凡纳滨对虾系统发生地位及适应性进化分析
|
摘要
甲壳动物是节肢动物门下仅次于六足亚门包含物种最丰富的一类物种，凡纳滨对虾（Litopenaeus vannamei）则隶属于甲壳亚门的十足目，是目前海水虾类中产量最高的单一海水经济养殖物种。目前，大量的研究工作都主要集中在水产养殖、病害防治和遗传育种等方面，对于对虾的系统发生问题以及进化过程中的各种生物学问题却少有研究。
随着二代测序技术的不断发展，各种虾类的基因组和转录组数据也不断释放，这为我们对对虾的系统发生学和进化生物学问题的研究提供了有力的数据支持。本研究论文基于海量基因组和转录组数据，对凡纳滨对虾在节肢动物门下的系统发生和分化时间，以及在甲壳动物亚门下的系统发生进行了深入分析，并对凡纳滨对虾进化过程中的适应性进化进行的深入研究。论文包括以下三个部分：
1.凡纳滨对虾的系统发生地位研究
我们从九种节肢动物的全基因序列中挑选出了19,982个基因家族，并从中找到了85个单拷贝基因用于节肢动物的系统发生分析。我们构建了一棵非常保守的系统发生树，修正了传统分子系统发生树之间产生的争议，说明这85个单拷贝基因可以作为很好的分子标记用于节肢动物系统发生分析。通过对分化时间的估计发现，甲壳动物的分化时期很早，大约在3.95亿年左右，而且从甲壳动物祖先分化形成水溞和对虾的过程中发生了大量基因家族的扩增和缺失，说明水溞与对虾之间存在巨大差异。凡纳滨对虾和斑节对虾的分化时间也较早，而且也存在大量的基因家族的扩增和缺失，说明两种对虾之间存在着较大差异，这进一步支持了《枝鳃虾类科属一世界对虾总科和樱虾总科虾类》专著中将对虾属的6个亚属提升至属级阶元的结论。此外，我们还发现两种对虾之间基因家族的扩增和缺失基本呈现一种“此消彼长”的关系，推测其与各自环境适应有关。其中细胞组成结构方面的基因家族的扩增对斑节对虾进化过程中环境适应非常重要，而神经系统方面基因家族在凡纳滨对虾的进化中相对扩增比较显著。
我们开发了一种基于短串序列（K-strings）构建后生动物系统发生树的方法，找到了23,223个对构建进化树贡献最大的关键进化元件（key K-strings）。该方法构建系统发生树不但能节省计算时间和空间，还能提升构树准确性，在物种分类方面优于其他方法。利用这种方法，我们构建了甲壳动物的系统发生树，结果显示凡纳滨对虾与美对虾属物种关系最近，而与对虾属斑节对虾关系相对较远，推测对虾各属的分化时间约在0.95亿年左右。此外，我们还提取到了427个甲壳动物关键进化元件key K-strings。这些key K-strings都位于其蛋白质序列的保守区，说明这些序列在漫长进化历史过程中，受到了进化选择压力而保留下来，并对物种的系统发生起着重要作用。
2.凡纳滨对虾的水平基因转移研究
水平基因转移事件的发生往往会使宿主获取新的性状和功能，以帮助宿主更好的适应新的环境。目前，越来越多的原核生物转移到真核生物的水平转移基因被报导，其中发现得最多的是在节肢动物中。通过对凡纳滨对虾的水平基因转移的研究，可以帮助我们了解对虾进化过程中的环境适应性机制。
我们通过一系列方法对对虾全基因组范围内的水平基因转移事件进行了研究，最终找到了14个水平转移基因，其中有12个是细菌起源的，另外两个是真菌起源的。通过对这些基因的结构进行分析，我们发现两个真菌起源的水平转移基因上的内含子在转移到对虾基因组上后被替换成了对虾特异性的内含子，而两个细菌起源的水平转移基因中则发现有对虾特异性的内含子的插入。此外，我们还发现有三个大片段的外源序列插入到了对虾基因组上，其中的一个是一个完整的转座子序列，而另外两个则是以操纵子的形式同时转移到对虾基因组上的，而且其上面的非编码区序列在转移到对虾基因组的过程中都被去除了，由此可以推测成熟的mRNA才是这些水平转移基因发生转移的基质。此外，大部分的水平转移基因都受到了强烈的负选择压力，推测他们在对虾基因组上都是具有一定功能的。通过对14个水平转移基因进行功能预测发现，其中有6个基因与能量代谢有关，还有4个基因与防御机制有关。而且大部分的水平转移基因在对虾的幼体发育不同时期展现出了差异基因表达，因此它们在对虾的生长发育过程中起着重要的作用。基于这14个基因功能方面的各种表现，我们推测这些水平转移基因可能有利于提升对虾的能量代谢和防御机制。
3、凡纳滨对虾适应性进化研究
在自然选择的作用力下，不同的虾会各自进化出适应周边环境的适应性机制。这些适应性机制直观地以新表型或新的生物性状的形式展现出来，但其本质还是分子水平上的遗传物质在随着选择压力的作用而产生的变化。
通过对转录组数据进行处理，我们获得了六种虾（凡纳滨对虾L. vannamei、中国明对虾Fenneropenaeus chinensis、斑节对虾Penaeus monodon、罗氏沼虾Macrobrachium rosenbergii、凯氏长额虾Pandalus latirostris以及狭螯螯虾Astacusleptodactylu）平均约12,000条去冗余的编码基因序列，并进一步从中挑选出了1,669组直系同源基因。利用这些直系同源基因我们成功构建了一棵保守的系统发生树，该系统发生树与传统的形态学分类以及分子标记系统发生学分析的结果一致。我们分别以三种对虾和两种真虾作为前景枝，探讨对虾和真虾在进化过程中的适应性机制差异；还分别以四种海水虾和两种淡水虾分别作为前景枝，探讨其在各自的水环境下的适应性机制。
我们分别在对虾和真虾中找到了231个和110个正选择基因。基因富集的结果显示对虾的正选择基因主要富集在跟核糖体合成、生物膜的组成以及应激反应等相关的功能中。正选择基因在核糖体合成及蛋白质翻译过程上的富集，推测对虾在蛋白质合成上受到较强的正选择作用；而在生物膜的组成上的富集，推测其可能是随蛋白质合成方面基因的正选择作用而产生的一种共同适应性进化的过程。对虾的正选择基因在应激反应相关的功能中富集正好与关于对虾拥有最快的生物信号冲动传导速度的观点不谋而合，说明对虾在面对应激因子刺激过程中逐渐产生出了较强的应激反应适应性。真虾的正选择基因则主要富集在甲基化相关的分类中，推测真虾可能通过甲基化修饰来提高其环境适应性。
通过分别以海水虾和淡水虾作为前景枝，我们分别找到了174个和360个正选择基因。渗透调控是虾类水环境适应过程中非常重要的一个生物学过程。我们从这些正选择基因中找到了海水虾中两个正向调控渗透作用的基因NKA和NKCC，它们都能有效的维持细胞较高的钠钾离子渗透梯度，提高海水虾在高盐环境的适应能力。此外，在淡水虾中也找到了一个负调控渗透作用的基因RhoGDI，它能有效的调整细胞内离子浓度，以维持细胞在淡水环境下的生存。因此，我们认为这些正选择基因中确实存在一些跟渗透调节有着直接关系的基因，它们分别有利于提升海水虾和淡水虾在各自的水环境中的适应性机制。
Except Insects, crustacean is one of the groups with most species in Athropoda.As a species in Crustacea, Pacific white shrimp, Litopenaeus vannamei, is animportant economic breeding species in China, which produce millions of tons everyyear. In present, most of the shrimp researches are focused on aquaculture, diseasecontrol and genetic breeding, while few of them are focused on phylogeny andevolutionary biology.
As the development of next-generation sequencing technology, a growingnumber of shrimp genomes and transcriptomes are sequenced and published gradually,which may provide good resources for the exhaustive research on shrimpphylogenetic and adaptive evolution analysis. In this study, we performedphylogenetic analysis of arthropods and estimated the divergence time of shrimpbased on the amount of transcriptome data. We also developed a new method toanalyze the phylogeny of shrimp under Crustacea. Besides, novel bioinformaticsmethods were implemented to analyze the adaptive evolution of shrimp. There arethree major sections included in this thesis as follows:
1. Phylogenetic analysis of L. vannamei
Through using TreeFam methodology, we extracted19,982gene families fromfull genes of nine arthropods. Then,85single-copy genes were selected from them forthe phylogenetic analysis of Athropoda. The phylogenetic tree constructed bysingle-copy genes was similar with the trees constructed by custom molecularmarkers, and also has high confidence on each branch, which indicated that these85single-copy genes could be used as good molecular marker for the Arthropodaphylogenetic analysis. After estimating the divergence time of each species, we foundthat Crustacea was divergent at about395million years ago. And there were a great many of gene gain and gene lose when the ancestor evolved to shrimp and Daphnia,indicating that there is significant bias between the genomes of Daphnia and shrimps.L. vannamei and Penaeus monodon were also divergent early and a lot of gained orlosed gene families were found between them, which suggest these two Penaeidea arequite different each other. These results rightly supported the opinion of upgrading thesix subgenus of Penaeus to the stage of genus. Furthermore, we found that there aremany GO term with one shrimp gene gain significantly while the other shrimp losesignificantly. Among these GO terms, cellular component related gene families weresignificantly gained in P. monodon, while nervous system related gene gamilies weresignificantly enriched in L. vannamei. The bias of gene gain and gene lose betweentwo shrimps may help them adapting to their new environments, respectively.
We developed a new method for the metazoans phylogenetic analysis based onthe short sequences segments, namely K-strings. We collected23,223key K-stringswhich make significant contribution for the phylogenetic tree construction. Throughusing this new method, we constructed a phylogenetic tree of Crustacea, and foundthat this tree is topological similar with the custom molecular phylogentic tree. L.vannamei was phylogentic close with Farfantepenaeus californiensis, while far fromP. monodon. The divergence time of Penaeidea was estimated at about95millionyears ago. Besides, we collected427key K-strings of Crustacea and map them on theoriginal protein sequences. The results showed that these phylogentic important keyK-strings are totally tend to accumulated at the conserved regions of the proteinsequences, which indicating that these key K-strings can be thought as evolutionaryelements that suffering selective pressure and play important role in crustaceansphylogeny.
2. Horizontal gene transfer analysis of L. vannamei
Generally, horizontal gene transfer (HGT) events could help receipients gainsome new phylotypes or functions to support for the receipients adapting to newenvironments. In recent years, a growing number of genes have been reported asbeing horizontally transferred from prokaryotes to eukaryotes, most of them involvingarthropods. As a member of the phylum Arthropoda, L. vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms,which provide a platform for horizontal gene transfer.
In this section, we analyzed the genome-wide HGT events in L. vannamei.Through homology search and phylogenetic analysis, followed by experimental PCRconfirmation,14genes with HGT event were identified:12of them were transferredfrom bacteria and two from fungi. Structure analysis of these genes showed that theintrons of the two fungi-originated genes were substituted by shrimp DNA fragment,two genes transferred from bacteria had shrimp specific introns inserted in them.Furthermore, around other three bacteria-originated genes, there were three largeDNA segments inserted into the shrimp genome. One segment was a transposon thatfully transferred, and the other two segments contained only coding regions ofbacteria. These structure alterations provide evidence that mature RNA may be thesubstrate for HGT events. Among14HGT genes, most of them were detected to beexposed to negative selection pressure and they appeared to be functional. Functionalprediction of these14genes showed that6of them might be related to energymetabolism, and4others related to defense of the organism. And most of themexpressed differently at five development stage of shrimp laveral, which indicatingthese genes are important for the shrimp development. Considering the functions ofthese14HGT genes, we thought they may helpful for the improvements of shrimpenergy metabolism and defense mechanism.
3. Adaptive evolution analysis of L. vannamei
During the long evolutionary history, because of the natural selection, shrimpswill evolve some adaptive mechanisms for the environment adaptation. Generally,these adaptive mechanisms can be directly displyed on the newly generatedphylotypes or biological characters, but it was actually displayed on the geneticmaterials mutations.
We collected many transcriptomes of six shrimps: L. vannamei, Fenneropenaeuschinensis, P. monodon, Pandalus latirostris, Macrobrachium rosenbergii, Astacusleptodactylus. After removing redundant sequences, we finally obtained average12,000protein-coding genes, and select1,669groups of orthologs from them. Based on these orthologs, we constructed a conserved phylogenetic tree of these six shrimps.The topology of this tree is similar with normal trees constructed by molecularmarkers, and also correspondent with the custom morphological classification. Then,we set the branches of three Penaeidea and two Caridea as foreground branchesrespectively to analyze the bias of adaptive mechanisms between Penaeidea andCaridea. We also set the branches of four seawater shrimps and two freshwatershrimps as foreground branches respectively to analyze the adaptive mechanisms ofdifferent water environments.
We obtained231and110positive selected genes from Penaeidea and Caridea,respectively. It was found that most of the positive selected genes in Penaeidea areenriched in the functional related GO terms of ribosome biogenesis, membrane andresponse to stimulus. The genes enriched in the ribosome biogenesis and proteintranslation suffer positive selection pressure may be benefit for the protein synthesisin Penaeidea, while the positive selected genes enriched in membrane compositionmay be co-evolved with the genes in protein synthesis. It was interesting to find thatmany positive selected genes are enriched in stimulus response related GO terms inPenaeidea. As Penaeidea have excellent giant nerve fibers to conduct impulses at thevelocity highest among animals, it seems the nervous systems of Penaeidea wereadaptive evolved during the long evolution history. When compared with Penaeidea,the positive selected genes in Caridea are primarily enriched in methylation relatedfunctions, which suggest that Caridea may improve its adaptation through methylationmodification.
When analyze the adaptive evolution of the shrimps under seawater or freshwater,we obtained174and360positive selected genes among them, respectively. Becauseosmoregulation is one of the most important biological processes in water adaptationof shrimps, we surveyed genes related to osmoregulation among these positiveselected genes. As expected, we found two genes, NKA and NKCC, positive regulatethe osmoregulation in seawater shrimps. Both genes are responsible for establishingelectrochemical gradients across biological membrane, which were considered benefitfor the seawater shrimps adapt to high salinity environments. In contrast, there is a positive selected gene RHOGTP8in freshwater shrimps can negative regulateosmoregulation procedures. RHOGTP8can maintain the intracellular ionconcentration, which may helpful for the freshwater adaptation. Therefore, all theseosmoregulation related positive selected genes are considered to play important rolein the improvements of water environment adaptation mechanisms.
随着二代测序技术的不断发展，各种虾类的基因组和转录组数据也不断释放，这为我们对对虾的系统发生学和进化生物学问题的研究提供了有力的数据支持。本研究论文基于海量基因组和转录组数据，对凡纳滨对虾在节肢动物门下的系统发生和分化时间，以及在甲壳动物亚门下的系统发生进行了深入分析，并对凡纳滨对虾进化过程中的适应性进化进行的深入研究。论文包括以下三个部分：
1.凡纳滨对虾的系统发生地位研究
我们从九种节肢动物的全基因序列中挑选出了19,982个基因家族，并从中找到了85个单拷贝基因用于节肢动物的系统发生分析。我们构建了一棵非常保守的系统发生树，修正了传统分子系统发生树之间产生的争议，说明这85个单拷贝基因可以作为很好的分子标记用于节肢动物系统发生分析。通过对分化时间的估计发现，甲壳动物的分化时期很早，大约在3.95亿年左右，而且从甲壳动物祖先分化形成水溞和对虾的过程中发生了大量基因家族的扩增和缺失，说明水溞与对虾之间存在巨大差异。凡纳滨对虾和斑节对虾的分化时间也较早，而且也存在大量的基因家族的扩增和缺失，说明两种对虾之间存在着较大差异，这进一步支持了《枝鳃虾类科属一世界对虾总科和樱虾总科虾类》专著中将对虾属的6个亚属提升至属级阶元的结论。此外，我们还发现两种对虾之间基因家族的扩增和缺失基本呈现一种“此消彼长”的关系，推测其与各自环境适应有关。其中细胞组成结构方面的基因家族的扩增对斑节对虾进化过程中环境适应非常重要，而神经系统方面基因家族在凡纳滨对虾的进化中相对扩增比较显著。
我们开发了一种基于短串序列（K-strings）构建后生动物系统发生树的方法，找到了23,223个对构建进化树贡献最大的关键进化元件（key K-strings）。该方法构建系统发生树不但能节省计算时间和空间，还能提升构树准确性，在物种分类方面优于其他方法。利用这种方法，我们构建了甲壳动物的系统发生树，结果显示凡纳滨对虾与美对虾属物种关系最近，而与对虾属斑节对虾关系相对较远，推测对虾各属的分化时间约在0.95亿年左右。此外，我们还提取到了427个甲壳动物关键进化元件key K-strings。这些key K-strings都位于其蛋白质序列的保守区，说明这些序列在漫长进化历史过程中，受到了进化选择压力而保留下来，并对物种的系统发生起着重要作用。
2.凡纳滨对虾的水平基因转移研究
水平基因转移事件的发生往往会使宿主获取新的性状和功能，以帮助宿主更好的适应新的环境。目前，越来越多的原核生物转移到真核生物的水平转移基因被报导，其中发现得最多的是在节肢动物中。通过对凡纳滨对虾的水平基因转移的研究，可以帮助我们了解对虾进化过程中的环境适应性机制。
我们通过一系列方法对对虾全基因组范围内的水平基因转移事件进行了研究，最终找到了14个水平转移基因，其中有12个是细菌起源的，另外两个是真菌起源的。通过对这些基因的结构进行分析，我们发现两个真菌起源的水平转移基因上的内含子在转移到对虾基因组上后被替换成了对虾特异性的内含子，而两个细菌起源的水平转移基因中则发现有对虾特异性的内含子的插入。此外，我们还发现有三个大片段的外源序列插入到了对虾基因组上，其中的一个是一个完整的转座子序列，而另外两个则是以操纵子的形式同时转移到对虾基因组上的，而且其上面的非编码区序列在转移到对虾基因组的过程中都被去除了，由此可以推测成熟的mRNA才是这些水平转移基因发生转移的基质。此外，大部分的水平转移基因都受到了强烈的负选择压力，推测他们在对虾基因组上都是具有一定功能的。通过对14个水平转移基因进行功能预测发现，其中有6个基因与能量代谢有关，还有4个基因与防御机制有关。而且大部分的水平转移基因在对虾的幼体发育不同时期展现出了差异基因表达，因此它们在对虾的生长发育过程中起着重要的作用。基于这14个基因功能方面的各种表现，我们推测这些水平转移基因可能有利于提升对虾的能量代谢和防御机制。
3、凡纳滨对虾适应性进化研究
在自然选择的作用力下，不同的虾会各自进化出适应周边环境的适应性机制。这些适应性机制直观地以新表型或新的生物性状的形式展现出来，但其本质还是分子水平上的遗传物质在随着选择压力的作用而产生的变化。
通过对转录组数据进行处理，我们获得了六种虾（凡纳滨对虾L. vannamei、中国明对虾Fenneropenaeus chinensis、斑节对虾Penaeus monodon、罗氏沼虾Macrobrachium rosenbergii、凯氏长额虾Pandalus latirostris以及狭螯螯虾Astacusleptodactylu）平均约12,000条去冗余的编码基因序列，并进一步从中挑选出了1,669组直系同源基因。利用这些直系同源基因我们成功构建了一棵保守的系统发生树，该系统发生树与传统的形态学分类以及分子标记系统发生学分析的结果一致。我们分别以三种对虾和两种真虾作为前景枝，探讨对虾和真虾在进化过程中的适应性机制差异；还分别以四种海水虾和两种淡水虾分别作为前景枝，探讨其在各自的水环境下的适应性机制。
我们分别在对虾和真虾中找到了231个和110个正选择基因。基因富集的结果显示对虾的正选择基因主要富集在跟核糖体合成、生物膜的组成以及应激反应等相关的功能中。正选择基因在核糖体合成及蛋白质翻译过程上的富集，推测对虾在蛋白质合成上受到较强的正选择作用；而在生物膜的组成上的富集，推测其可能是随蛋白质合成方面基因的正选择作用而产生的一种共同适应性进化的过程。对虾的正选择基因在应激反应相关的功能中富集正好与关于对虾拥有最快的生物信号冲动传导速度的观点不谋而合，说明对虾在面对应激因子刺激过程中逐渐产生出了较强的应激反应适应性。真虾的正选择基因则主要富集在甲基化相关的分类中，推测真虾可能通过甲基化修饰来提高其环境适应性。
通过分别以海水虾和淡水虾作为前景枝，我们分别找到了174个和360个正选择基因。渗透调控是虾类水环境适应过程中非常重要的一个生物学过程。我们从这些正选择基因中找到了海水虾中两个正向调控渗透作用的基因NKA和NKCC，它们都能有效的维持细胞较高的钠钾离子渗透梯度，提高海水虾在高盐环境的适应能力。此外，在淡水虾中也找到了一个负调控渗透作用的基因RhoGDI，它能有效的调整细胞内离子浓度，以维持细胞在淡水环境下的生存。因此，我们认为这些正选择基因中确实存在一些跟渗透调节有着直接关系的基因，它们分别有利于提升海水虾和淡水虾在各自的水环境中的适应性机制。
Except Insects, crustacean is one of the groups with most species in Athropoda.As a species in Crustacea, Pacific white shrimp, Litopenaeus vannamei, is animportant economic breeding species in China, which produce millions of tons everyyear. In present, most of the shrimp researches are focused on aquaculture, diseasecontrol and genetic breeding, while few of them are focused on phylogeny andevolutionary biology.
As the development of next-generation sequencing technology, a growingnumber of shrimp genomes and transcriptomes are sequenced and published gradually,which may provide good resources for the exhaustive research on shrimpphylogenetic and adaptive evolution analysis. In this study, we performedphylogenetic analysis of arthropods and estimated the divergence time of shrimpbased on the amount of transcriptome data. We also developed a new method toanalyze the phylogeny of shrimp under Crustacea. Besides, novel bioinformaticsmethods were implemented to analyze the adaptive evolution of shrimp. There arethree major sections included in this thesis as follows:
1. Phylogenetic analysis of L. vannamei
Through using TreeFam methodology, we extracted19,982gene families fromfull genes of nine arthropods. Then,85single-copy genes were selected from them forthe phylogenetic analysis of Athropoda. The phylogenetic tree constructed bysingle-copy genes was similar with the trees constructed by custom molecularmarkers, and also has high confidence on each branch, which indicated that these85single-copy genes could be used as good molecular marker for the Arthropodaphylogenetic analysis. After estimating the divergence time of each species, we foundthat Crustacea was divergent at about395million years ago. And there were a great many of gene gain and gene lose when the ancestor evolved to shrimp and Daphnia,indicating that there is significant bias between the genomes of Daphnia and shrimps.L. vannamei and Penaeus monodon were also divergent early and a lot of gained orlosed gene families were found between them, which suggest these two Penaeidea arequite different each other. These results rightly supported the opinion of upgrading thesix subgenus of Penaeus to the stage of genus. Furthermore, we found that there aremany GO term with one shrimp gene gain significantly while the other shrimp losesignificantly. Among these GO terms, cellular component related gene families weresignificantly gained in P. monodon, while nervous system related gene gamilies weresignificantly enriched in L. vannamei. The bias of gene gain and gene lose betweentwo shrimps may help them adapting to their new environments, respectively.
We developed a new method for the metazoans phylogenetic analysis based onthe short sequences segments, namely K-strings. We collected23,223key K-stringswhich make significant contribution for the phylogenetic tree construction. Throughusing this new method, we constructed a phylogenetic tree of Crustacea, and foundthat this tree is topological similar with the custom molecular phylogentic tree. L.vannamei was phylogentic close with Farfantepenaeus californiensis, while far fromP. monodon. The divergence time of Penaeidea was estimated at about95millionyears ago. Besides, we collected427key K-strings of Crustacea and map them on theoriginal protein sequences. The results showed that these phylogentic important keyK-strings are totally tend to accumulated at the conserved regions of the proteinsequences, which indicating that these key K-strings can be thought as evolutionaryelements that suffering selective pressure and play important role in crustaceansphylogeny.
2. Horizontal gene transfer analysis of L. vannamei
Generally, horizontal gene transfer (HGT) events could help receipients gainsome new phylotypes or functions to support for the receipients adapting to newenvironments. In recent years, a growing number of genes have been reported asbeing horizontally transferred from prokaryotes to eukaryotes, most of them involvingarthropods. As a member of the phylum Arthropoda, L. vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms,which provide a platform for horizontal gene transfer.
In this section, we analyzed the genome-wide HGT events in L. vannamei.Through homology search and phylogenetic analysis, followed by experimental PCRconfirmation,14genes with HGT event were identified:12of them were transferredfrom bacteria and two from fungi. Structure analysis of these genes showed that theintrons of the two fungi-originated genes were substituted by shrimp DNA fragment,two genes transferred from bacteria had shrimp specific introns inserted in them.Furthermore, around other three bacteria-originated genes, there were three largeDNA segments inserted into the shrimp genome. One segment was a transposon thatfully transferred, and the other two segments contained only coding regions ofbacteria. These structure alterations provide evidence that mature RNA may be thesubstrate for HGT events. Among14HGT genes, most of them were detected to beexposed to negative selection pressure and they appeared to be functional. Functionalprediction of these14genes showed that6of them might be related to energymetabolism, and4others related to defense of the organism. And most of themexpressed differently at five development stage of shrimp laveral, which indicatingthese genes are important for the shrimp development. Considering the functions ofthese14HGT genes, we thought they may helpful for the improvements of shrimpenergy metabolism and defense mechanism.
3. Adaptive evolution analysis of L. vannamei
During the long evolutionary history, because of the natural selection, shrimpswill evolve some adaptive mechanisms for the environment adaptation. Generally,these adaptive mechanisms can be directly displyed on the newly generatedphylotypes or biological characters, but it was actually displayed on the geneticmaterials mutations.
We collected many transcriptomes of six shrimps: L. vannamei, Fenneropenaeuschinensis, P. monodon, Pandalus latirostris, Macrobrachium rosenbergii, Astacusleptodactylus. After removing redundant sequences, we finally obtained average12,000protein-coding genes, and select1,669groups of orthologs from them. Based on these orthologs, we constructed a conserved phylogenetic tree of these six shrimps.The topology of this tree is similar with normal trees constructed by molecularmarkers, and also correspondent with the custom morphological classification. Then,we set the branches of three Penaeidea and two Caridea as foreground branchesrespectively to analyze the bias of adaptive mechanisms between Penaeidea andCaridea. We also set the branches of four seawater shrimps and two freshwatershrimps as foreground branches respectively to analyze the adaptive mechanisms ofdifferent water environments.
We obtained231and110positive selected genes from Penaeidea and Caridea,respectively. It was found that most of the positive selected genes in Penaeidea areenriched in the functional related GO terms of ribosome biogenesis, membrane andresponse to stimulus. The genes enriched in the ribosome biogenesis and proteintranslation suffer positive selection pressure may be benefit for the protein synthesisin Penaeidea, while the positive selected genes enriched in membrane compositionmay be co-evolved with the genes in protein synthesis. It was interesting to find thatmany positive selected genes are enriched in stimulus response related GO terms inPenaeidea. As Penaeidea have excellent giant nerve fibers to conduct impulses at thevelocity highest among animals, it seems the nervous systems of Penaeidea wereadaptive evolved during the long evolution history. When compared with Penaeidea,the positive selected genes in Caridea are primarily enriched in methylation relatedfunctions, which suggest that Caridea may improve its adaptation through methylationmodification.
When analyze the adaptive evolution of the shrimps under seawater or freshwater,we obtained174and360positive selected genes among them, respectively. Becauseosmoregulation is one of the most important biological processes in water adaptationof shrimps, we surveyed genes related to osmoregulation among these positiveselected genes. As expected, we found two genes, NKA and NKCC, positive regulatethe osmoregulation in seawater shrimps. Both genes are responsible for establishingelectrochemical gradients across biological membrane, which were considered benefitfor the seawater shrimps adapt to high salinity environments. In contrast, there is a positive selected gene RHOGTP8in freshwater shrimps can negative regulateosmoregulation procedures. RHOGTP8can maintain the intracellular ionconcentration, which may helpful for the freshwater adaptation. Therefore, all theseosmoregulation related positive selected genes are considered to play important rolein the improvements of water environment adaptation mechanisms.
引文
A.Gheyas, I. and LeslieS.Smith (2009)."Feature subset selection in largedimensionality domains." Pattern Recognition43:5-13.
Ackerly, D. D.(2003)."Community assembly, niche conservatism, and adaptiveevolution in changing environments." International Journal of Plant Sciences164(3): S165-S184.
Adams, M. D., S. E. Celniker, et al.(2000)."The genome sequence of Drosophilamelanogaster." Science287(5461):2185-2195.
Adoutte, A., G. Balavoine, et al.(2000)."The new animal phylogeny: reliability andimplications." Proc Natl Acad Sci U S A97(9):4453-4456.
Aguinaldo, A. M., J. M. Turbeville, et al.(1997)."Evidence for a clade of nematodes,arthropods and other moulting animals." Nature387(6632):489-493.
Ahyong, S. T. and D. O'Meally (2004)."Phylogeny of the Decapoda reptantia:Resolution using three molecular loci and morphology." Raffles Bulletin ofZoology52(2):673-693.
Aikawa, T., H. Anbutsu, et al.(2009)."Longicorn beetle that vectors pinewoodnematode carries many Wolbachia genes on an autosome." Proceedings of theRoyal Society B-Biological Sciences276(1674):3791-3798.
Alba, M. M., R. Das, et al.(2001)."Genomewide function conservation andphylogeny in the Herpesviridae." Genome Res11(1):43-54.
Alderton, G. K.(2014)."Neuroblastoma: A new gene that promotes NMYC activity."Nat Rev Cancer14(3):155.
Allen, G. C. and A. Kornberg (1993)."Assembly of the Primosome ofDNA-Replication in Escherichia-Coli." Journal of Biological Chemistry268(26):19204-19209.
Altincicek, B., J. L. Kovacs, et al.(2012)."Horizontally transferred fungal carotenoidgenes in the two-spotted spider mite Tetranychus urticae." Biol Lett8(2):253-257.
Andersson, J. O., A. M. Sjogren, et al.(2003)."Phylogenetic analyses of diplomonadgenes reveal frequent lateral gene transfers affecting eukaryotes." Curr Biol13(2):94-104.
Andriantahina, F., X. Liu, et al.(2013)."Current status of genetics and genomics ofreared penaeid shrimp: information relevant to access and benefit sharing." MarBiotechnol (NY)15(4):399-412.
Assavalapsakul, W. and S. Panyim (2012)."Molecular cloning and tissue distributionof the Toll receptor in the black tiger shrimp, Penaeus monodon." Genet Mol Res11(1):484-493.
Atum, Y., I. Gareis, et al.(2010)."Genetic feature selection to optimally detect P300in brain computer interfaces." Conf Proc IEEE Eng Med Biol Soc1:3289-3292.
Auch, A. F., S. R. Henz, et al.(2006)."Genome BLAST distance phylogenies inferredfrom whole plastid and whole mitochondrion genome sequences." BMCBioinformatics7:350.
Averof, M. and M. Akam (1995)."Hox Genes and the Diversification of Insect andCrustacean Body Plans." Nature376(6539):420-423.
Babbitt, C. C. and N. H. Patel (2005)."Relationships within the Pancrustacea:examining the influence of additional malacostracan18S and28S rDNA." Crust.Issues16(275-294).
Bachmann, S., T. Saritas, et al.(2013)."STE20-like kinase SPAK differentiallyregulates Na-(K)-Cl cotransporters along the distal nephron under the endocrinecontrol of AVP." Faseb Journal27.
Baele, G., P. Lemey, et al.(2012)."Improving the accuracy of demographic andmolecular clock model comparison while accommodating phylogeneticuncertainty." Mol Biol Evol29(9):2157-2167.
Bafna, V. and P. A. Pevzner (1995)."Sorting by reversals：Genome rearrangement inplant organelles and evolutionary history of X chromosome." Mol Biol Evol12：239—24.
Bao, R. and M. Friedrich (2009)."Molecular evolution of the Drosophila retinome:exceptional gene gain in the higher Diptera." Mol Biol Evol26(6):1273-1287.
Bapteste, E., Y. Boucher, et al.(2004)."Phylogenetic reconstruction and lateral genetransfer." Trends Microbiol12(9):406-411.
Baralis, E., G. Bruno, et al.(2008)."Minimum number of genes for microarray featureselection." Conf Proc IEEE Eng Med Biol Soc2008:5692-5695.
Baranski, M., G. Gopikrishna, et al.(2014)."The Development of a High DensityLinkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs."PLoS One9(1).
Baranski, M., G. Gopikrishna, et al.(2014)."The Development of a High DensityLinkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs."PLoS One9(1): e85413.
Beaber, J. W., B. Hochhut, et al.(2004)."SOS response promotes horizontaldissemination of antibiotic resistance genes." Nature427(6969):72-74.
Beiko, R. G., T. J. Harlow, et al.(2005)."Highways of gene sharing in prokaryotes."Proc Natl Acad Sci U S A102(40):14332-14337.
Belda, E., A. Moya, et al.(2005)."Genome rearrangement distances and gene orderphylogeny in gamma-Proteobacteria." Mol Biol Evol22(6):1456-1467.
Benjamini, Y. and Y. Hochberg (1995)."Controlling the false discovery rate-apractical and powerful approach to multiple testing." Journal of the RoyalStatistical Society Series B-Methodological57(1):289-300.
Bird, A. P.(1986)."Cpg-Rich Islands and the Function of DNA Methylation." Nature321(6067):209-213.
Blanchette, M. and M. Tompa (2002)."Discovery of regulatory elements by acomputational method for phylogenetic footprinting." Genome Res12(5):739-748.
Boas, F. E. V.(1880)."Studier over decapodernes slaegtskabsforhold." DanskVidenskabernes Seksjeab, Copenhagen, Skrifter, Naturvidenskabelig ogmatematisek Afdeling1:26-210.
Boore, J. L., T. M. Collins, et al.(1995)."Deducing the Pattern of ArthropodPhylogeny from Mitochondrial-DNA Rearrangements." Nature376(6536):163-165.
Bork, P.(1993)."Hundreds of ankyrin-like repeats in functionally diverse proteins-mobile modules that cross phyla horizontally." Proteins-Structure Function andGenetics17(4):363-374.
Bracken, H. D., S. De Grave, et al.(2010)."Phylogenetic position, systematic status,and divergence time of the Procarididea (Crustacea: Decapoda)." ZoologicaScripta39(2):198-212.
Brooks, W. K.(1883)."The Phylogeny of the Higher Crustacea." Science2(46):790-793.
Bullard, J. H., E. Purdom, et al.(2010)."Evaluation of statistical methods fornormalization and differential expression in mRNA-Seq experiments." BMCBioinformatics11:94.
Burge, C. and S. Karlin (1997)."Prediction of complete gene structures in humangenomic DNA." J Mol Biol268(1):78-94.
Burge, E. J., D. J. Madigan, et al.(2007)."Lysozyme gene expression by hemocytesof Pacific white shrimp, Litopenaeus vannamei, after injection with Vibrio." FishShellfish Immunol22(4):327-339.
Burkenroad, M. D.(1981)."The higher taxonomy and evolution of Decapoda(Crustacea)." Transactions of the San Diego Society of Natural History19:251-268.
Cao, Z., Y. Yu, et al.(2013)."The genome of Mesobuthus martensii reveals a uniqueadaptation model of arthropods." Nat Commun4:2602.
Castresana, J.(2000)."Selection of conserved blocks from multiple alignments fortheir use in phylogenetic analysis." Mol Biol Evol17(4):540-552.
Center, G. S. L.(2012, August6)."The brine shrimp life cycle." Learn. Genetics.
Chan, C. X., D. Bhattacharya, et al.(2012)."Endosymbiotic and horizontal genetransfer in microbial eukaryotes: Impacts on cell evolution and the tree of life."Mob Genet Elements2(2):101-105.
Chapman, J. A., E. F. Kirkness, et al.(2010)."The dynamic genome of Hydra."Nature464(7288):592-596.
Chen, H. and M. Blanchette (2007)."Detecting non-coding selective pressure incoding regions." BMC Evol Biol7Suppl1: S9.
Chen, H. W., Z. B. Zhao, et al.(2001)."Insights into the branched-chain formation ofmycarose: Methylation catalyzed by an (S)-adenosylmethionine-dependentmethyltransferase." Angewandte Chemie-International Edition40(3):607-610.
Chen, J. C., J. N. Lin, et al.(1996)."Survival, growth and intermolt period of juvenilePenaeus chinensis (Osbeck) reared at different combinations of salinity andtemperature." Journal of Experimental Marine Biology and Ecology204(1-2):169-178.
Chen, M. J., T. Shimada, et al.(1984)."The Functional HumanDihydrofolate-Reductase Gene." Journal of Biological Chemistry259(6):3933-3943.
Chen, S., G. Zhang, et al.(2014)."Whole-genome sequence of a flatfish providesinsights into ZW sex chromosome evolution and adaptation to a benthiclifestyle." Nat Genet46(3):253-260.
Chen, X. H., D. G. Zeng, et al.(2013)."Transcriptome Analysis of Litopenaeusvannamei in Response to White Spot Syndrome Virus Infection." PLoS One8(8).
Chiba, S., K. Yoshino, et al.(2013)."Maladaptive sex ratio adjustment by asex-changing shrimp in selective-fishing environments." Journal of AnimalEcology82(3):632-641.
Chien, Y. H.(1992)."Water-Quality Requirements and Management for MarineShrimp Culture." Proceedings of the Special Session on Shrimp Farming:144-156.
Chiron, H., A. Drouet, et al.(2000)."Molecular cloning and functional expression of astress-induced multifunctional O-methyltransferase with pinosylvinmethyltransferase activity from Scots pine (Pinus sylvestris L.)." Plant MolecularBiology44(6):733-745.
Cho, B. H., H. Yu, et al.(2008)."Application of irregular and unbalanced data topredict diabetic nephropathy using visualization and feature selection methods."Artif Intell Med42(1):37-53.
Choi, I. G. and S. H. Kim (2007)."Global extent of horizontal gene transfer." ProcNatl Acad Sci U S A104(11):4489-4494.
Choudhary, A., M. Brun, et al.(2006)."Genetic test bed for feature selection."Bioinformatics22(7):837-842.
Chu, K. H., L. M. Tsang, et al.(2008)."Decapod phylogeny: what can protein codinggenes tell us?" Decapod Crustacean Phylogenetics18:89-99.
Chuang, L. Y., C. H. Ke, et al.(2009)."A two-stage feature selection method for geneexpression data." OMICS13(2):127-137.
Colbourne, J. K., M. E. Pfrender, et al.(2011)."The ecoresponsive genome ofDaphnia pulex." Science331(6017):555-561.
Cover, T. M. and J. A. Thomas (1991)."Elements of Information Theory."(New York:Wiley).
Crandall, K. A., D. J. Harris, et al.(2000)."The monophyletic origin of freshwatercrayfish estimated from nuclear and mitochondrial DNA sequences." Proceedingsof the Royal Society B-Biological Sciences267(1453):1679-1686.
Creevey, C. J., J. Muller, et al.(2011)."Identifying Single Copy Orthologs inMetazoa." Plos Computational Biology7(12).
Cruz, P., A. M. Ibarra, et al.(2004)."Genetic variability assessed by microsatellites ina breeding program of Pacific white shrimp (Litopenaeus vannamei)." MarBiotechnol (NY)6(2):157-164.
Cutler, C. P., A. S. Martinez, et al.(2007)."The role of aquaporin3in teleost fish."Comparative Biochemistry and Physiology a-Molecular&Integrative Physiology148(1):82-91.
Dam, P., V. Olman, et al.(2007)."Operon prediction using both genome-specific andgeneral genomic information." Nucleic Acids Res35(1):288-298.
Dang, L. T., T. Koyama, et al.(2010)."Involvement of WSSV-shrimp homologs inWSSV infectivity in kuruma shrimp: Marsupenaeus japonicus." Antiviral Res88(2):217-226.
De Bie, T., N. Cristianini, et al.(2006)."CAFE: a computational tool for the study ofgene family evolution." Bioinformatics22(10):1269-1271.
DeFaveri, J., T. Shikano, et al.(2011)."Global Analysis of Genes Involved inFreshwater Adaptation in Threespine Sticklebacks (Gasterosteus Aculeatus)."Evolution65(6):1800-1807.
Delsuc, F., H. Brinkmann, et al.(2005)."Phylogenomics and the reconstruction of thetree of life." Nat Rev Genet6(5):361-375.
Denton, E. J. and J. Gray (1985)."Lateral-Line-Like Antennae of Certain of thePenaeidea (Crustacea, Decapoda, Natantia)." Proceedings of the Royal SocietySeries B-Biological Sciences226(1244):249-+.
DeSalle, R. and B. Schierwater (2008)."An even "newer" animal phylogeny."Bioessays30(11-12):1043-1047.
Desper, R. and O. Gascuel (2006)."Getting a tree fast: Neighbor Joining, FastME,and distance-based methods." Curr Protoc Bioinformatics Chapter6: Unit63.
Dickerson, R. E.(1971)."The structures of cytochrome c and the rates of molecularevolution." J Mol Evol1(1):26-45.
DiGuistini, S., Y. Wang, et al.(2011)."Genome and transcriptome analyses of themountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pinepathogen." Proc Natl Acad Sci U S A108(6):2504-2509.
Doudoumis, V., U. Alam, et al.(2013)."Tsetse-Wolbachia symbiosis: Comes of ageand has great potential for pest and disease control." Journal of InvertebratePathology112: S94-S103.
Dougherty, E. R., J. Hua, et al.(2009)."Performance of feature selection methods."Curr Genomics10(6):365-374.
Du, Z. Q., D. C. Ciobanu, et al.(2010)."A gene-based SNP linkage map for pacificwhite shrimp, Litopenaeus vannamei." Anim Genet41(3):286-294.
Duarte, J. M., P. K. Wall, et al.(2010)."Identification of shared single copy nucleargenes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utilityacross various taxonomic levels." BMC Evol Biol10:61.
Dunning Hotopp, J. C.(2011)."Horizontal gene transfer between bacteria andanimals." Trends Genet27(4):157-163.
Dunning Hotopp, J. C., M. E. Clark, et al.(2007)."Widespread lateral gene transferfrom intracellular bacteria to multicellular eukaryotes." Science317(5845):1753-1756.
Dyall, S. D., M. T. Brown, et al.(2004)."Ancient invasions: from endosymbionts toorganelles." Science304(5668):253-257.
Eden, S., T. Hashimshony, et al.(1998)."DNA methylation models histoneacetylation." Nature394(6696):842-842.
Edgar, R. C.(2004)."MUSCLE: multiple sequence alignment with high accuracy andhigh throughput." Nucleic Acids Res32(5):1792-1797.
Eick-Helmerich, K. and V. Braun (1989)."Import of biopolymers into Escherichiacoli: nucleotide sequences of the exbB and exbD genes are homologous to thoseof the tolQ and tolR genes, respectively." Journal of Bacteriology171(9):5117-5126.
Eizaguirre, C., T. L. Lenz, et al.(2012)."Rapid and adaptive evolution of MHC genesunder parasite selection in experimental vertebrate populations." Nat Commun3:621.
Escobedo-Bonilla, C. M., M. Wille, et al.(2007)."Pathogenesis of a Thai strain ofwhite spot syndrome virus (WSSV) in juvenile, specific pathogen-freeLitopenaeus vannamei." Dis Aquat Organ74(2):85-94.
Escobedo-Bonilla, C. M., M. Wille, et al.(2005)."In vivo titration of white spotsyndrome virus (WSSV) in specific pathogen-free Litopenaeus vannamei byintramuscular and oral routes." Dis Aquat Organ66(2):163-170.
Esteban, D. J. and A. P. Hutchinson (2011)."Genes in the terminal regions oforthopoxvirus genomes experience adaptive molecular evolution." BMCGenomics12.
Evans, D. H., P. M. Piermarini, et al.(2005)."The multifunctional fish gill: Dominantsite of gas exchange, osmoregulation, acid-base regulation, and excretion ofnitrogenous waste." Physiological Reviews85(1):97-177.
Eyre-Walker, A. and P. D. Keightley (2007)."The distribution of fitness effects of newmutations." Nature Reviews Genetics8(8):610-618.
Farfante, I. P. and B. Kensley (1997)."Penaeoid and Sergestoid Shrimps and Prawnsof the World: Keys and Diagnoses for the Families and Genera." Washington,D.C.: National Museum of Natural History ISBN2-85653-510-0.
Farfante, I. P. and B. Kensley (1997)."Penaeoid and Sergestoid Shrimps and Prawnsof the World: Keys and Diagnoses for the Families and Genera." Memoires duMuseum National d'Histoire Naturelle175:223.
Field, K. G., G. J. Olsen, et al.(1988)."Molecular Phylogeny of the AnimalKingdom." Science239(4841):748-753.
Flegel, T. W. and K. Sritunyalucksana (2011)."Shrimp molecular responses to viralpathogens." Mar Biotechnol (NY)13(4):587-607.
Freire, C. A., F. Cavassin, et al.(2003)."Adaptive patterns of osmotic and ionicregulation, and the invasion of fresh water by the palaemonid shrimps." CompBiochem Physiol A Mol Integr Physiol136(3):771-778.
Freire, C. A., F. Cavassin, et al.(2003)."Adaptive patterns of osmotic and ionicregulation, and the invasion of fresh water by the palaemonid shrimps."Comparative Biochemistry and Physiology a-Molecular&Integrative Physiology136(3):771-778.
Friedrich, M. and D. Tautz (1995)."Ribosomal DNA Phylogeny of the Major ExtantArthropod Classes and the Evolution of Myriapods." Nature376(6536):165-167.
Friesen, T. L., E. H. Stukenbrock, et al.(2006)."Emergence of a new disease as aresult of interspecific virulence gene transfer." Nat Genet38(8):953-956.
Fuks, F.(2005)."DNA methylation and histone modifications: teaming up to silencegenes." Current Opinion in Genetics&Development15(5):490-495.
G., K.(2012)."Cell and Molecular Biology." Wiley5th Ed.
Galtier, N.(2007)."A model of horizontal gene transfer and the bacterial phylogenyproblem." Syst Biol56(4):633-642.
Gardner, A. E. and R. E. Dutch (2007)."A conserved region in the F(2) subunit ofparamyxovirus fusion proteins is involved in fusion regulation." J Virol81(15):8303-8314.
Gaucher, E. A., J. T. Kratzer, et al.(2010)."Deep phylogeny--how a tree can helpcharacterize early life on Earth." Cold Spring Harb Perspect Biol2(1): a002238.
Gerrish, P. J., A. Colato, et al.(2013)."Genomic mutation rates that neutralizeadaptive evolution and natural selection." Journal of the Royal Society Interface10(85).
Gil-Turnes, M. S., M. E. Hay, et al.(1989)."Symbiotic marine bacteria chemicallydefend crustacean embryos from a pathogenic fungus." Science246(4926):116-118.
Gilbert, C., S. Schaack, et al.(2010)."A role for host-parasite interactions in thehorizontal transfer of transposons across phyla." Nature464(7293):1347-1350.
Giordani, R. and J. Buc (2004)."Evidence for two different electron transfer pathwaysin the same enzyme, nitrate reductase A from Escherichia coli." Eur J Biochem271(12):2400-2407.
Giribet, G. and C. Ribera (1998)."The position of arthropods in the animal kingdom:A search for a reliable outgroup for internal arthropod phylogeny." MolPhylogenet Evol9(3):481-488.
Giribet, G. and W. C. Wheeler (1999)."The position of arthropods in the animalkingdom: Ecdysozoa, islands, trees, and the "parsimony ratchet"." MolPhylogenet Evol13(3):619-623.
Gogarten, J. P., W. F. Doolittle, et al.(2002)."Prokaryotic evolution in light of genetransfer." Mol Biol Evol19(12):2226-2238.
Goodman, D., N. Ollikainen, et al.(2007)."Baculovirus Phylogeny Based on GenomeRearrangements." LNBI4751：69—82.
Grabherr, M. G., B. J. Haas, et al.(2011)."Full-length transcriptome assembly fromRNA-Seq data without a reference genome." Nat Biotechnol29(7):644-652.
Grabherr, M. G., B. J. Haas, et al.(2011)."Full-length transcriptome assembly fromRNA-Seq data without a reference genome." Nature Biotechnology29(7):644-U130.
Grbic, M., T. Van Leeuwen, et al.(2011)."The genome of Tetranychus urticae revealsherbivorous pest adaptations." Nature479(7374):487-492.
Gribaldo, S. and C. Brochier (2009)."Phylogeny of prokaryotes: does it exist and whyshould we care?" Res Microbiol160(7):513-21.
Gross, P. S., T. C. Bartlett, et al.(2001)."Immune gene discovery by expressedsequence tag analysis of hemocytes and hepatopancreas in the Pacific WhiteShrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus." DevComp Immunol25(7):565-577.
Gu, H. F., J. H. Xiao, et al.(2014)."Adaptive evolution of the circadian gene timeoutin insects." Sci Rep4:4212.
Guan, X., P. Silva, et al.(2009)."The mitochondrial genome sequence and molecularphylogeny of the turkey, Meleagris gallopavo." Anim Genet40(2):134-141.
Gubser, C., S. Hue, et al.(2004)."Poxvirus genomes: a phylogenetic analysis." J GenVirol85(Pt1):105-117.
Gueguen, Y., J. Garnier, et al.(2006)."PenBase, the shrimp antimicrobial peptidepenaeidin database: sequence-based classification and recommendednomenclature." Dev Comp Immunol30(3):283-288.
Guindon, S., J. F. Dufayard, et al.(2010)."New algorithms and methods to estimatemaximum-likelihood phylogenies: assessing the performance of PhyML3.0."Syst Biol59(3):307-321.
Gutkin, M., R. Shamir, et al.(2009)."SlimPLS: a method for feature selection in geneexpression-based disease classification." PLoS One4(7): e6416.
Guyon, I. and A. e. Elisseeff (2003)."An Introduction to Variable and FeatureSelection." Journal of Machine Learning Research3,1157-1182.
Haas, B. J., A. Papanicolaou, et al.(2013)."De novo transcript sequencereconstruction from RNA-seq using the Trinity platform for reference generationand analysis." Nat Protoc8(8):1494-1512.
Haas, M. and B. Forbush (1998)."The Na-K-Cl cotransporters." Journal ofBioenergetics and Biomembranes30(2):161-172.
Hahlbrock, K. and D. Scheel (1989)."Physiology and molecular-biology ofphenylpropanoid metabolism." Annual Review of Plant Physiology and PlantMolecular Biology40:347-369.
Hahn, M. W., J. P. Demuth, et al.(2007)."Accelerated rate of gene gain and loss inprimates." Genetics177(3):1941-1949.
Han, B., Z. Obradovic, et al.(2006)."Substring selection for biomedical documentclassification." Bioinformatics22(17):2136-2142.
Han, M., S. Qin, et al.(2013)."Evolutionary rate patterns of genes involved in theDrosophila Toll and Imd signaling pathway." BMC Evol Biol13:245.
Hao, B. and J. Qi (2004)."Prokaryote phylogeny without sequence alignment: fromavoidance signature to composition distance." J Bioinform Comput Biol2(1):1-19.
Harwood, J. H. and D. H. Smith (1969)."Resistance factor-mediated streptomycinresistance." Journal of Bacteriology97(3):1262-1271.
Havird, J. C., R. P. Henry, et al.(2013)."Altered expression of Na+/K+-ATPase andother osmoregulatory genes in the gills of euryhaline animals in response tosalinity transfer: A meta-analysis of59quantitative PCR studies over10years."Comparative Biochemistry and Physiology D-Genomics&Proteomics8(2):131-140.
He, A., Y. Luo, et al.(2010)."Complete mitochondrial DNA sequences of the Niletilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): genomecharacterization and phylogeny applications." Mol Biol Rep.
Heather D. Bracken, Alicia Toon, et al.(2009)."The Decapod Tree of Life: Compilingthe Data and Moving toward a Consensus of Decapod Evolution." ArthropodSystematics&Phylogeny67(1):99-116.
Henz, S. R., D. H. Huson, et al.(2005)."Whole-genome prokaryotic phylogeny."Bioinformatics21(10):2329-2335.
Hessler, R. and W. Newman (1975)." A trilobitomorph origin for the Crustacea."
Heymons, R.(1901)."Die Entwicklungsgeschichte der Scolopender." Zoologica.Original-Abhandlungen aus dem gesammtgebliete der Zoologie33:244.
Higgs, P. I., R. A. Larsen, et al.(2002)."Quantification of known components of theEscherichia coli TonB energy transduction system: TonB, ExbB, ExbD andFepA." Mol Microbiol44(1):271-281.
Hill, C. A. and S. K. Wikel (2005)."The Ixodes scapularis Genome Project: anopportunity for advancing tick research." Trends Parasitol21(4):151-153.
Hirono, I., F. F. Fagutao, et al.(2011)."Uncovering the mechanisms of shrimp innateimmune response by RNA interference." Mar Biotechnol (NY)13(4):622-628.
Holt, R. A., G. M. Subramanian, et al.(2002)."The genome sequence of the malariamosquito Anopheles gambiae." Science298(5591):129-149.
Hotopp, J. C. D., M. E. Clark, et al.(2007)."Widespread lateral gene transfer fromintracellular bacteria to multicellular eukaryotes." Science317(5845):1753-1756.
Hsu, K. and S. Terakawa (1996)."Fenestration in the myelin sheath of nerve fibers ofthe shrimp: A novel node of excitation for saltatory conduction." Journal ofNeurobiology30(3):397-409.
Huang, S. W., Y. Y. Lin, et al.(2011)."Fosmid library end sequencing reveals a rarelyknown genome structure of marine shrimp Penaeus monodon." BMC Genomics12:242.
Huang, W., H. Xu, et al.(2012)."Characterization of Yatakemycin Gene ClusterRevealing a Radical S-Adenosylmethionine Dependent Methyltransferase andHighlighting Spirocyclopropane Biosynthesis." Journal of the AmericanChemical Society134(21):8831-8840.
Huang, W. J., J. H. Leu, et al.(2011)."Differential expression of LvHSP60in shrimpin response to environmental stress." Fish&Shellfish Immunology30(2):576-582.
Huang, X. and A. Madan (1999)."CAP3: A DNA sequence assembly program."Genome Res9(9):868-877.
Huelsenbeck, J. P., B. Larget, et al.(2000)."A compound poisson process for relaxingthe molecular clock." Genetics154(4):1879-1892.
Huelsenbeck, J. P. and F. Ronquist (2001)."MRBAYES: Bayesian inference ofphylogenetic trees." Bioinformatics17(8):754-755.
Hughes, A. L.(1999)."Adaptive Evolution of Genes and Genomes." OxfordUniversity Press:1-265.
Hughes, A. L. and R. Friedman (2005)."Poxvirus genome evolution by gene gain andloss." Mol Phylogenet Evol35(1):186-195.
Huynen, M. A. and P. Bork (1998)."Measuring genome evolution." Proc Natl AcadSci U S A95(11):5849-5856.
Huynh, K. D. and J. T. Lee (2005)."X-chromosome inactivation: a hypothesis linkingontogeny and phylogeny." Nat Rev Genet6(5):410-418.
Inoue, N., T. Soga, et al.(2000)."Mechanism of regulation of sodium pump isoformactivities in cultured cerebral neurons." Na/K-Atpase and Related Atpases1207:583-586.
Iwasaki, W. and T. Takagi (2007)."Reconstruction of highly heterogeneousgene-content evolution across the three domains of life." Bioinformatics23(13):i230-239.
Iyer, L. M., L. Aravind, et al.(2004)."Evolution of cell-cell signaling in animals: didlate horizontal gene transfer from bacteria have a role?" Trends Genet20(7):292-299.
James, T. Y., F. Kauff, et al.(2006)."Reconstructing the early evolution of Fungiusing a six-gene phylogeny." Nature443(7113):818-822.
Jang, K. H. and U. W. Hwang (2009)."Complete mitochondrial genome of Bugulaneritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position ofBryozoa and phylogeny of lophophorates within the Lophotrochozoa." BMCGenomics10:167.
Jeffares, D. C., T. Mourier, et al.(2006)."The biology of intron gain and loss." TrendsGenet22(1):16-22.
Jeffrey, E. C.(1906)."Morphology and Phylogeny." Science23(582):291-297.
Jelonek, J. and J. Stefanowski (1997)."Feature subset selection for classification ofhistological images." Artif Intell Med9(3):227-239.
Johnson, S. C.(1967)."Hierarchical clustering schemes." Psychometrika32(3):241-254.
Jung, H., R. E. Lyons, et al.(2011)."Transcriptomics of a Giant Freshwater Prawn(Macrobrachium rosenbergii): De Novo Assembly, Annotation and MarkerDiscovery." PLoS One6(12).
Kalujnaia, S., I. S. McWilliam, et al.(2007)."Transcriptomic approach to the study ofosmoregulation in the European eel Anguilla anguilla." Physiol Genomics31(3):385-401.
Kan, X. Z., J. K. Yang, et al.(2010)."Phylogeny of major lineages of galliform birds(Aves: Galliformes) based on complete mitochondrial genomes." Genet Mol Res9(3):1625-1633.
Kawahara-Miki, R., K. Wada, et al.(2011)."Expression Profiling without GenomeSequence Information in a Non-Model Species, Pandalid Shrimp (Pandaluslatirostris), by Next-Generation Sequencing." PLoS One6(10).
Keeling, P. J. and J. D. Palmer (2008)."Horizontal gene transfer in eukaryoticevolution." Nat Rev Genet9(8):605-618.
Kent, W. J.(2002)."BLAT--the BLAST-like alignment tool." Genome Res12(4):656-664.
Kim, H. and T. J. Crow (1999)."Identification and phylogeny of novel humanendogenous retroviral sequences belonging to the HERV-W family on the humanX chromosome." Arch Virol144(12):2403-2413.
Kimura, M. and T. Ohta (1973)."Eukaryotes-prokaryotes divergence estimated by5Sribosomal RNA sequences." Nat New Biol243(128):199-200.
Klaoudatos, S. D. and D. S. Klaoudatos (2008)."Phylogeny biology and ecology ofCrustaceans(Phylum Arthropoda; Subphylum Crusacea)." Reproductive Biologyof Crustaceans, Case studies of Decapod Crustaceans. Science Publishers, NewHampshire, USA: pp.
Klasson, L., Z. Kambris, et al.(2009)."Horizontal gene transfer between Wolbachiaand the mosquito Aedes aegypti." BMC Genomics10.
Klintworth, G. K.(1968)."The comparative anatomy and phylogeny of the tentoriumcerebelli." Anat Rec160(3):635-642.
Koch, I. and K. Naito (2007)."Dimension selection for feature selection anddimension reduction with principal and independent component analysis." NeuralComput19(2):513-545.
Komoto, N., K. Yukuhiro, et al.(2010)."Exploring the molecular phylogeny ofphasmids with whole mitochondrial genome sequences." Mol Phylogenet Evol.
Kondo, N., N. Nikoh, et al.(2002)."Genome fragment of Wolbachia endosymbionttransferred to X chromosome of host insect." Proc Natl Acad Sci U S A99(22):14280-14285.
Kornberg, H. L.(1987)."Krebs citric-acid cycle-half a century and still turning-introductory." Biochemical Society Symposium(54):1-2.
Kumar, D., P. Carvalho, et al.(2010)."Heart murmur classification with featureselection." Conf Proc IEEE Eng Med Biol Soc1:4566-4569.
Kunin, V. and C. A. Ouzounis (2003)."GeneTRACE-reconstruction of gene contentof ancestral species." Bioinformatics19(11):1412-1416.
Kurtz, S., A. Phillippy, et al.(2004)."Versatile and open software for comparing largegenomes." Genome Biol5(2): R12.
Lavery, S., T. Y. Chan, et al.(2004)."Phylogenetic relationships and evolutionaryhistory of the shrimp genus Penaeus s.l. derived from mitochondrial DNA." MolPhylogenet Evol31(1):39-49.
Lavrov, D. V., W. M. Brown, et al.(2004)."Phylogenetic position of the Pentastomidaand (pan)crustacean relationships." Proc Biol Sci271(1538):537-544.
Lavrov, D. V. and B. F. Lang (2005)."Poriferan mtDNA and animal phylogeny basedon mitochondrial gene arrangements." Syst Biol54(4):651-659.
Lawrence, J. G. and H. Ochman (1998)."Molecular archaeology of the Escherichiacoli genome." Proc Natl Acad Sci U S A95(16):9413-9417.
Letain, T. E. and K. Postle (1997)."TonB protein appears to transduce energy byshuttling between the cytoplasmic membrane and the outer membrane inEscherichia coli." Mol Microbiol24(2):271-283.
Li, C., S. Weng, et al.(2012)."Analysis of Litopenaeus vannamei TranscriptomeUsing the Next-Generation DNA Sequencing Technique." PLoS One7(10):e47442.
Li, C. Z., S. P. Weng, et al.(2012)."Analysis of Litopenaeus vannamei TranscriptomeUsing the Next-Generation DNA Sequencing Technique." PLoS One7(10).
Li, D. X., X. J. Du, et al.(2006)."Cloning and expression analysis of ano-methyltransferase (OMT) gene from Chinese shrimp, Fenneropenaeuschinensis." Fish Shellfish Immunol21(3):284-292.
Li, F. and J. Xiang (2013)."Recent advances in researches on the innate immunity ofshrimp in China." Dev Comp Immunol39(1-2):11-26.
Li, F. H. and J. H. Xiang (2013)."Signaling pathways regulating innate immuneresponses in shrimp." Fish&Shellfish Immunology34(4):973-980.
Li, G. L. and T. Y. Leong (2005)."Feature selection for the prediction of translationinitiation sites." Genomics Proteomics Bioinformatics3(2):73-83.
Li, H., A. Coghlan, et al.(2006)."TreeFam: a curated database of phylogenetic treesof animal gene families." Nucleic Acids Res34(Database issue): D572-580.
Li, M., J. H. Badger, et al.(2001)."An information-based sequence distance and itsapplication to whole mitochondrial genome phylogeny." Bioinformatics17(2):149-154.
Li, Q., Q. H. Liu, et al.(2013)."FATP synthase b-chain of Litopenaeus vannameiinvolved in White Spot Syndrome Virus infection." Virus Genes.
Li, R., W. Fan, et al.(2010)."The sequence and de novo assembly of the giant pandagenome." Nature463(7279):311-317.
Li, R., C. Yu, et al.(2009)."SOAP2: an improved ultrafast tool for short readalignment." Bioinformatics25(15):1966-1967.
Li, S.-T. and F.-C. Tsai (2011)."Noise control in document classification based onfuzzy formal concept analysis " Fuzzy Systems (FUZZ),2011IEEE InternationalConference on (27-30June):2583-2588.
Li, S., X. Zhang, et al.(2013)."Transcriptome Analysis on Chinese ShrimpFenneropenaeus chinensis during WSSV Acute Infection." PLoS One8(3):e58627.
Li, S. H., X. J. Zhang, et al.(2013)."Transcriptome Analysis on Chinese ShrimpFenneropenaeus chinensis during WSSV Acute Infection." PLoS One8(3).
Li, X. Z., Q. W. Luo, et al.(2009)."A Molybdopterin Oxidoreductase Is Involved inH-2Oxidation in Desulfovibrio desulfuricans G20." Journal of Bacteriology191(8):2675-2682.
Li, Z. W., Y. H. Shen, et al.(2011)."Pathogen-origin horizontally transferred genescontribute to the evolution of Lepidopteran insects." BMC Evol Biol11:356.
Liang, L., Y. Y. Shen, et al.(2013)."Adaptive Evolution of the Hox Gene Family forDevelopment in Bats and Dolphins." PLoS One8(6).
Lightner, D. V.(1985)."A review of the diseases of cultured penaeid shrimps andprawns with emphasis on recent discoveries and developments." Proceedings ofthe First International Conference on the Culture of Penaeid Prawns/Shrimps,4-7December1984, Iloilo City, Philippines: pp.79-103.
Lightner, D. V., R. P. Hedrick, et al.(1987)."A Survey of Cultured Penaeid Shrimp inTaiwan for Viral and Other Important Diseases." Fish Pathology22(3):127-140.
Lim, A. and L. Zhang (1999)."WebPHYLIP: a web interface to PHYLIP."Bioinformatics15(12):1068-1069.
Lin, F. J., Y. Liu, et al.(2012)."Evolution and phylogeny of the mud shrimps(Crustacea: Decapoda) revealed from complete mitochondrial genomes." BMCGenomics13.
Lin, J. and M. Gerstein (2000)."Whole-genome trees based on the occurrence of foldsand orthologs: implications for comparing genomes on different levels." GenomeRes10(6):808-818.
Lin, Y. F., S. R. Jing, et al.(2003)."The potential use of constructed wetlands in arecirculating aquaculture system for shrimp culture." Environmental Pollution123(1):107-113.
Lipson, R. S. and S. G. Clarke (2007)."S-adenosylmethionine-dependent proteinmethylation in mammalian cytosol via tyrphostin modification bycatechol-O-methyltransferase." Journal of Biological Chemistry282(42):31094-31102.
Little, J. W., D. W. Mount, et al.(1981)."Purified Lexa Protein Is a Repressor of theReca and Lexa Genes." Proceedings of the National Academy of Sciences of theUnited States of America-Biological Sciences78(7):4199-4203.
Logacheva, M. D., A. A. Penin, et al.(2007)."Phylogeny of flowering plants by thechloroplast genome sequences: in search of a "lucky gene"." Biochemistry (Mosc)72(12):1324-1330.
Long, M., N. W. VanKuren, et al.(2013)."New gene evolution: little did we know."Annu Rev Genet47:307-333.
Lopes, F. M., D. C. Martins, Jr., et al.(2008)."Feature selection environment forgenomic applications." BMC Bioinformatics9:451.
Lopez, P. and E. Bapteste (2009)."Molecular phylogeny: reconstructing the forest." CR Biol332(2-3):171-182.
Luo, H., J. Shi, et al.(2008)."Gene order phylogeny of the genus Prochlorococcus."PLoS One3(12): e3837.
Luo, R., B. Liu, et al.(2012)."SOAPdenovo2: an empirically improvedmemory-efficient short-read de novo assembler." Gigascience1(1):18.
Lustgarten, J. L., V. Gopalakrishnan, et al.(2009)."Measuring stability of featureselection in biomedical datasets." AMIA Annu Symp Proc2009:406-410.
Ma, K. Y., T.-Y. Chan, et al.(2009)."Phylogeny of penaeoid shrimps (Decapoda:Penaeoidea) inferred from nuclear protein-coding genes." MolecularPhylogenetics and Evolution53(1):45–55.
Ma, S. and J. Huang (2008)."Penalized feature selection and classification inbioinformatics." Brief Bioinform9(5):392-403.
Maggioni, R., A. D. Rogers, et al.(2001)."Molecular phylogeny of western AtlanticFarfantepenaeus and Litopenaeus shrimp based on mitochondrial16S partialsequences." Mol Phylogenet Evol18(1):66-73.
Magnan, C. N., A. Randall, et al.(2009)."SOLpro: accurate sequence-basedprediction of protein solubility." Bioinformatics25(17):2200-2207.
Maizels, N. and A. M. Weiner (1994)."Phylogeny from function: evidence from themolecular fossil record that tRNA originated in replication, not translation." ProcNatl Acad Sci U S A91(15):6729-6734.
Majoros, W. H., M. Pertea, et al.(2004)."TigrScan and GlimmerHMM: two opensource ab initio eukaryotic gene-finders." Bioinformatics20(16):2878-2879.
Manfrin, C., M. Tom, et al.(2013)."Application of D-Crustacean HyperglycemicHormone Induces Peptidases Transcription and Suppresses Glycolysis-RelatedTranscripts in the Hepatopancreas of the Crayfish Pontastacus leptodactylus-Results of a Transcriptomic Study." PLoS One8(6).
Manton, S.(1972)."The evolution of arthropod locomotory mechanisms." Zool. J.Linn. Soc.51:203-400.
Manton, S.(1979)."Functional morphology and the evolution of the hexapod classesin Arthropod Phylogeny." In: Gupta A P. Arthropod Phylogeny:387-466.
Manton, S. M. and J. P. Harding (1964)."Mandibular mechanisms and the evolutionof arthropods." Phil. Trans. R. Soc. Lond. B247(737):1-183.
Mardis, E. R.(2006)."Anticipating the1,000dollar genome." Genome Biol7(7):112.
Margulies, M., M. Egholm, et al.(2005)."Genome sequencing in microfabricatedhigh-density picolitre reactors." Nature437(7057):376-380.
Martin, J. L. and F. M. McMillan (2002)."SAM (dependent) I AM: theS-adenosylmethionine-dependent methyltransferase fold." Current Opinion inStructural Biology12(6):783-793.
Masai, H. and K. Arai (1988)."Operon structure of dnaT and dnaC genes essential fornormal and stable DNA replication of Escherichia coli chromosome." Journal ofBiological Chemistry263(29):15083-15093.
Matsui, A., F. Rakotondraparany, et al.(2009)."Molecular phylogeny and evolutionof prosimians based on complete sequences of mitochondrial DNAs." Gene441(1-2):53-66.
McInerney, J. O., J. A. Cotton, et al.(2008)."The prokaryotic tree of life: past,present... and future?" Trends Ecol Evol23(5):276-281.
Mclaughl.Pj and M. O. Dayhoff (1970)."Eukaryotes Versus Prokaryotes-an Estimateof Evolutionary Distance." Science168(3938):1469-&.
McLysaght, A., P. F. Baldi, et al.(2003)."Extensive gene gain associated withadaptive evolution of poxviruses." Proc Natl Acad Sci U S A100(26):15655-15660.
McNamara, J. C. and S. C. Faria (2012)."Evolution of osmoregulatory patterns andgill ion transport mechanisms in the decapod Crustacea: a review." Journal ofComparative Physiology B-Biochemical Systemic and Environmental Physiology182(8):997-1014.
McNulty, S. N., J. M. Foster, et al.(2010)."Endosymbiont DNA in endobacteria-freefilarial nematodes indicates ancient horizontal genetic transfer." PLoS One5(6):e11029.
Meehan, D., Z. Xu, et al.(2003)."High frequency and large number of polymorphicmicrosatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei[Crustacea:Decapoda]." Mar Biotechnol (NY)5(4):311-330.
Merget, B. and M. Wolf (2010)."A molecular phylogeny of Hypnales (Bryophyta)inferred from ITS2sequence-structure data." BMC Res Notes3:320.
Metzker, M. L.(2005)."Emerging technologies in DNA sequencing." Genome Res15(12):1767-1776.
Miao, S. and S. C. Tu (1996)."Modeling effect of thermic amplitude on growingChinese shrimp, Penaeus chinensis (Osbeck)." Ecological Modelling88(1-3):93-100.
Moran, N. A. and T. Jarvik (2010)."Lateral transfer of genes from fungi underliescarotenoid production in aphids." Science328(5978):624-627.
Morozov, A., E. Yung, et al.(1998)."Structure-function analysis of integraseinteractor1/hSNF5L1reveals differential properties of two repeat motifs presentin the highly conserved region." Proc Natl Acad Sci U S A95(3):1120-1125.
Moss, S. M., D. R. Moss, et al.(2012)."The role of selective breeding and biosecurityin the prevention of disease in penaeid shrimp aquaculture." J Invertebr Pathol110(2):247-250.
Murphy, W. J., D. M. Larkin, et al.(2005)."Dynamics of mammalian chromosomeevolution inferred from multispecies comparative maps." Science309(5734):613-617.
Narayanan, Y.(1973)."The phylogenetic relationships of the members of theDrosophila robusta group." Genetics73(2):319-350.
Nei, M. and S. Kumar (2000)."Molecular evolution and phylogenetics " OxfordUniversity Press:1-333.
Nikoh, N., J. P. McCutcheon, et al.(2010)."Bacterial genes in the aphid genome:absence of functional gene transfer from Buchnera to its host." PLoS Genet6(2):e1000827.
Nikoh, N. and A. Nakabachi (2009)."Aphids acquired symbiotic genes via lateralgene transfer." BMC Biol7:12.
Nikoh, N., K. Tanaka, et al.(2008)."Wolbachia genome integrated in an insectchromosome: evolution and fate of laterally transferred endosymbiont genes."Genome Res18(2):272-280.
Nye, T. M., P. Lio, et al.(2006)."A novel algorithm and web-based tool forcomparing two alternative phylogenetic trees." Bioinformatics22(1):117-119.
O'Leary, N. A., H. F. Trent,3rd, et al.(2006)."Analysis of multiple tissue-specificcDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei." IntegrComp Biol46(6):931-939.
Ochman, H.(2001)."Lateral and oblique gene transfer." Current Opinion in Genetics&Development11(6):616-619.
Otu, H. H. and K. Sayood (2003)."A new sequence distance measure for phylogenetictree construction." Bioinformatics19(16):2122-2130.
Overstreet, R. M.(1973)."Parasites of some penaeid shrimps with emphasis on rearedhosts." Aquaculture2:105-140.
Ozkurt, T. E., M. Sun, et al.(2006)."Optimal feature selection for seizure detection: asubspace based approach." Conf Proc IEEE Eng Med Biol Soc1:2134-2137.
Padhi, A., B. Verghese, et al.(2007)."Adaptive evolution after duplication ofpenaeidin antimicrobial peptides." Fish Shellfish Immunol23(3):553-566.
Palermo, C., J. C. Hope, et al.(2008)."Importance of a C-terminal conserved regionof Chk1for checkpoint function." PLoS One3(1): e1427.
Panganiban, G., A. Sebring, et al.(1995)."The development of crustacean limbs andthe evolution of arthropod." Science270:1363-1366.
Pasyk, E. A., X. K. Morin, et al.(1998)."A conserved region of the R domain ofcystic fibrosis transmembrane conductance regulator is important in processingand function." J Biol Chem273(48):31759-31764.
Patel, R. K. and M. Jain (2012)."NGS QC Toolkit: a toolkit for quality control of nextgeneration sequencing data." PLoS One7(2): e30619.
Pennisi, E.(2002)."Bacteria Shared Photosynt hesis Genes." Science298:1616-1620.
Pertea, G., X. Huang, et al.(2003)."TIGR Gene Indices clustering tools (TGICL): asoftware system for fast clustering of large EST datasets." Bioinformatics19(5):651-652.
Peters, A. E., A. Bavishi, et al.(2012)."Evolutionary constraints and expressionanalysis of gene duplications in Rhodobacter sphaeroides2.4.1." BMC Res Notes5:192.
Podsiadlowski, L. and T. Bartolomaeus (2006)."Major rearrangements characterizethe mitochondrial genome of the isopod Idotea baltica (Crustacea: Peracarida)."Mol Phylogenet Evol40(3):893-899.
Pok, G., J. C. Liu, et al.(2010)."Effective feature selection framework for clusteranalysis of microarray data." Bioinformation4(8):385-389.
Porter, M. L., M. Perez-Losada, et al.(2005)."Model-based multi-locus estimation ofdecapod phylogeny and divergence times." Mol Phylogenet Evol37(2):355-369.
Pride, D. T., R. J. Meinersmann, et al.(2003)."Evolutionary implications of microbialgenome tetranucleotide frequency biases." Genome Res13(2):145-158.
Qi, J., H. Luo, et al.(2004)."CVTree: a phylogenetic tree reconstruction tool based onwhole genomes." Nucleic Acids Res32(Web Server issue): W45-47.
Qi, J., B. Wang, et al.(2004)."Whole proteome prokaryote phylogeny withoutsequence alignment: a K-string composition approach." J Mol Evol58(1):1-11.
Qi, Z. H., J. M. Wang, et al.(2009)."Classification analysis of dual nucleotides usingdimension reduction." J Theor Biol260(1):104-109.
Quan, J., Z. Zhuang, et al.(2004)."Phylogenetic relationships of12penaeoideashrimp species deduced from mitochondrial DNA sequences." Biochem Genet42(9-10):331-345.
Richards, S., R. A. Gibbs, et al.(2008)."The genome of the model beetle and pestTribolium castaneum." Nature452(7190):949-955.
Richards, T. A., D. M. Soanes, et al.(2011)."Horizontal gene transfer facilitated theevolution of plant parasitic mechanisms in the oomycetes." Proc Natl Acad Sci US A108(37):15258-15263.
Rizvi, S. B., A. K. Shukla, et al.(2009)."A simple method based on multiplealignment and phylogeny to derive a correlation between the protein fold andsequence via motif search." Interdiscip Sci1(3):235-243.
Robalino, J., J. S. Almeida, et al.(2007)."Insights into the immune transcriptome ofthe shrimp Litopenaeus vannamei: tissue-specific expression profiles andtranscriptomic responses to immune challenge." Physiol Genomics29(1):44-56.
Robinson, M. D., D. J. McCarthy, et al.(2010)."edgeR: a Bioconductor package fordifferential expression analysis of digital gene expression data." Bioinformatics26(1):139-140.
Robles, R., C. D. Schubart, et al.(2007)."Molecular phylogeny of the AmericanCallinectes Stimpson,1860(Brachyura: Portunidae), based on two partialmitochondrial genes." Marine Biology150(6):1265-1274.
Rodelsperger, C. and R. J. Sommer (2011)."Computational archaeology of thePristionchus pacificus genome reveals evidence of horizontal gene transfers frominsects." BMC Evol Biol11:239.
Rokas, A., B. L. Williams, et al.(2003)."Genome-scale approaches to resolvingincongruence in molecular phylogenies." Nature425(6960):798-804.
Ronquist, F., M. Teslenko, et al.(2012)."MrBayes3.2: efficient Bayesianphylogenetic inference and model choice across a large model space." Syst Biol61(3):539-542.
Rosten, E., R. Porter, et al.(2010)."Faster and better: a machine learning approach tocorner detection." IEEE Trans Pattern Anal Mach Intell32(1):105-119.
Ruan, J., H. Li, et al.(2008)."TreeFam:2008Update." Nucleic Acids Res36(Database issue): D735-740.
Rumpho, M. E., J. M. Worful, et al.(2008)."Horizontal gene transfer of the algalnuclear gene psbO to the photosynthetic sea slug Elysia chlorotica." Proc NatlAcad Sci U S A105(46):17867-17871.
Saeys, Y., I. Inza, et al.(2007)."A review of feature selection techniques inbioinformatics." Bioinformatics23(19):2507-2517.
Saitou, N. and M. Nei (1987)."The neighbor-joining method: a new method forreconstructing phylogenetic trees." Mol Biol Evol4(4):406-425.
Schierwater, B., S. O. Kolokotronis, et al.(2009)."The Diploblast-Bilateria Sisterhypothesis: parallel revolution of a nervous systems may have been a simplestep." Commun Integr Biol2(5):403-405.
Schnell, J. R., H. J. Dyson, et al.(2004)."Structure, dynamics, and catalytic functionof dihydrofolate reductase." Annual Review of Biophysics and BiomolecularStructure33:119-140.
Schram, F. R.(2001)."Phylogeny of decapods: moving towards a consensus."Hydrobiologia449(1-3):1-20.
Schwer, B., J. Bunkenborg, et al.(2006)."Reversible lysine acetylation controls theactivity of the mitochondrial enzyme acetyl-CoA synthetase2." Proc Natl AcadSci U S A103(27):10224-10229.
Semino, O., A. S. Santachiara-Benerecetti, et al.(2002)."Ethiopians and Khoisanshare the deepest clades of the human Y-chromosome phylogeny." Am J HumGenet70(1):265-268.
Sever, D. M.(1992)."Comparative anatomy and phylogeny of the cloacae ofsalamanders (Amphibia: Caudata). IV. Salamandridae." Anat Rec233(2):229-244.
Shapeero, W. L.(1961)."Phylogeny of Priapulida." Science133(3456):879-880.
Shaw, W. V., L. C. Packman, et al.(1979)."Primary structure of a chloramphenicolacetyltransferase specified by R plasmids." Nature282(5741):870-872.
Shen, L. and E. C. Tan (2005)."Dimension reduction-based penalized logisticregression for cancer classification using microarray data." IEEE/ACM TransComput Biol Bioinform2(2):166-175.
Shen, X., M. Sun, et al.(2009)."The complete mitochondrial genome of the ridgetailwhite prawn Exopalaemon carinicauda Holthuis,1950(Crustacean: Decapoda:Palaemonidae) revealed a novel rearrangement of tRNA genes." Gene437(1-2):1-8.
Shubo, Z. and L. Jian-huang (2010)."Bioinformatics approach for molocularevolution research." Computer Science37(8):47-51.
Sims, G. E., S. R. Jun, et al.(2009)."Alignment-free genome comparison with featurefrequency profiles (FFP) and optimal resolutions." Proc Natl Acad Sci U S A106(8):2677-2682.
Snel, B., P. Bork, et al.(2002)."Genomes in flux: the evolution of archaeal andproteobacterial gene content." Genome Res12(1):17-25.
Snodgrass, R.(1938)."Evolution of the Annelida, Onychophora and Arthropoda."Smithson. Misc. collect.97:1-159.
Sogin, S. J., M. L. Sogin, et al.(1971)."Phylogenetic measurement in procaryotes byprimary structural characterization." J Mol Evol1(1):173-184.
Stanhope, M. J., A. Lupas, et al.(2001)."Phylogenetic analyses do not supporthorizontal gene transfers from bacteria to vertebrates." Nature411(6840):940-944.
Stanke, M. and B. Morgenstern (2005)."AUGUSTUS: a web server for geneprediction in eukaryotes that allows user-defined constraints." Nucleic Acids Res33: W465-W467.
Stenderup, J. T., J. Olesen, et al.(2006)."Molecular phylogeny of the Branchiopoda(Crustacea)--multiple approaches suggest a 'diplostracan' ancestry of theNotostraca." Mol Phylogenet Evol41(1):182-194.
Struck, T. H. and F. Fisse (2008)."Phylogenetic position of Nemertea derived fromphylogenomic data." Mol Biol Evol25(4):728-736.
Stuart, G. W., K. Moffett, et al.(2002)."Integrated gene and species phylogenies fromunaligned whole genome protein sequences." Bioinformatics18(1):100-108.
Stuart, G. W., K. Moffett, et al.(2002)."A comprehensive vertebrate phylogeny usingvector representations of protein sequences from whole genomes." Mol Biol Evol19(4):554-562.
Studer, R. A., P. A. Christin, et al.(2014)."Stability-activity tradeoffs constrain theadaptive evolution of RubisCO." Proc Natl Acad Sci U S A111(6):2223-2228.
Sudar, E., M. Velebit, et al.(2008)."Hypothetical mechanism of sodium pumpregulation by estradiol under primary hypertension." Journal of TheoreticalBiology251(4):584-592.
Sung, Y. Y., T. H. MacRae, et al.(2011)."Stress response for disease control inaquaculture." Reviews in Aquaculture3(3):120-137.
Supek, F., M. Bosnjak, et al.(2011)."REVIGO summarizes and visualizes long listsof gene ontology terms." PLoS One6(7): e21800.
Sutton, B. C.(1993)."Mitosporic fungi (Deuteromycetes) in thefictionary-of-the-fungi." Fungal Holomorph: Mitotic, Meiotic and PleomorphicSpeciation in Fungal Systematics:27-55.
Tagle, D. A., B. F. Koop, et al.(1988)."Embryonic epsilon and gamma globin genesof a prosimian primate (Galago crassicaudatus). Nucleotide and amino acidsequences, developmental regulation and phylogenetic footprints." J Mol Biol203(2):439-455.
Tamura, K., J. Dudley, et al.(2007)."MEGA4: Molecular Evolutionary GeneticsAnalysis (MEGA) software version4.0." Mol Biol Evol24(8):1596-1599.
Tekaia, F., A. Lazcano, et al.(1999)."The genomic tree as revealed from wholeproteome comparisons." Genome Res9(6):550-557.
Thompson, J. D., T. J. Gibson, et al.(2002)."Multiple sequence alignment usingClustalW and ClustalX." Curr Protoc Bioinformatics Chapter2: Unit23.
Tsagkogeorga, G., X. Turon, et al.(2009)."An updated18S rRNA phylogeny oftunicates based on mixture and secondary structure models." BMC Evol Biol9:187.
Tsang, L. M., K. Y. Ma, et al.(2008)."Phylogeny of Decapoda using two nuclearprotein-coding genes: Origin and evolution of the Reptantia." Mol PhylogenetEvol48(1):359-368.
Tsuji, J., M. C. Frith, et al.(2012)."Mammalian NUMT insertion is non-random."Nucleic Acids Res40(18):9073-9088.
Tudge, C. C.(1997)."Phylogeny of the Anomura (Decapoda, Crustacea):Spermatozoa and spermatophore morphological evidence." Contributions toZoology67(2):125-141.
Turbeville, J. M., D. M. Pfeifer, et al.(1991)."The Phylogenetic Status of Arthropods,as Inferred from18s Ribosomal-Rna Sequences." Mol Biol Evol8(5):669-686.
Twine, N. A., K. Janitz, et al.(2011)."Whole transcriptome sequencing reveals geneexpression and splicing differences in brain regions affected by Alzheimer'sdisease." PLoS One6(1): e16266.
Umetsu, K., N. Iwabuchi, et al.(2002)."Complete mitochondrial DNA sequence of atadpole shrimp (Triops cancriformis) and analysis of museum samples."Electrophoresis23(24):4080-4084.
Wang, L., W. N. Wang, et al.(2012)."Two types of ATPases from the Pacific whiteshrimp, Litopenaeus vannamei in response to environmental stress." MolecularBiology Reports39(6):6427-6438.
Wang, P. H., D. H. Wan, et al.(2011)."Litopenaeus vannamei tumor necrosis factorreceptor-associated factor6(TRAF6) responds to Vibrio alginolyticus and whitespot syndrome virus (WSSV) infection and activates antimicrobial peptidegenes." Dev Comp Immunol35(1):105-114.
Wang, W., Y. Tian, et al.(2012)."Integration genetic linkage map construction andseveral potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis)based on three types of molecular markers." Genetika48(4):508-521.
Wang, X., S. Bandyopadhyay, et al.(2007)."Prediction of transcription start sitesbased on feature selection using AMOSA." Comput Syst Bioinformatics Conf6:183-193.
Wang, X., X. Fang, et al.(2014)."The locust genome provides insight into swarmformation and long-distance flight." Nat Commun5:2957.
Warnock, R. C., Z. Yang, et al.(2012)."Exploring uncertainty in the calibration of themolecular clock." Biol Lett8(1):156-159.
Waters, S. B., S. Lin, et al.(2003)."A novel S-adenosylmethionine-dependentmethyltransferase from rat liver cytosol catalyzes the formation of methylatedarsenicals." Arsenic Exposure and Health Effects V:255-266.
Wei, H. L. and S. A. Billings (2007)."Feature subset selection and ranking for datadimensionality reduction." IEEE Trans Pattern Anal Mach Intell29(1):162-166.
Weinstock, G. M., G. E. Robinson, et al.(2006)."Insights into social insects from thegenome of the honeybee Apis mellifera." Nature443(7114):931-949.
Wicker, T., E. Schlagenhauf, et al.(2006)."454sequencing put to the test using thecomplex genome of barley." BMC Genomics7:275.
Wills, M. A.(2002)."The tree of life and the rock of ages: are we getting better atestimating phylogeny?" Bioessays24(3):203-207.
Winbush, A., D. Reed, et al.(2012)."Identification of gene expression changesassociated with long-term memory of courtship rejection in Drosophila males."G3(Bethesda)2(11):1437-1445.
Woese, C. R., O. Kandler, et al.(1990)."Towards a natural system of organisms:proposal for the domains Archaea, Bacteria, and Eucarya." Proc Natl Acad Sci US A87(12):4576-4579.
Wolf, Y. I., I. B. Rogozin, et al.(2001)."Genome alignment, evolution of prokaryoticgenome organization, and prediction of gene function using genomic context."Genome Res11(3):356-372.
Woolfit, M., I. Iturbe-Ormaetxe, et al.(2009)."An Ancient Horizontal Gene Transferbetween Mosquito and the Endosymbiotic Bacterium Wolbachia pipientis." MolBiol Evol26(2):367-374.
Worm, J. and P. Guldberg (2002)."DNA methylation: an epigenetic pathway to cancerand a promising target for anticancer therapy." Journal of Oral Pathology&Medicine31(8):443-449.
Wu, D. D., G. M. Li, et al.(2012)."Positive Selection on the Osteoarthritis-Risk andDecreased-Height Associated Variants at the GDF5Gene in East Asians." PLoSOne7(8).
Wu, X. and P. A. Sharp (2013)."Divergent transcription: a driving force for new geneorigination?" Cell155(5):990-996.
Xia, Q., Y. Guo, et al.(2009)."Complete resequencing of40genomes revealsdomestication events and genes in silkworm (Bombyx)." Science326(5951):433-436.
Xilin, D., Z. Weiling, et al.(1999)."Effects of temperature and dissolved oxygencontent on oxygen consumption rate of Chinese prawn, giant tiger prawn andgiant freshwater prawn." Chinese Journal of Oceanology and Limnology17(2):119-127.
Xiong, H., D. Capurso, et al.(2011)."Sequence-based classification usingdiscriminatory motif feature selection." PLoS One6(11): e27382.
Xu, Z. and B. Hao (2009)."CVTree update: a newly designed phylogenetic studyplatform using composition vectors and whole genomes." Nucleic Acids Res37(Web Server issue): W174-178.
Xue, S. X., Y. C. Liu, et al.(2013)."Sequencing and De Novo Analysis of theHemocytes Transcriptome in Litopenaeus vannamei Response to White SpotSyndrome Virus Infection." PLoS One8(10).
Yang, L. S., Z. X. Yin, et al.(2007)."A Toll receptor in shrimp." Mol Immunol44(8):1999-2008.
Yang, Z.(1997)."PAML: a program package for phylogenetic analysis by maximumlikelihood." Comput Appl Biosci13(5):555-556.
Yang, Z.(2007)."PAML4: phylogenetic analysis by maximum likelihood." Mol BiolEvol24(8):1586-1591.
Yang, Z., R. Nielsen, et al.(2000)."Codon-substitution models for heterogeneousselection pressure at amino acid sites." Genetics155(1):431-449.
Yang, Z. and W. J. Swanson (2002)."Codon-substitution models to detect adaptiveevolution that account for heterogeneous selective pressures among site classes."Mol Biol Evol19(1):49-57.
Yu, Z. a. Z., Li-Qian and Anh, Vo V. and Chu, K. H. and Li, C. P. and Chen, Y. J.(2007)."Distance-based analysis to reveal vertebrate phylogeny withoutsequence alignment using complete mitochondrial genomes." Proceedings11thWorld Multi-Conference on Systemics, Cybernetics and Informatics: WMSCI2007,:206-211.
Yu, Z. G., L. Q. Zhou, et al.(2005)."Phylogeny of prokaryotes and chloroplastsrevealed by a simple composition approach on all protein sequences fromcomplete genomes without sequence alignment." J Mol Evol60(4):538-545.
Yushkevich, P., S. Joshi, et al.(2003)."Feature selection for shape-based classificationof biological objects." Inf Process Med Imaging18:114-125.
Zablen, L., L. Bonen, et al.(1975)."The phylogenetic status of Pasteurella pestis." JMol Evol4(4):347-358.
Zeng, F., R. H. Yap, et al.(2002)."Using feature generation and feature selection foraccurate prediction of translation initiation sites." Genome Inform13:192-200.
Zenteno-Savin, T.(2005)."Oxidative stress in response to environmentalhypoxia/reoxygenation in two crustacean species, Pacific white shrimp(Litopenaeus vannamei) and red claw crayfish (Cherax quadricarinatus)." FreeRadical Biology and Medicine39: S177-S177.
Zhan, S., C. Merlin, et al.(2011)."The Monarch Butterfly Genome Yields Insightsinto Long-Distance Migration." Cell147(5):1171-1185.
Zhang, C., M. Zhao, et al.(2011)."An improved algorithm for corner detection "Electronic and Mechanical Engineering and Information Technology (EMEIT),2011International Conference on(12-14Aug.):4639-4641
Zhang, G., X. Fang, et al.(2012)."The oyster genome reveals stress adaptation andcomplexity of shell formation." Nature490(7418):49-54.
Zhang, X., Y. Zhang, et al.(2010)."Construction and characterization of a bacterialartificial chromosome (BAC) library of Pacific white shrimp, Litopenaeusvannamei." Mar Biotechnol (NY)12(2):141-149.
Zhang, Z., J. Li, et al.(2006)."KaKs_Calculator: calculating Ka and Ks throughmodel selection and model averaging." Genomics Proteomics Bioinformatics4(4):259-263.
Zhaxybayeva, O., C. L. Nesbo, et al.(2007)."Systematic overestimation of gene gainthrough false diagnosis of gene absence." Genome Biol8(2).
Zhu, B., M. M. Lou, et al.(2011)."Horizontal gene transfer in silkworm, Bombyxmori." BMC Genomics12:248.
Zimmermann, K., M. Engeser, et al.(2009)."Pederin-type pathways of uncultivatedbacterial symbionts: analysis of o-methyltransferases and generation of abiosynthetic hybrid." J Am Chem Soc131(8):2780-2781.
Zrzavy, J. and P. Stys (1997)."The basic body plan of arthropods: Insights fromevolutionary morphology and developmental biology." Journal of EvolutionaryBiology10(3):353-367.
Zuckerkandl, E. and L. B. Pauling (1962)."Molecular disease, evolution, and geneticheterogeneity." New York: Horizons in Biochemistry:189-225.
岑伯明,胡洲, et al.(2012)."凡纳滨对虾养殖池塘水温预测模型研究."宁波大学学报：理工版25(1):7-12.
刘培生(1995)."适应性进化与物种形成."化石2:19-21.
刘帅,李墨非, et al.(2012)."基于线粒体16S rRNA和COI基因序列探讨对虾属(Penaeus)物种系统发生关系."生物学杂志29(5):37-42.
沈文英,阳会军, et al.(2004)."南美白对虾的病害及防治研究现状."水利渔业24(1):58-60.
朱玉贤(2013)."现代分子生物学(第4版)."高等教育出版社4:1-484.
Ackerly, D. D.(2003)."Community assembly, niche conservatism, and adaptiveevolution in changing environments." International Journal of Plant Sciences164(3): S165-S184.
Adams, M. D., S. E. Celniker, et al.(2000)."The genome sequence of Drosophilamelanogaster." Science287(5461):2185-2195.
Adoutte, A., G. Balavoine, et al.(2000)."The new animal phylogeny: reliability andimplications." Proc Natl Acad Sci U S A97(9):4453-4456.
Aguinaldo, A. M., J. M. Turbeville, et al.(1997)."Evidence for a clade of nematodes,arthropods and other moulting animals." Nature387(6632):489-493.
Ahyong, S. T. and D. O'Meally (2004)."Phylogeny of the Decapoda reptantia:Resolution using three molecular loci and morphology." Raffles Bulletin ofZoology52(2):673-693.
Aikawa, T., H. Anbutsu, et al.(2009)."Longicorn beetle that vectors pinewoodnematode carries many Wolbachia genes on an autosome." Proceedings of theRoyal Society B-Biological Sciences276(1674):3791-3798.
Alba, M. M., R. Das, et al.(2001)."Genomewide function conservation andphylogeny in the Herpesviridae." Genome Res11(1):43-54.
Alderton, G. K.(2014)."Neuroblastoma: A new gene that promotes NMYC activity."Nat Rev Cancer14(3):155.
Allen, G. C. and A. Kornberg (1993)."Assembly of the Primosome ofDNA-Replication in Escherichia-Coli." Journal of Biological Chemistry268(26):19204-19209.
Altincicek, B., J. L. Kovacs, et al.(2012)."Horizontally transferred fungal carotenoidgenes in the two-spotted spider mite Tetranychus urticae." Biol Lett8(2):253-257.
Andersson, J. O., A. M. Sjogren, et al.(2003)."Phylogenetic analyses of diplomonadgenes reveal frequent lateral gene transfers affecting eukaryotes." Curr Biol13(2):94-104.
Andriantahina, F., X. Liu, et al.(2013)."Current status of genetics and genomics ofreared penaeid shrimp: information relevant to access and benefit sharing." MarBiotechnol (NY)15(4):399-412.
Assavalapsakul, W. and S. Panyim (2012)."Molecular cloning and tissue distributionof the Toll receptor in the black tiger shrimp, Penaeus monodon." Genet Mol Res11(1):484-493.
Atum, Y., I. Gareis, et al.(2010)."Genetic feature selection to optimally detect P300in brain computer interfaces." Conf Proc IEEE Eng Med Biol Soc1:3289-3292.
Auch, A. F., S. R. Henz, et al.(2006)."Genome BLAST distance phylogenies inferredfrom whole plastid and whole mitochondrion genome sequences." BMCBioinformatics7:350.
Averof, M. and M. Akam (1995)."Hox Genes and the Diversification of Insect andCrustacean Body Plans." Nature376(6539):420-423.
Babbitt, C. C. and N. H. Patel (2005)."Relationships within the Pancrustacea:examining the influence of additional malacostracan18S and28S rDNA." Crust.Issues16(275-294).
Bachmann, S., T. Saritas, et al.(2013)."STE20-like kinase SPAK differentiallyregulates Na-(K)-Cl cotransporters along the distal nephron under the endocrinecontrol of AVP." Faseb Journal27.
Baele, G., P. Lemey, et al.(2012)."Improving the accuracy of demographic andmolecular clock model comparison while accommodating phylogeneticuncertainty." Mol Biol Evol29(9):2157-2167.
Bafna, V. and P. A. Pevzner (1995)."Sorting by reversals：Genome rearrangement inplant organelles and evolutionary history of X chromosome." Mol Biol Evol12：239—24.
Bao, R. and M. Friedrich (2009)."Molecular evolution of the Drosophila retinome:exceptional gene gain in the higher Diptera." Mol Biol Evol26(6):1273-1287.
Bapteste, E., Y. Boucher, et al.(2004)."Phylogenetic reconstruction and lateral genetransfer." Trends Microbiol12(9):406-411.
Baralis, E., G. Bruno, et al.(2008)."Minimum number of genes for microarray featureselection." Conf Proc IEEE Eng Med Biol Soc2008:5692-5695.
Baranski, M., G. Gopikrishna, et al.(2014)."The Development of a High DensityLinkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs."PLoS One9(1).
Baranski, M., G. Gopikrishna, et al.(2014)."The Development of a High DensityLinkage Map for Black Tiger Shrimp (Penaeus monodon) Based on cSNPs."PLoS One9(1): e85413.
Beaber, J. W., B. Hochhut, et al.(2004)."SOS response promotes horizontaldissemination of antibiotic resistance genes." Nature427(6969):72-74.
Beiko, R. G., T. J. Harlow, et al.(2005)."Highways of gene sharing in prokaryotes."Proc Natl Acad Sci U S A102(40):14332-14337.
Belda, E., A. Moya, et al.(2005)."Genome rearrangement distances and gene orderphylogeny in gamma-Proteobacteria." Mol Biol Evol22(6):1456-1467.
Benjamini, Y. and Y. Hochberg (1995)."Controlling the false discovery rate-apractical and powerful approach to multiple testing." Journal of the RoyalStatistical Society Series B-Methodological57(1):289-300.
Bird, A. P.(1986)."Cpg-Rich Islands and the Function of DNA Methylation." Nature321(6067):209-213.
Blanchette, M. and M. Tompa (2002)."Discovery of regulatory elements by acomputational method for phylogenetic footprinting." Genome Res12(5):739-748.
Boas, F. E. V.(1880)."Studier over decapodernes slaegtskabsforhold." DanskVidenskabernes Seksjeab, Copenhagen, Skrifter, Naturvidenskabelig ogmatematisek Afdeling1:26-210.
Boore, J. L., T. M. Collins, et al.(1995)."Deducing the Pattern of ArthropodPhylogeny from Mitochondrial-DNA Rearrangements." Nature376(6536):163-165.
Bork, P.(1993)."Hundreds of ankyrin-like repeats in functionally diverse proteins-mobile modules that cross phyla horizontally." Proteins-Structure Function andGenetics17(4):363-374.
Bracken, H. D., S. De Grave, et al.(2010)."Phylogenetic position, systematic status,and divergence time of the Procarididea (Crustacea: Decapoda)." ZoologicaScripta39(2):198-212.
Brooks, W. K.(1883)."The Phylogeny of the Higher Crustacea." Science2(46):790-793.
Bullard, J. H., E. Purdom, et al.(2010)."Evaluation of statistical methods fornormalization and differential expression in mRNA-Seq experiments." BMCBioinformatics11:94.
Burge, C. and S. Karlin (1997)."Prediction of complete gene structures in humangenomic DNA." J Mol Biol268(1):78-94.
Burge, E. J., D. J. Madigan, et al.(2007)."Lysozyme gene expression by hemocytesof Pacific white shrimp, Litopenaeus vannamei, after injection with Vibrio." FishShellfish Immunol22(4):327-339.
Burkenroad, M. D.(1981)."The higher taxonomy and evolution of Decapoda(Crustacea)." Transactions of the San Diego Society of Natural History19:251-268.
Cao, Z., Y. Yu, et al.(2013)."The genome of Mesobuthus martensii reveals a uniqueadaptation model of arthropods." Nat Commun4:2602.
Castresana, J.(2000)."Selection of conserved blocks from multiple alignments fortheir use in phylogenetic analysis." Mol Biol Evol17(4):540-552.
Center, G. S. L.(2012, August6)."The brine shrimp life cycle." Learn. Genetics.
Chan, C. X., D. Bhattacharya, et al.(2012)."Endosymbiotic and horizontal genetransfer in microbial eukaryotes: Impacts on cell evolution and the tree of life."Mob Genet Elements2(2):101-105.
Chapman, J. A., E. F. Kirkness, et al.(2010)."The dynamic genome of Hydra."Nature464(7288):592-596.
Chen, H. and M. Blanchette (2007)."Detecting non-coding selective pressure incoding regions." BMC Evol Biol7Suppl1: S9.
Chen, H. W., Z. B. Zhao, et al.(2001)."Insights into the branched-chain formation ofmycarose: Methylation catalyzed by an (S)-adenosylmethionine-dependentmethyltransferase." Angewandte Chemie-International Edition40(3):607-610.
Chen, J. C., J. N. Lin, et al.(1996)."Survival, growth and intermolt period of juvenilePenaeus chinensis (Osbeck) reared at different combinations of salinity andtemperature." Journal of Experimental Marine Biology and Ecology204(1-2):169-178.
Chen, M. J., T. Shimada, et al.(1984)."The Functional HumanDihydrofolate-Reductase Gene." Journal of Biological Chemistry259(6):3933-3943.
Chen, S., G. Zhang, et al.(2014)."Whole-genome sequence of a flatfish providesinsights into ZW sex chromosome evolution and adaptation to a benthiclifestyle." Nat Genet46(3):253-260.
Chen, X. H., D. G. Zeng, et al.(2013)."Transcriptome Analysis of Litopenaeusvannamei in Response to White Spot Syndrome Virus Infection." PLoS One8(8).
Chiba, S., K. Yoshino, et al.(2013)."Maladaptive sex ratio adjustment by asex-changing shrimp in selective-fishing environments." Journal of AnimalEcology82(3):632-641.
Chien, Y. H.(1992)."Water-Quality Requirements and Management for MarineShrimp Culture." Proceedings of the Special Session on Shrimp Farming:144-156.
Chiron, H., A. Drouet, et al.(2000)."Molecular cloning and functional expression of astress-induced multifunctional O-methyltransferase with pinosylvinmethyltransferase activity from Scots pine (Pinus sylvestris L.)." Plant MolecularBiology44(6):733-745.
Cho, B. H., H. Yu, et al.(2008)."Application of irregular and unbalanced data topredict diabetic nephropathy using visualization and feature selection methods."Artif Intell Med42(1):37-53.
Choi, I. G. and S. H. Kim (2007)."Global extent of horizontal gene transfer." ProcNatl Acad Sci U S A104(11):4489-4494.
Choudhary, A., M. Brun, et al.(2006)."Genetic test bed for feature selection."Bioinformatics22(7):837-842.
Chu, K. H., L. M. Tsang, et al.(2008)."Decapod phylogeny: what can protein codinggenes tell us?" Decapod Crustacean Phylogenetics18:89-99.
Chuang, L. Y., C. H. Ke, et al.(2009)."A two-stage feature selection method for geneexpression data." OMICS13(2):127-137.
Colbourne, J. K., M. E. Pfrender, et al.(2011)."The ecoresponsive genome ofDaphnia pulex." Science331(6017):555-561.
Cover, T. M. and J. A. Thomas (1991)."Elements of Information Theory."(New York:Wiley).
Crandall, K. A., D. J. Harris, et al.(2000)."The monophyletic origin of freshwatercrayfish estimated from nuclear and mitochondrial DNA sequences." Proceedingsof the Royal Society B-Biological Sciences267(1453):1679-1686.
Creevey, C. J., J. Muller, et al.(2011)."Identifying Single Copy Orthologs inMetazoa." Plos Computational Biology7(12).
Cruz, P., A. M. Ibarra, et al.(2004)."Genetic variability assessed by microsatellites ina breeding program of Pacific white shrimp (Litopenaeus vannamei)." MarBiotechnol (NY)6(2):157-164.
Cutler, C. P., A. S. Martinez, et al.(2007)."The role of aquaporin3in teleost fish."Comparative Biochemistry and Physiology a-Molecular&Integrative Physiology148(1):82-91.
Dam, P., V. Olman, et al.(2007)."Operon prediction using both genome-specific andgeneral genomic information." Nucleic Acids Res35(1):288-298.
Dang, L. T., T. Koyama, et al.(2010)."Involvement of WSSV-shrimp homologs inWSSV infectivity in kuruma shrimp: Marsupenaeus japonicus." Antiviral Res88(2):217-226.
De Bie, T., N. Cristianini, et al.(2006)."CAFE: a computational tool for the study ofgene family evolution." Bioinformatics22(10):1269-1271.
DeFaveri, J., T. Shikano, et al.(2011)."Global Analysis of Genes Involved inFreshwater Adaptation in Threespine Sticklebacks (Gasterosteus Aculeatus)."Evolution65(6):1800-1807.
Delsuc, F., H. Brinkmann, et al.(2005)."Phylogenomics and the reconstruction of thetree of life." Nat Rev Genet6(5):361-375.
Denton, E. J. and J. Gray (1985)."Lateral-Line-Like Antennae of Certain of thePenaeidea (Crustacea, Decapoda, Natantia)." Proceedings of the Royal SocietySeries B-Biological Sciences226(1244):249-+.
DeSalle, R. and B. Schierwater (2008)."An even "newer" animal phylogeny."Bioessays30(11-12):1043-1047.
Desper, R. and O. Gascuel (2006)."Getting a tree fast: Neighbor Joining, FastME,and distance-based methods." Curr Protoc Bioinformatics Chapter6: Unit63.
Dickerson, R. E.(1971)."The structures of cytochrome c and the rates of molecularevolution." J Mol Evol1(1):26-45.
DiGuistini, S., Y. Wang, et al.(2011)."Genome and transcriptome analyses of themountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pinepathogen." Proc Natl Acad Sci U S A108(6):2504-2509.
Doudoumis, V., U. Alam, et al.(2013)."Tsetse-Wolbachia symbiosis: Comes of ageand has great potential for pest and disease control." Journal of InvertebratePathology112: S94-S103.
Dougherty, E. R., J. Hua, et al.(2009)."Performance of feature selection methods."Curr Genomics10(6):365-374.
Du, Z. Q., D. C. Ciobanu, et al.(2010)."A gene-based SNP linkage map for pacificwhite shrimp, Litopenaeus vannamei." Anim Genet41(3):286-294.
Duarte, J. M., P. K. Wall, et al.(2010)."Identification of shared single copy nucleargenes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utilityacross various taxonomic levels." BMC Evol Biol10:61.
Dunning Hotopp, J. C.(2011)."Horizontal gene transfer between bacteria andanimals." Trends Genet27(4):157-163.
Dunning Hotopp, J. C., M. E. Clark, et al.(2007)."Widespread lateral gene transferfrom intracellular bacteria to multicellular eukaryotes." Science317(5845):1753-1756.
Dyall, S. D., M. T. Brown, et al.(2004)."Ancient invasions: from endosymbionts toorganelles." Science304(5668):253-257.
Eden, S., T. Hashimshony, et al.(1998)."DNA methylation models histoneacetylation." Nature394(6696):842-842.
Edgar, R. C.(2004)."MUSCLE: multiple sequence alignment with high accuracy andhigh throughput." Nucleic Acids Res32(5):1792-1797.
Eick-Helmerich, K. and V. Braun (1989)."Import of biopolymers into Escherichiacoli: nucleotide sequences of the exbB and exbD genes are homologous to thoseof the tolQ and tolR genes, respectively." Journal of Bacteriology171(9):5117-5126.
Eizaguirre, C., T. L. Lenz, et al.(2012)."Rapid and adaptive evolution of MHC genesunder parasite selection in experimental vertebrate populations." Nat Commun3:621.
Escobedo-Bonilla, C. M., M. Wille, et al.(2007)."Pathogenesis of a Thai strain ofwhite spot syndrome virus (WSSV) in juvenile, specific pathogen-freeLitopenaeus vannamei." Dis Aquat Organ74(2):85-94.
Escobedo-Bonilla, C. M., M. Wille, et al.(2005)."In vivo titration of white spotsyndrome virus (WSSV) in specific pathogen-free Litopenaeus vannamei byintramuscular and oral routes." Dis Aquat Organ66(2):163-170.
Esteban, D. J. and A. P. Hutchinson (2011)."Genes in the terminal regions oforthopoxvirus genomes experience adaptive molecular evolution." BMCGenomics12.
Evans, D. H., P. M. Piermarini, et al.(2005)."The multifunctional fish gill: Dominantsite of gas exchange, osmoregulation, acid-base regulation, and excretion ofnitrogenous waste." Physiological Reviews85(1):97-177.
Eyre-Walker, A. and P. D. Keightley (2007)."The distribution of fitness effects of newmutations." Nature Reviews Genetics8(8):610-618.
Farfante, I. P. and B. Kensley (1997)."Penaeoid and Sergestoid Shrimps and Prawnsof the World: Keys and Diagnoses for the Families and Genera." Washington,D.C.: National Museum of Natural History ISBN2-85653-510-0.
Farfante, I. P. and B. Kensley (1997)."Penaeoid and Sergestoid Shrimps and Prawnsof the World: Keys and Diagnoses for the Families and Genera." Memoires duMuseum National d'Histoire Naturelle175:223.
Field, K. G., G. J. Olsen, et al.(1988)."Molecular Phylogeny of the AnimalKingdom." Science239(4841):748-753.
Flegel, T. W. and K. Sritunyalucksana (2011)."Shrimp molecular responses to viralpathogens." Mar Biotechnol (NY)13(4):587-607.
Freire, C. A., F. Cavassin, et al.(2003)."Adaptive patterns of osmotic and ionicregulation, and the invasion of fresh water by the palaemonid shrimps." CompBiochem Physiol A Mol Integr Physiol136(3):771-778.
Freire, C. A., F. Cavassin, et al.(2003)."Adaptive patterns of osmotic and ionicregulation, and the invasion of fresh water by the palaemonid shrimps."Comparative Biochemistry and Physiology a-Molecular&Integrative Physiology136(3):771-778.
Friedrich, M. and D. Tautz (1995)."Ribosomal DNA Phylogeny of the Major ExtantArthropod Classes and the Evolution of Myriapods." Nature376(6536):165-167.
Friesen, T. L., E. H. Stukenbrock, et al.(2006)."Emergence of a new disease as aresult of interspecific virulence gene transfer." Nat Genet38(8):953-956.
Fuks, F.(2005)."DNA methylation and histone modifications: teaming up to silencegenes." Current Opinion in Genetics&Development15(5):490-495.
G., K.(2012)."Cell and Molecular Biology." Wiley5th Ed.
Galtier, N.(2007)."A model of horizontal gene transfer and the bacterial phylogenyproblem." Syst Biol56(4):633-642.
Gardner, A. E. and R. E. Dutch (2007)."A conserved region in the F(2) subunit ofparamyxovirus fusion proteins is involved in fusion regulation." J Virol81(15):8303-8314.
Gaucher, E. A., J. T. Kratzer, et al.(2010)."Deep phylogeny--how a tree can helpcharacterize early life on Earth." Cold Spring Harb Perspect Biol2(1): a002238.
Gerrish, P. J., A. Colato, et al.(2013)."Genomic mutation rates that neutralizeadaptive evolution and natural selection." Journal of the Royal Society Interface10(85).
Gil-Turnes, M. S., M. E. Hay, et al.(1989)."Symbiotic marine bacteria chemicallydefend crustacean embryos from a pathogenic fungus." Science246(4926):116-118.
Gilbert, C., S. Schaack, et al.(2010)."A role for host-parasite interactions in thehorizontal transfer of transposons across phyla." Nature464(7293):1347-1350.
Giordani, R. and J. Buc (2004)."Evidence for two different electron transfer pathwaysin the same enzyme, nitrate reductase A from Escherichia coli." Eur J Biochem271(12):2400-2407.
Giribet, G. and C. Ribera (1998)."The position of arthropods in the animal kingdom:A search for a reliable outgroup for internal arthropod phylogeny." MolPhylogenet Evol9(3):481-488.
Giribet, G. and W. C. Wheeler (1999)."The position of arthropods in the animalkingdom: Ecdysozoa, islands, trees, and the "parsimony ratchet"." MolPhylogenet Evol13(3):619-623.
Gogarten, J. P., W. F. Doolittle, et al.(2002)."Prokaryotic evolution in light of genetransfer." Mol Biol Evol19(12):2226-2238.
Goodman, D., N. Ollikainen, et al.(2007)."Baculovirus Phylogeny Based on GenomeRearrangements." LNBI4751：69—82.
Grabherr, M. G., B. J. Haas, et al.(2011)."Full-length transcriptome assembly fromRNA-Seq data without a reference genome." Nat Biotechnol29(7):644-652.
Grabherr, M. G., B. J. Haas, et al.(2011)."Full-length transcriptome assembly fromRNA-Seq data without a reference genome." Nature Biotechnology29(7):644-U130.
Grbic, M., T. Van Leeuwen, et al.(2011)."The genome of Tetranychus urticae revealsherbivorous pest adaptations." Nature479(7374):487-492.
Gribaldo, S. and C. Brochier (2009)."Phylogeny of prokaryotes: does it exist and whyshould we care?" Res Microbiol160(7):513-21.
Gross, P. S., T. C. Bartlett, et al.(2001)."Immune gene discovery by expressedsequence tag analysis of hemocytes and hepatopancreas in the Pacific WhiteShrimp, Litopenaeus vannamei, and the Atlantic White Shrimp, L. setiferus." DevComp Immunol25(7):565-577.
Gu, H. F., J. H. Xiao, et al.(2014)."Adaptive evolution of the circadian gene timeoutin insects." Sci Rep4:4212.
Guan, X., P. Silva, et al.(2009)."The mitochondrial genome sequence and molecularphylogeny of the turkey, Meleagris gallopavo." Anim Genet40(2):134-141.
Gubser, C., S. Hue, et al.(2004)."Poxvirus genomes: a phylogenetic analysis." J GenVirol85(Pt1):105-117.
Gueguen, Y., J. Garnier, et al.(2006)."PenBase, the shrimp antimicrobial peptidepenaeidin database: sequence-based classification and recommendednomenclature." Dev Comp Immunol30(3):283-288.
Guindon, S., J. F. Dufayard, et al.(2010)."New algorithms and methods to estimatemaximum-likelihood phylogenies: assessing the performance of PhyML3.0."Syst Biol59(3):307-321.
Gutkin, M., R. Shamir, et al.(2009)."SlimPLS: a method for feature selection in geneexpression-based disease classification." PLoS One4(7): e6416.
Guyon, I. and A. e. Elisseeff (2003)."An Introduction to Variable and FeatureSelection." Journal of Machine Learning Research3,1157-1182.
Haas, B. J., A. Papanicolaou, et al.(2013)."De novo transcript sequencereconstruction from RNA-seq using the Trinity platform for reference generationand analysis." Nat Protoc8(8):1494-1512.
Haas, M. and B. Forbush (1998)."The Na-K-Cl cotransporters." Journal ofBioenergetics and Biomembranes30(2):161-172.
Hahlbrock, K. and D. Scheel (1989)."Physiology and molecular-biology ofphenylpropanoid metabolism." Annual Review of Plant Physiology and PlantMolecular Biology40:347-369.
Hahn, M. W., J. P. Demuth, et al.(2007)."Accelerated rate of gene gain and loss inprimates." Genetics177(3):1941-1949.
Han, B., Z. Obradovic, et al.(2006)."Substring selection for biomedical documentclassification." Bioinformatics22(17):2136-2142.
Han, M., S. Qin, et al.(2013)."Evolutionary rate patterns of genes involved in theDrosophila Toll and Imd signaling pathway." BMC Evol Biol13:245.
Hao, B. and J. Qi (2004)."Prokaryote phylogeny without sequence alignment: fromavoidance signature to composition distance." J Bioinform Comput Biol2(1):1-19.
Harwood, J. H. and D. H. Smith (1969)."Resistance factor-mediated streptomycinresistance." Journal of Bacteriology97(3):1262-1271.
Havird, J. C., R. P. Henry, et al.(2013)."Altered expression of Na+/K+-ATPase andother osmoregulatory genes in the gills of euryhaline animals in response tosalinity transfer: A meta-analysis of59quantitative PCR studies over10years."Comparative Biochemistry and Physiology D-Genomics&Proteomics8(2):131-140.
He, A., Y. Luo, et al.(2010)."Complete mitochondrial DNA sequences of the Niletilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): genomecharacterization and phylogeny applications." Mol Biol Rep.
Heather D. Bracken, Alicia Toon, et al.(2009)."The Decapod Tree of Life: Compilingthe Data and Moving toward a Consensus of Decapod Evolution." ArthropodSystematics&Phylogeny67(1):99-116.
Henz, S. R., D. H. Huson, et al.(2005)."Whole-genome prokaryotic phylogeny."Bioinformatics21(10):2329-2335.
Hessler, R. and W. Newman (1975)." A trilobitomorph origin for the Crustacea."
Heymons, R.(1901)."Die Entwicklungsgeschichte der Scolopender." Zoologica.Original-Abhandlungen aus dem gesammtgebliete der Zoologie33:244.
Higgs, P. I., R. A. Larsen, et al.(2002)."Quantification of known components of theEscherichia coli TonB energy transduction system: TonB, ExbB, ExbD andFepA." Mol Microbiol44(1):271-281.
Hill, C. A. and S. K. Wikel (2005)."The Ixodes scapularis Genome Project: anopportunity for advancing tick research." Trends Parasitol21(4):151-153.
Hirono, I., F. F. Fagutao, et al.(2011)."Uncovering the mechanisms of shrimp innateimmune response by RNA interference." Mar Biotechnol (NY)13(4):622-628.
Holt, R. A., G. M. Subramanian, et al.(2002)."The genome sequence of the malariamosquito Anopheles gambiae." Science298(5591):129-149.
Hotopp, J. C. D., M. E. Clark, et al.(2007)."Widespread lateral gene transfer fromintracellular bacteria to multicellular eukaryotes." Science317(5845):1753-1756.
Hsu, K. and S. Terakawa (1996)."Fenestration in the myelin sheath of nerve fibers ofthe shrimp: A novel node of excitation for saltatory conduction." Journal ofNeurobiology30(3):397-409.
Huang, S. W., Y. Y. Lin, et al.(2011)."Fosmid library end sequencing reveals a rarelyknown genome structure of marine shrimp Penaeus monodon." BMC Genomics12:242.
Huang, W., H. Xu, et al.(2012)."Characterization of Yatakemycin Gene ClusterRevealing a Radical S-Adenosylmethionine Dependent Methyltransferase andHighlighting Spirocyclopropane Biosynthesis." Journal of the AmericanChemical Society134(21):8831-8840.
Huang, W. J., J. H. Leu, et al.(2011)."Differential expression of LvHSP60in shrimpin response to environmental stress." Fish&Shellfish Immunology30(2):576-582.
Huang, X. and A. Madan (1999)."CAP3: A DNA sequence assembly program."Genome Res9(9):868-877.
Huelsenbeck, J. P., B. Larget, et al.(2000)."A compound poisson process for relaxingthe molecular clock." Genetics154(4):1879-1892.
Huelsenbeck, J. P. and F. Ronquist (2001)."MRBAYES: Bayesian inference ofphylogenetic trees." Bioinformatics17(8):754-755.
Hughes, A. L.(1999)."Adaptive Evolution of Genes and Genomes." OxfordUniversity Press:1-265.
Hughes, A. L. and R. Friedman (2005)."Poxvirus genome evolution by gene gain andloss." Mol Phylogenet Evol35(1):186-195.
Huynen, M. A. and P. Bork (1998)."Measuring genome evolution." Proc Natl AcadSci U S A95(11):5849-5856.
Huynh, K. D. and J. T. Lee (2005)."X-chromosome inactivation: a hypothesis linkingontogeny and phylogeny." Nat Rev Genet6(5):410-418.
Inoue, N., T. Soga, et al.(2000)."Mechanism of regulation of sodium pump isoformactivities in cultured cerebral neurons." Na/K-Atpase and Related Atpases1207:583-586.
Iwasaki, W. and T. Takagi (2007)."Reconstruction of highly heterogeneousgene-content evolution across the three domains of life." Bioinformatics23(13):i230-239.
Iyer, L. M., L. Aravind, et al.(2004)."Evolution of cell-cell signaling in animals: didlate horizontal gene transfer from bacteria have a role?" Trends Genet20(7):292-299.
James, T. Y., F. Kauff, et al.(2006)."Reconstructing the early evolution of Fungiusing a six-gene phylogeny." Nature443(7113):818-822.
Jang, K. H. and U. W. Hwang (2009)."Complete mitochondrial genome of Bugulaneritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position ofBryozoa and phylogeny of lophophorates within the Lophotrochozoa." BMCGenomics10:167.
Jeffares, D. C., T. Mourier, et al.(2006)."The biology of intron gain and loss." TrendsGenet22(1):16-22.
Jeffrey, E. C.(1906)."Morphology and Phylogeny." Science23(582):291-297.
Jelonek, J. and J. Stefanowski (1997)."Feature subset selection for classification ofhistological images." Artif Intell Med9(3):227-239.
Johnson, S. C.(1967)."Hierarchical clustering schemes." Psychometrika32(3):241-254.
Jung, H., R. E. Lyons, et al.(2011)."Transcriptomics of a Giant Freshwater Prawn(Macrobrachium rosenbergii): De Novo Assembly, Annotation and MarkerDiscovery." PLoS One6(12).
Kalujnaia, S., I. S. McWilliam, et al.(2007)."Transcriptomic approach to the study ofosmoregulation in the European eel Anguilla anguilla." Physiol Genomics31(3):385-401.
Kan, X. Z., J. K. Yang, et al.(2010)."Phylogeny of major lineages of galliform birds(Aves: Galliformes) based on complete mitochondrial genomes." Genet Mol Res9(3):1625-1633.
Kawahara-Miki, R., K. Wada, et al.(2011)."Expression Profiling without GenomeSequence Information in a Non-Model Species, Pandalid Shrimp (Pandaluslatirostris), by Next-Generation Sequencing." PLoS One6(10).
Keeling, P. J. and J. D. Palmer (2008)."Horizontal gene transfer in eukaryoticevolution." Nat Rev Genet9(8):605-618.
Kent, W. J.(2002)."BLAT--the BLAST-like alignment tool." Genome Res12(4):656-664.
Kim, H. and T. J. Crow (1999)."Identification and phylogeny of novel humanendogenous retroviral sequences belonging to the HERV-W family on the humanX chromosome." Arch Virol144(12):2403-2413.
Kimura, M. and T. Ohta (1973)."Eukaryotes-prokaryotes divergence estimated by5Sribosomal RNA sequences." Nat New Biol243(128):199-200.
Klaoudatos, S. D. and D. S. Klaoudatos (2008)."Phylogeny biology and ecology ofCrustaceans(Phylum Arthropoda; Subphylum Crusacea)." Reproductive Biologyof Crustaceans, Case studies of Decapod Crustaceans. Science Publishers, NewHampshire, USA: pp.
Klasson, L., Z. Kambris, et al.(2009)."Horizontal gene transfer between Wolbachiaand the mosquito Aedes aegypti." BMC Genomics10.
Klintworth, G. K.(1968)."The comparative anatomy and phylogeny of the tentoriumcerebelli." Anat Rec160(3):635-642.
Koch, I. and K. Naito (2007)."Dimension selection for feature selection anddimension reduction with principal and independent component analysis." NeuralComput19(2):513-545.
Komoto, N., K. Yukuhiro, et al.(2010)."Exploring the molecular phylogeny ofphasmids with whole mitochondrial genome sequences." Mol Phylogenet Evol.
Kondo, N., N. Nikoh, et al.(2002)."Genome fragment of Wolbachia endosymbionttransferred to X chromosome of host insect." Proc Natl Acad Sci U S A99(22):14280-14285.
Kornberg, H. L.(1987)."Krebs citric-acid cycle-half a century and still turning-introductory." Biochemical Society Symposium(54):1-2.
Kumar, D., P. Carvalho, et al.(2010)."Heart murmur classification with featureselection." Conf Proc IEEE Eng Med Biol Soc1:4566-4569.
Kunin, V. and C. A. Ouzounis (2003)."GeneTRACE-reconstruction of gene contentof ancestral species." Bioinformatics19(11):1412-1416.
Kurtz, S., A. Phillippy, et al.(2004)."Versatile and open software for comparing largegenomes." Genome Biol5(2): R12.
Lavery, S., T. Y. Chan, et al.(2004)."Phylogenetic relationships and evolutionaryhistory of the shrimp genus Penaeus s.l. derived from mitochondrial DNA." MolPhylogenet Evol31(1):39-49.
Lavrov, D. V., W. M. Brown, et al.(2004)."Phylogenetic position of the Pentastomidaand (pan)crustacean relationships." Proc Biol Sci271(1538):537-544.
Lavrov, D. V. and B. F. Lang (2005)."Poriferan mtDNA and animal phylogeny basedon mitochondrial gene arrangements." Syst Biol54(4):651-659.
Lawrence, J. G. and H. Ochman (1998)."Molecular archaeology of the Escherichiacoli genome." Proc Natl Acad Sci U S A95(16):9413-9417.
Letain, T. E. and K. Postle (1997)."TonB protein appears to transduce energy byshuttling between the cytoplasmic membrane and the outer membrane inEscherichia coli." Mol Microbiol24(2):271-283.
Li, C., S. Weng, et al.(2012)."Analysis of Litopenaeus vannamei TranscriptomeUsing the Next-Generation DNA Sequencing Technique." PLoS One7(10):e47442.
Li, C. Z., S. P. Weng, et al.(2012)."Analysis of Litopenaeus vannamei TranscriptomeUsing the Next-Generation DNA Sequencing Technique." PLoS One7(10).
Li, D. X., X. J. Du, et al.(2006)."Cloning and expression analysis of ano-methyltransferase (OMT) gene from Chinese shrimp, Fenneropenaeuschinensis." Fish Shellfish Immunol21(3):284-292.
Li, F. and J. Xiang (2013)."Recent advances in researches on the innate immunity ofshrimp in China." Dev Comp Immunol39(1-2):11-26.
Li, F. H. and J. H. Xiang (2013)."Signaling pathways regulating innate immuneresponses in shrimp." Fish&Shellfish Immunology34(4):973-980.
Li, G. L. and T. Y. Leong (2005)."Feature selection for the prediction of translationinitiation sites." Genomics Proteomics Bioinformatics3(2):73-83.
Li, H., A. Coghlan, et al.(2006)."TreeFam: a curated database of phylogenetic treesof animal gene families." Nucleic Acids Res34(Database issue): D572-580.
Li, M., J. H. Badger, et al.(2001)."An information-based sequence distance and itsapplication to whole mitochondrial genome phylogeny." Bioinformatics17(2):149-154.
Li, Q., Q. H. Liu, et al.(2013)."FATP synthase b-chain of Litopenaeus vannameiinvolved in White Spot Syndrome Virus infection." Virus Genes.
Li, R., W. Fan, et al.(2010)."The sequence and de novo assembly of the giant pandagenome." Nature463(7279):311-317.
Li, R., C. Yu, et al.(2009)."SOAP2: an improved ultrafast tool for short readalignment." Bioinformatics25(15):1966-1967.
Li, S.-T. and F.-C. Tsai (2011)."Noise control in document classification based onfuzzy formal concept analysis " Fuzzy Systems (FUZZ),2011IEEE InternationalConference on (27-30June):2583-2588.
Li, S., X. Zhang, et al.(2013)."Transcriptome Analysis on Chinese ShrimpFenneropenaeus chinensis during WSSV Acute Infection." PLoS One8(3):e58627.
Li, S. H., X. J. Zhang, et al.(2013)."Transcriptome Analysis on Chinese ShrimpFenneropenaeus chinensis during WSSV Acute Infection." PLoS One8(3).
Li, X. Z., Q. W. Luo, et al.(2009)."A Molybdopterin Oxidoreductase Is Involved inH-2Oxidation in Desulfovibrio desulfuricans G20." Journal of Bacteriology191(8):2675-2682.
Li, Z. W., Y. H. Shen, et al.(2011)."Pathogen-origin horizontally transferred genescontribute to the evolution of Lepidopteran insects." BMC Evol Biol11:356.
Liang, L., Y. Y. Shen, et al.(2013)."Adaptive Evolution of the Hox Gene Family forDevelopment in Bats and Dolphins." PLoS One8(6).
Lightner, D. V.(1985)."A review of the diseases of cultured penaeid shrimps andprawns with emphasis on recent discoveries and developments." Proceedings ofthe First International Conference on the Culture of Penaeid Prawns/Shrimps,4-7December1984, Iloilo City, Philippines: pp.79-103.
Lightner, D. V., R. P. Hedrick, et al.(1987)."A Survey of Cultured Penaeid Shrimp inTaiwan for Viral and Other Important Diseases." Fish Pathology22(3):127-140.
Lim, A. and L. Zhang (1999)."WebPHYLIP: a web interface to PHYLIP."Bioinformatics15(12):1068-1069.
Lin, F. J., Y. Liu, et al.(2012)."Evolution and phylogeny of the mud shrimps(Crustacea: Decapoda) revealed from complete mitochondrial genomes." BMCGenomics13.
Lin, J. and M. Gerstein (2000)."Whole-genome trees based on the occurrence of foldsand orthologs: implications for comparing genomes on different levels." GenomeRes10(6):808-818.
Lin, Y. F., S. R. Jing, et al.(2003)."The potential use of constructed wetlands in arecirculating aquaculture system for shrimp culture." Environmental Pollution123(1):107-113.
Lipson, R. S. and S. G. Clarke (2007)."S-adenosylmethionine-dependent proteinmethylation in mammalian cytosol via tyrphostin modification bycatechol-O-methyltransferase." Journal of Biological Chemistry282(42):31094-31102.
Little, J. W., D. W. Mount, et al.(1981)."Purified Lexa Protein Is a Repressor of theReca and Lexa Genes." Proceedings of the National Academy of Sciences of theUnited States of America-Biological Sciences78(7):4199-4203.
Logacheva, M. D., A. A. Penin, et al.(2007)."Phylogeny of flowering plants by thechloroplast genome sequences: in search of a "lucky gene"." Biochemistry (Mosc)72(12):1324-1330.
Long, M., N. W. VanKuren, et al.(2013)."New gene evolution: little did we know."Annu Rev Genet47:307-333.
Lopes, F. M., D. C. Martins, Jr., et al.(2008)."Feature selection environment forgenomic applications." BMC Bioinformatics9:451.
Lopez, P. and E. Bapteste (2009)."Molecular phylogeny: reconstructing the forest." CR Biol332(2-3):171-182.
Luo, H., J. Shi, et al.(2008)."Gene order phylogeny of the genus Prochlorococcus."PLoS One3(12): e3837.
Luo, R., B. Liu, et al.(2012)."SOAPdenovo2: an empirically improvedmemory-efficient short-read de novo assembler." Gigascience1(1):18.
Lustgarten, J. L., V. Gopalakrishnan, et al.(2009)."Measuring stability of featureselection in biomedical datasets." AMIA Annu Symp Proc2009:406-410.
Ma, K. Y., T.-Y. Chan, et al.(2009)."Phylogeny of penaeoid shrimps (Decapoda:Penaeoidea) inferred from nuclear protein-coding genes." MolecularPhylogenetics and Evolution53(1):45–55.
Ma, S. and J. Huang (2008)."Penalized feature selection and classification inbioinformatics." Brief Bioinform9(5):392-403.
Maggioni, R., A. D. Rogers, et al.(2001)."Molecular phylogeny of western AtlanticFarfantepenaeus and Litopenaeus shrimp based on mitochondrial16S partialsequences." Mol Phylogenet Evol18(1):66-73.
Magnan, C. N., A. Randall, et al.(2009)."SOLpro: accurate sequence-basedprediction of protein solubility." Bioinformatics25(17):2200-2207.
Maizels, N. and A. M. Weiner (1994)."Phylogeny from function: evidence from themolecular fossil record that tRNA originated in replication, not translation." ProcNatl Acad Sci U S A91(15):6729-6734.
Majoros, W. H., M. Pertea, et al.(2004)."TigrScan and GlimmerHMM: two opensource ab initio eukaryotic gene-finders." Bioinformatics20(16):2878-2879.
Manfrin, C., M. Tom, et al.(2013)."Application of D-Crustacean HyperglycemicHormone Induces Peptidases Transcription and Suppresses Glycolysis-RelatedTranscripts in the Hepatopancreas of the Crayfish Pontastacus leptodactylus-Results of a Transcriptomic Study." PLoS One8(6).
Manton, S.(1972)."The evolution of arthropod locomotory mechanisms." Zool. J.Linn. Soc.51:203-400.
Manton, S.(1979)."Functional morphology and the evolution of the hexapod classesin Arthropod Phylogeny." In: Gupta A P. Arthropod Phylogeny:387-466.
Manton, S. M. and J. P. Harding (1964)."Mandibular mechanisms and the evolutionof arthropods." Phil. Trans. R. Soc. Lond. B247(737):1-183.
Mardis, E. R.(2006)."Anticipating the1,000dollar genome." Genome Biol7(7):112.
Margulies, M., M. Egholm, et al.(2005)."Genome sequencing in microfabricatedhigh-density picolitre reactors." Nature437(7057):376-380.
Martin, J. L. and F. M. McMillan (2002)."SAM (dependent) I AM: theS-adenosylmethionine-dependent methyltransferase fold." Current Opinion inStructural Biology12(6):783-793.
Masai, H. and K. Arai (1988)."Operon structure of dnaT and dnaC genes essential fornormal and stable DNA replication of Escherichia coli chromosome." Journal ofBiological Chemistry263(29):15083-15093.
Matsui, A., F. Rakotondraparany, et al.(2009)."Molecular phylogeny and evolutionof prosimians based on complete sequences of mitochondrial DNAs." Gene441(1-2):53-66.
McInerney, J. O., J. A. Cotton, et al.(2008)."The prokaryotic tree of life: past,present... and future?" Trends Ecol Evol23(5):276-281.
Mclaughl.Pj and M. O. Dayhoff (1970)."Eukaryotes Versus Prokaryotes-an Estimateof Evolutionary Distance." Science168(3938):1469-&.
McLysaght, A., P. F. Baldi, et al.(2003)."Extensive gene gain associated withadaptive evolution of poxviruses." Proc Natl Acad Sci U S A100(26):15655-15660.
McNamara, J. C. and S. C. Faria (2012)."Evolution of osmoregulatory patterns andgill ion transport mechanisms in the decapod Crustacea: a review." Journal ofComparative Physiology B-Biochemical Systemic and Environmental Physiology182(8):997-1014.
McNulty, S. N., J. M. Foster, et al.(2010)."Endosymbiont DNA in endobacteria-freefilarial nematodes indicates ancient horizontal genetic transfer." PLoS One5(6):e11029.
Meehan, D., Z. Xu, et al.(2003)."High frequency and large number of polymorphicmicrosatellites in cultured shrimp, Penaeus (Litopenaeus) vannamei[Crustacea:Decapoda]." Mar Biotechnol (NY)5(4):311-330.
Merget, B. and M. Wolf (2010)."A molecular phylogeny of Hypnales (Bryophyta)inferred from ITS2sequence-structure data." BMC Res Notes3:320.
Metzker, M. L.(2005)."Emerging technologies in DNA sequencing." Genome Res15(12):1767-1776.
Miao, S. and S. C. Tu (1996)."Modeling effect of thermic amplitude on growingChinese shrimp, Penaeus chinensis (Osbeck)." Ecological Modelling88(1-3):93-100.
Moran, N. A. and T. Jarvik (2010)."Lateral transfer of genes from fungi underliescarotenoid production in aphids." Science328(5978):624-627.
Morozov, A., E. Yung, et al.(1998)."Structure-function analysis of integraseinteractor1/hSNF5L1reveals differential properties of two repeat motifs presentin the highly conserved region." Proc Natl Acad Sci U S A95(3):1120-1125.
Moss, S. M., D. R. Moss, et al.(2012)."The role of selective breeding and biosecurityin the prevention of disease in penaeid shrimp aquaculture." J Invertebr Pathol110(2):247-250.
Murphy, W. J., D. M. Larkin, et al.(2005)."Dynamics of mammalian chromosomeevolution inferred from multispecies comparative maps." Science309(5734):613-617.
Narayanan, Y.(1973)."The phylogenetic relationships of the members of theDrosophila robusta group." Genetics73(2):319-350.
Nei, M. and S. Kumar (2000)."Molecular evolution and phylogenetics " OxfordUniversity Press:1-333.
Nikoh, N., J. P. McCutcheon, et al.(2010)."Bacterial genes in the aphid genome:absence of functional gene transfer from Buchnera to its host." PLoS Genet6(2):e1000827.
Nikoh, N. and A. Nakabachi (2009)."Aphids acquired symbiotic genes via lateralgene transfer." BMC Biol7:12.
Nikoh, N., K. Tanaka, et al.(2008)."Wolbachia genome integrated in an insectchromosome: evolution and fate of laterally transferred endosymbiont genes."Genome Res18(2):272-280.
Nye, T. M., P. Lio, et al.(2006)."A novel algorithm and web-based tool forcomparing two alternative phylogenetic trees." Bioinformatics22(1):117-119.
O'Leary, N. A., H. F. Trent,3rd, et al.(2006)."Analysis of multiple tissue-specificcDNA libraries from the Pacific whiteleg shrimp, Litopenaeus vannamei." IntegrComp Biol46(6):931-939.
Ochman, H.(2001)."Lateral and oblique gene transfer." Current Opinion in Genetics&Development11(6):616-619.
Otu, H. H. and K. Sayood (2003)."A new sequence distance measure for phylogenetictree construction." Bioinformatics19(16):2122-2130.
Overstreet, R. M.(1973)."Parasites of some penaeid shrimps with emphasis on rearedhosts." Aquaculture2:105-140.
Ozkurt, T. E., M. Sun, et al.(2006)."Optimal feature selection for seizure detection: asubspace based approach." Conf Proc IEEE Eng Med Biol Soc1:2134-2137.
Padhi, A., B. Verghese, et al.(2007)."Adaptive evolution after duplication ofpenaeidin antimicrobial peptides." Fish Shellfish Immunol23(3):553-566.
Palermo, C., J. C. Hope, et al.(2008)."Importance of a C-terminal conserved regionof Chk1for checkpoint function." PLoS One3(1): e1427.
Panganiban, G., A. Sebring, et al.(1995)."The development of crustacean limbs andthe evolution of arthropod." Science270:1363-1366.
Pasyk, E. A., X. K. Morin, et al.(1998)."A conserved region of the R domain ofcystic fibrosis transmembrane conductance regulator is important in processingand function." J Biol Chem273(48):31759-31764.
Patel, R. K. and M. Jain (2012)."NGS QC Toolkit: a toolkit for quality control of nextgeneration sequencing data." PLoS One7(2): e30619.
Pennisi, E.(2002)."Bacteria Shared Photosynt hesis Genes." Science298:1616-1620.
Pertea, G., X. Huang, et al.(2003)."TIGR Gene Indices clustering tools (TGICL): asoftware system for fast clustering of large EST datasets." Bioinformatics19(5):651-652.
Peters, A. E., A. Bavishi, et al.(2012)."Evolutionary constraints and expressionanalysis of gene duplications in Rhodobacter sphaeroides2.4.1." BMC Res Notes5:192.
Podsiadlowski, L. and T. Bartolomaeus (2006)."Major rearrangements characterizethe mitochondrial genome of the isopod Idotea baltica (Crustacea: Peracarida)."Mol Phylogenet Evol40(3):893-899.
Pok, G., J. C. Liu, et al.(2010)."Effective feature selection framework for clusteranalysis of microarray data." Bioinformation4(8):385-389.
Porter, M. L., M. Perez-Losada, et al.(2005)."Model-based multi-locus estimation ofdecapod phylogeny and divergence times." Mol Phylogenet Evol37(2):355-369.
Pride, D. T., R. J. Meinersmann, et al.(2003)."Evolutionary implications of microbialgenome tetranucleotide frequency biases." Genome Res13(2):145-158.
Qi, J., H. Luo, et al.(2004)."CVTree: a phylogenetic tree reconstruction tool based onwhole genomes." Nucleic Acids Res32(Web Server issue): W45-47.
Qi, J., B. Wang, et al.(2004)."Whole proteome prokaryote phylogeny withoutsequence alignment: a K-string composition approach." J Mol Evol58(1):1-11.
Qi, Z. H., J. M. Wang, et al.(2009)."Classification analysis of dual nucleotides usingdimension reduction." J Theor Biol260(1):104-109.
Quan, J., Z. Zhuang, et al.(2004)."Phylogenetic relationships of12penaeoideashrimp species deduced from mitochondrial DNA sequences." Biochem Genet42(9-10):331-345.
Richards, S., R. A. Gibbs, et al.(2008)."The genome of the model beetle and pestTribolium castaneum." Nature452(7190):949-955.
Richards, T. A., D. M. Soanes, et al.(2011)."Horizontal gene transfer facilitated theevolution of plant parasitic mechanisms in the oomycetes." Proc Natl Acad Sci US A108(37):15258-15263.
Rizvi, S. B., A. K. Shukla, et al.(2009)."A simple method based on multiplealignment and phylogeny to derive a correlation between the protein fold andsequence via motif search." Interdiscip Sci1(3):235-243.
Robalino, J., J. S. Almeida, et al.(2007)."Insights into the immune transcriptome ofthe shrimp Litopenaeus vannamei: tissue-specific expression profiles andtranscriptomic responses to immune challenge." Physiol Genomics29(1):44-56.
Robinson, M. D., D. J. McCarthy, et al.(2010)."edgeR: a Bioconductor package fordifferential expression analysis of digital gene expression data." Bioinformatics26(1):139-140.
Robles, R., C. D. Schubart, et al.(2007)."Molecular phylogeny of the AmericanCallinectes Stimpson,1860(Brachyura: Portunidae), based on two partialmitochondrial genes." Marine Biology150(6):1265-1274.
Rodelsperger, C. and R. J. Sommer (2011)."Computational archaeology of thePristionchus pacificus genome reveals evidence of horizontal gene transfers frominsects." BMC Evol Biol11:239.
Rokas, A., B. L. Williams, et al.(2003)."Genome-scale approaches to resolvingincongruence in molecular phylogenies." Nature425(6960):798-804.
Ronquist, F., M. Teslenko, et al.(2012)."MrBayes3.2: efficient Bayesianphylogenetic inference and model choice across a large model space." Syst Biol61(3):539-542.
Rosten, E., R. Porter, et al.(2010)."Faster and better: a machine learning approach tocorner detection." IEEE Trans Pattern Anal Mach Intell32(1):105-119.
Ruan, J., H. Li, et al.(2008)."TreeFam:2008Update." Nucleic Acids Res36(Database issue): D735-740.
Rumpho, M. E., J. M. Worful, et al.(2008)."Horizontal gene transfer of the algalnuclear gene psbO to the photosynthetic sea slug Elysia chlorotica." Proc NatlAcad Sci U S A105(46):17867-17871.
Saeys, Y., I. Inza, et al.(2007)."A review of feature selection techniques inbioinformatics." Bioinformatics23(19):2507-2517.
Saitou, N. and M. Nei (1987)."The neighbor-joining method: a new method forreconstructing phylogenetic trees." Mol Biol Evol4(4):406-425.
Schierwater, B., S. O. Kolokotronis, et al.(2009)."The Diploblast-Bilateria Sisterhypothesis: parallel revolution of a nervous systems may have been a simplestep." Commun Integr Biol2(5):403-405.
Schnell, J. R., H. J. Dyson, et al.(2004)."Structure, dynamics, and catalytic functionof dihydrofolate reductase." Annual Review of Biophysics and BiomolecularStructure33:119-140.
Schram, F. R.(2001)."Phylogeny of decapods: moving towards a consensus."Hydrobiologia449(1-3):1-20.
Schwer, B., J. Bunkenborg, et al.(2006)."Reversible lysine acetylation controls theactivity of the mitochondrial enzyme acetyl-CoA synthetase2." Proc Natl AcadSci U S A103(27):10224-10229.
Semino, O., A. S. Santachiara-Benerecetti, et al.(2002)."Ethiopians and Khoisanshare the deepest clades of the human Y-chromosome phylogeny." Am J HumGenet70(1):265-268.
Sever, D. M.(1992)."Comparative anatomy and phylogeny of the cloacae ofsalamanders (Amphibia: Caudata). IV. Salamandridae." Anat Rec233(2):229-244.
Shapeero, W. L.(1961)."Phylogeny of Priapulida." Science133(3456):879-880.
Shaw, W. V., L. C. Packman, et al.(1979)."Primary structure of a chloramphenicolacetyltransferase specified by R plasmids." Nature282(5741):870-872.
Shen, L. and E. C. Tan (2005)."Dimension reduction-based penalized logisticregression for cancer classification using microarray data." IEEE/ACM TransComput Biol Bioinform2(2):166-175.
Shen, X., M. Sun, et al.(2009)."The complete mitochondrial genome of the ridgetailwhite prawn Exopalaemon carinicauda Holthuis,1950(Crustacean: Decapoda:Palaemonidae) revealed a novel rearrangement of tRNA genes." Gene437(1-2):1-8.
Shubo, Z. and L. Jian-huang (2010)."Bioinformatics approach for molocularevolution research." Computer Science37(8):47-51.
Sims, G. E., S. R. Jun, et al.(2009)."Alignment-free genome comparison with featurefrequency profiles (FFP) and optimal resolutions." Proc Natl Acad Sci U S A106(8):2677-2682.
Snel, B., P. Bork, et al.(2002)."Genomes in flux: the evolution of archaeal andproteobacterial gene content." Genome Res12(1):17-25.
Snodgrass, R.(1938)."Evolution of the Annelida, Onychophora and Arthropoda."Smithson. Misc. collect.97:1-159.
Sogin, S. J., M. L. Sogin, et al.(1971)."Phylogenetic measurement in procaryotes byprimary structural characterization." J Mol Evol1(1):173-184.
Stanhope, M. J., A. Lupas, et al.(2001)."Phylogenetic analyses do not supporthorizontal gene transfers from bacteria to vertebrates." Nature411(6840):940-944.
Stanke, M. and B. Morgenstern (2005)."AUGUSTUS: a web server for geneprediction in eukaryotes that allows user-defined constraints." Nucleic Acids Res33: W465-W467.
Stenderup, J. T., J. Olesen, et al.(2006)."Molecular phylogeny of the Branchiopoda(Crustacea)--multiple approaches suggest a 'diplostracan' ancestry of theNotostraca." Mol Phylogenet Evol41(1):182-194.
Struck, T. H. and F. Fisse (2008)."Phylogenetic position of Nemertea derived fromphylogenomic data." Mol Biol Evol25(4):728-736.
Stuart, G. W., K. Moffett, et al.(2002)."Integrated gene and species phylogenies fromunaligned whole genome protein sequences." Bioinformatics18(1):100-108.
Stuart, G. W., K. Moffett, et al.(2002)."A comprehensive vertebrate phylogeny usingvector representations of protein sequences from whole genomes." Mol Biol Evol19(4):554-562.
Studer, R. A., P. A. Christin, et al.(2014)."Stability-activity tradeoffs constrain theadaptive evolution of RubisCO." Proc Natl Acad Sci U S A111(6):2223-2228.
Sudar, E., M. Velebit, et al.(2008)."Hypothetical mechanism of sodium pumpregulation by estradiol under primary hypertension." Journal of TheoreticalBiology251(4):584-592.
Sung, Y. Y., T. H. MacRae, et al.(2011)."Stress response for disease control inaquaculture." Reviews in Aquaculture3(3):120-137.
Supek, F., M. Bosnjak, et al.(2011)."REVIGO summarizes and visualizes long listsof gene ontology terms." PLoS One6(7): e21800.
Sutton, B. C.(1993)."Mitosporic fungi (Deuteromycetes) in thefictionary-of-the-fungi." Fungal Holomorph: Mitotic, Meiotic and PleomorphicSpeciation in Fungal Systematics:27-55.
Tagle, D. A., B. F. Koop, et al.(1988)."Embryonic epsilon and gamma globin genesof a prosimian primate (Galago crassicaudatus). Nucleotide and amino acidsequences, developmental regulation and phylogenetic footprints." J Mol Biol203(2):439-455.
Tamura, K., J. Dudley, et al.(2007)."MEGA4: Molecular Evolutionary GeneticsAnalysis (MEGA) software version4.0." Mol Biol Evol24(8):1596-1599.
Tekaia, F., A. Lazcano, et al.(1999)."The genomic tree as revealed from wholeproteome comparisons." Genome Res9(6):550-557.
Thompson, J. D., T. J. Gibson, et al.(2002)."Multiple sequence alignment usingClustalW and ClustalX." Curr Protoc Bioinformatics Chapter2: Unit23.
Tsagkogeorga, G., X. Turon, et al.(2009)."An updated18S rRNA phylogeny oftunicates based on mixture and secondary structure models." BMC Evol Biol9:187.
Tsang, L. M., K. Y. Ma, et al.(2008)."Phylogeny of Decapoda using two nuclearprotein-coding genes: Origin and evolution of the Reptantia." Mol PhylogenetEvol48(1):359-368.
Tsuji, J., M. C. Frith, et al.(2012)."Mammalian NUMT insertion is non-random."Nucleic Acids Res40(18):9073-9088.
Tudge, C. C.(1997)."Phylogeny of the Anomura (Decapoda, Crustacea):Spermatozoa and spermatophore morphological evidence." Contributions toZoology67(2):125-141.
Turbeville, J. M., D. M. Pfeifer, et al.(1991)."The Phylogenetic Status of Arthropods,as Inferred from18s Ribosomal-Rna Sequences." Mol Biol Evol8(5):669-686.
Twine, N. A., K. Janitz, et al.(2011)."Whole transcriptome sequencing reveals geneexpression and splicing differences in brain regions affected by Alzheimer'sdisease." PLoS One6(1): e16266.
Umetsu, K., N. Iwabuchi, et al.(2002)."Complete mitochondrial DNA sequence of atadpole shrimp (Triops cancriformis) and analysis of museum samples."Electrophoresis23(24):4080-4084.
Wang, L., W. N. Wang, et al.(2012)."Two types of ATPases from the Pacific whiteshrimp, Litopenaeus vannamei in response to environmental stress." MolecularBiology Reports39(6):6427-6438.
Wang, P. H., D. H. Wan, et al.(2011)."Litopenaeus vannamei tumor necrosis factorreceptor-associated factor6(TRAF6) responds to Vibrio alginolyticus and whitespot syndrome virus (WSSV) infection and activates antimicrobial peptidegenes." Dev Comp Immunol35(1):105-114.
Wang, W., Y. Tian, et al.(2012)."Integration genetic linkage map construction andseveral potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis)based on three types of molecular markers." Genetika48(4):508-521.
Wang, X., S. Bandyopadhyay, et al.(2007)."Prediction of transcription start sitesbased on feature selection using AMOSA." Comput Syst Bioinformatics Conf6:183-193.
Wang, X., X. Fang, et al.(2014)."The locust genome provides insight into swarmformation and long-distance flight." Nat Commun5:2957.
Warnock, R. C., Z. Yang, et al.(2012)."Exploring uncertainty in the calibration of themolecular clock." Biol Lett8(1):156-159.
Waters, S. B., S. Lin, et al.(2003)."A novel S-adenosylmethionine-dependentmethyltransferase from rat liver cytosol catalyzes the formation of methylatedarsenicals." Arsenic Exposure and Health Effects V:255-266.
Wei, H. L. and S. A. Billings (2007)."Feature subset selection and ranking for datadimensionality reduction." IEEE Trans Pattern Anal Mach Intell29(1):162-166.
Weinstock, G. M., G. E. Robinson, et al.(2006)."Insights into social insects from thegenome of the honeybee Apis mellifera." Nature443(7114):931-949.
Wicker, T., E. Schlagenhauf, et al.(2006)."454sequencing put to the test using thecomplex genome of barley." BMC Genomics7:275.
Wills, M. A.(2002)."The tree of life and the rock of ages: are we getting better atestimating phylogeny?" Bioessays24(3):203-207.
Winbush, A., D. Reed, et al.(2012)."Identification of gene expression changesassociated with long-term memory of courtship rejection in Drosophila males."G3(Bethesda)2(11):1437-1445.
Woese, C. R., O. Kandler, et al.(1990)."Towards a natural system of organisms:proposal for the domains Archaea, Bacteria, and Eucarya." Proc Natl Acad Sci US A87(12):4576-4579.
Wolf, Y. I., I. B. Rogozin, et al.(2001)."Genome alignment, evolution of prokaryoticgenome organization, and prediction of gene function using genomic context."Genome Res11(3):356-372.
Woolfit, M., I. Iturbe-Ormaetxe, et al.(2009)."An Ancient Horizontal Gene Transferbetween Mosquito and the Endosymbiotic Bacterium Wolbachia pipientis." MolBiol Evol26(2):367-374.
Worm, J. and P. Guldberg (2002)."DNA methylation: an epigenetic pathway to cancerand a promising target for anticancer therapy." Journal of Oral Pathology&Medicine31(8):443-449.
Wu, D. D., G. M. Li, et al.(2012)."Positive Selection on the Osteoarthritis-Risk andDecreased-Height Associated Variants at the GDF5Gene in East Asians." PLoSOne7(8).
Wu, X. and P. A. Sharp (2013)."Divergent transcription: a driving force for new geneorigination?" Cell155(5):990-996.
Xia, Q., Y. Guo, et al.(2009)."Complete resequencing of40genomes revealsdomestication events and genes in silkworm (Bombyx)." Science326(5951):433-436.
Xilin, D., Z. Weiling, et al.(1999)."Effects of temperature and dissolved oxygencontent on oxygen consumption rate of Chinese prawn, giant tiger prawn andgiant freshwater prawn." Chinese Journal of Oceanology and Limnology17(2):119-127.
Xiong, H., D. Capurso, et al.(2011)."Sequence-based classification usingdiscriminatory motif feature selection." PLoS One6(11): e27382.
Xu, Z. and B. Hao (2009)."CVTree update: a newly designed phylogenetic studyplatform using composition vectors and whole genomes." Nucleic Acids Res37(Web Server issue): W174-178.
Xue, S. X., Y. C. Liu, et al.(2013)."Sequencing and De Novo Analysis of theHemocytes Transcriptome in Litopenaeus vannamei Response to White SpotSyndrome Virus Infection." PLoS One8(10).
Yang, L. S., Z. X. Yin, et al.(2007)."A Toll receptor in shrimp." Mol Immunol44(8):1999-2008.
Yang, Z.(1997)."PAML: a program package for phylogenetic analysis by maximumlikelihood." Comput Appl Biosci13(5):555-556.
Yang, Z.(2007)."PAML4: phylogenetic analysis by maximum likelihood." Mol BiolEvol24(8):1586-1591.
Yang, Z., R. Nielsen, et al.(2000)."Codon-substitution models for heterogeneousselection pressure at amino acid sites." Genetics155(1):431-449.
Yang, Z. and W. J. Swanson (2002)."Codon-substitution models to detect adaptiveevolution that account for heterogeneous selective pressures among site classes."Mol Biol Evol19(1):49-57.
Yu, Z. a. Z., Li-Qian and Anh, Vo V. and Chu, K. H. and Li, C. P. and Chen, Y. J.(2007)."Distance-based analysis to reveal vertebrate phylogeny withoutsequence alignment using complete mitochondrial genomes." Proceedings11thWorld Multi-Conference on Systemics, Cybernetics and Informatics: WMSCI2007,:206-211.
Yu, Z. G., L. Q. Zhou, et al.(2005)."Phylogeny of prokaryotes and chloroplastsrevealed by a simple composition approach on all protein sequences fromcomplete genomes without sequence alignment." J Mol Evol60(4):538-545.
Yushkevich, P., S. Joshi, et al.(2003)."Feature selection for shape-based classificationof biological objects." Inf Process Med Imaging18:114-125.
Zablen, L., L. Bonen, et al.(1975)."The phylogenetic status of Pasteurella pestis." JMol Evol4(4):347-358.
Zeng, F., R. H. Yap, et al.(2002)."Using feature generation and feature selection foraccurate prediction of translation initiation sites." Genome Inform13:192-200.
Zenteno-Savin, T.(2005)."Oxidative stress in response to environmentalhypoxia/reoxygenation in two crustacean species, Pacific white shrimp(Litopenaeus vannamei) and red claw crayfish (Cherax quadricarinatus)." FreeRadical Biology and Medicine39: S177-S177.
Zhan, S., C. Merlin, et al.(2011)."The Monarch Butterfly Genome Yields Insightsinto Long-Distance Migration." Cell147(5):1171-1185.
Zhang, C., M. Zhao, et al.(2011)."An improved algorithm for corner detection "Electronic and Mechanical Engineering and Information Technology (EMEIT),2011International Conference on(12-14Aug.):4639-4641
Zhang, G., X. Fang, et al.(2012)."The oyster genome reveals stress adaptation andcomplexity of shell formation." Nature490(7418):49-54.
Zhang, X., Y. Zhang, et al.(2010)."Construction and characterization of a bacterialartificial chromosome (BAC) library of Pacific white shrimp, Litopenaeusvannamei." Mar Biotechnol (NY)12(2):141-149.
Zhang, Z., J. Li, et al.(2006)."KaKs_Calculator: calculating Ka and Ks throughmodel selection and model averaging." Genomics Proteomics Bioinformatics4(4):259-263.
Zhaxybayeva, O., C. L. Nesbo, et al.(2007)."Systematic overestimation of gene gainthrough false diagnosis of gene absence." Genome Biol8(2).
Zhu, B., M. M. Lou, et al.(2011)."Horizontal gene transfer in silkworm, Bombyxmori." BMC Genomics12:248.
Zimmermann, K., M. Engeser, et al.(2009)."Pederin-type pathways of uncultivatedbacterial symbionts: analysis of o-methyltransferases and generation of abiosynthetic hybrid." J Am Chem Soc131(8):2780-2781.
Zrzavy, J. and P. Stys (1997)."The basic body plan of arthropods: Insights fromevolutionary morphology and developmental biology." Journal of EvolutionaryBiology10(3):353-367.
Zuckerkandl, E. and L. B. Pauling (1962)."Molecular disease, evolution, and geneticheterogeneity." New York: Horizons in Biochemistry:189-225.
岑伯明,胡洲, et al.(2012)."凡纳滨对虾养殖池塘水温预测模型研究."宁波大学学报：理工版25(1):7-12.
刘培生(1995)."适应性进化与物种形成."化石2:19-21.
刘帅,李墨非, et al.(2012)."基于线粒体16S rRNA和COI基因序列探讨对虾属(Penaeus)物种系统发生关系."生物学杂志29(5):37-42.
沈文英,阳会军, et al.(2004)."南美白对虾的病害及防治研究现状."水利渔业24(1):58-60.
朱玉贤(2013)."现代分子生物学(第4版)."高等教育出版社4:1-484.