利用高通量测序技术对东方鲀杂交优势的初步解析
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摘要
杂交优势是指遗传基础不同的亲本杂交产生的后代，其各项性状继承综合了亲本的优势性状甚至产生优于亲本性状的广泛存在的生物学现象。利用杂交优势服务于农业生产已有几千年历史，对杂交优势的科学研究也持续了一个多世纪，但对其产生的原因一直存在争议。冀研一号作为重要经济鱼类红鳍东方鲀和菊黄东方鲀的杂交子一代，表现出生长速度快、存活率高等明显的杂交优势。本研究首先对亲本之一的菊黄东方鲀进行全基因组测序和组装，并进行了基因组水平的结构特征解析、基因预测和功能注释；其次对冀研一号及两个亲本进行了全转录组测序和比对研究，从基因表达模式、差异表达转录本功能注释和新转录剪接体注释三方面对杂交优势的机制进行了转录组水平的初步解析。
本研究使用菊黄东方鲀基因组DNA构建了三个不同插入片段长度的Mate-Pair文库，文库使用SOLiD4测序，得到测序总长度76.0Gb，平均测序深度超过190。利用辅助拼接策略对基因组进行组装，共得到50，947条scaffolds， scaffold N50为305,741bp。菊黄东方鲀基因组平均GC含量为45.2%，重复序列总长占全基因组的6.87%。结构特征分析表明菊黄东方鲀基因组在GC含量和重复序列等多方面与红鳍东方鲀基因组相似，同样为小而紧密的基因组。通过基因组序列对比发现菊黄东方鲀基因组序列与红鳍东方鲀基因组序列存在明显的共线性关系。
菊黄东方鲀基因组中共含有1,253个非编码RNA基因。其中包括659个tRNA基因，可编码50种反密码子。而miRNA基因的种类数和拷贝数均多于已知河鲀miRNA基因，表明miRNA的基因扩张在物种分化后仍在进行。菊黄东方鲀基因组中共有30,285个蛋白编码基因，蛋白平均长度为519.9个氨基酸，平均每个基因含7.2个内含子，75%的内含子长度小于543bp。菊黄东方鲀中有11,142个蛋白簇与红鳍东方鲀中蛋白序列相似，有8,819个蛋白簇与斑点绿河鲀中蛋白序列相似。利用全蛋白组序列进行系统进化分析，证明菊黄东方鲀与红鳍东方鲀分化时间较晚，为近缘物种。对菊黄东方鲀进行蛋白质功能注释，鉴定负责黑色、黄色和红色等色素颗粒的合成的相关基因共16个，微管运输相关基因116个，Brinker编码基因42个，基因拷贝数远超过红鳍东方鲀。另外，菊黄东方鲀中脂联素受体编码基因和去甲肾上腺素转运蛋白编码基因也具有较多的拷贝数。
对冀研一号、红鳍东方鲀、菊黄东方鲀进行全转录组测序，测序总长度为12,189Mb，共覆盖44,305个转录本。冀研一号68.7%的差异转录本表达水平显著高于两亲本，19.8%的差异转录本表达水平与亲本中的一方相接近，4.6%的差异转录本表达水平与两亲本表达水平的平均值相近。表明在冀研一号中，超显性效应、显性效应和累加效应共同存在。另外共鉴定14,148个差异表达转录本，仅存在于冀研一号与两亲本之间的差异表达转录本为2,024个。对该部分转录本进行富集分析和功能注释，多数具有新陈代谢相关功能，表明冀研一号活跃的代谢活性可能与其较快的生长速度等杂交优势表征相关。对潜在的杂交优势相关基因进行KEGG通路富集，共得到80条通路，其中含有三个以上差异表达转录本的通路35条。细胞色素P450介导的外源性化学物代谢通路和碳水化合物、氨基酸、脂类代谢通路所含差异表达转录本多数为上调表达，其活跃的代谢活性可能与冀研一号的高抗逆性和快速生长速度有关。而对新转录剪接体的鉴定，表明冀研一号中存在大量未知的转录可变剪接形式。对新转录剪接体进行功能预测，其功能涵盖信号转导、新陈代谢和物质跨膜运输等多个生物过程，也提示杂交优势并非起源于单一机制，而是由多通路多层次差异的积累而形成。
本研究对亲本菊黄东方鲀进行基因组草图的搭建和分析，完善了亲本的遗传背景信息，也为进行转录组水平的研究提供了数据支持；对冀研一号及亲本进行转录组对比分析，证明杂交优势为超显性、显性和累加多种效应共存的结果，并由多个基因、多条通路共同参与调控。
Heterosis refers to the improved biological qualities in the hybrid offspringof two distinct species, which has been used to increase yields and vigor inagricultural production for thousands of years. The mechanism study ofheterosis has been processding since1900’s, however there is stillcontroversy. Jiyan-1is the hybrid offspring of Takifugu rubripes and Takifuguflavidus, which exhibits obvious heterosis in the fields of growth performance,flavor and stress tolerance. In the present study, the genome of T. flavidus wassequenced and assembled, and the characteristic features were also analyzed.In addition, the transcriptomes of Jiyan-1and both parental species werecomparatively studied. The potential mechanisms of heterosis were discussedin the fields of gene action modes, function annotation of differentiallyexpressed transcripts and prediction of novel transcript isoforms.
Firstly, three Mate-Pair libraries with different insert sizes were constructedfrom genomic DNA of T. flavidus, and sequenced using SOLiD4platform. Thecombined sequencing length was76.0Gb, and the average sequencing depthwas more than190-fold. The genome was assembled with assisted-assemblywhich generated50,947scaffolds with N50value of305.7kb. The average GCcontent was45.2%, and the proportion of repetive sequences was6.87%ofthe genome, which indicated the genome of T. flavidus was as compact as thegenome of T. rubripes. Sequence comparison of scaffolds showed obvioussynteny between the genomes of T. flavidus and T. rubripes.
There were1,253non-coding RNA genes, including649tRNA genes whichwere capable of encoding50anticodons for all species of amino acids. Thenumbers of species and copies of miRNA genes were more than that in the genomes of T. rubripes and T. nigroviridus, indicating the gene expression wasunder more rigorous monitor and the gene expasion had been ongoing afterthe speciation of T. flavidus. There were30,285protein-encoding genes whoseprotein products had an average length of519.9aa. There were average7.2introns per gene, and75%of introns were with length less than543bp. Thelengths of introns in T. flavidus were greater than that of T. rubripes, while nosignificant difference was found for the number of protein-encoding genes andintrons, the sequences of proteins and the length distribution of proteinsbetween T. flavidus and T. rubripes. The phylogenetic analysis of wholeproteomes indicated T. flavidus and T. rubripes were closely allied species.
There were16genes related to the biosynthesis of pigment granules and116genes evolved in the microtubule-dependent transport system. The copynumbers of these genes were much more that in the T. rubripes, indicating themicrotubule-dependent transport system might play a role in the color patternvariation during the growth. The T. flavidus genome contained42genesencoding Brinker which was an importance suppressor for Dpp signalingpathway. Besides, the more copy numbers of adiponectin receptor gene andnoradrenaline transporter gene suggested the activities of lipid mobilizationand metabolism were up-regulated in T. flavidus. The genomic level analysiscontributed to better understanding of the relationship between the genotypeand phenotype, and also provided valuable data resource for heterosis studyin transcriptomic level.
Whole transcriptomes of Jiyan-1, T. rubripes and T. flavidus weresequenced by SOLiD4platform. The combined sequencing length was12.2Gb. A total of44,305transcripts were identified, among which there were14,148differentially expressed transcripts (DTs). In Jiyan-1,68.7%DTs wereclassified as “above high parent”,19.8%DTs were classified as “low parent” or“high parent”, and4.6%DTs were classified as “mid parent”. The coexistenceof overdominance, dominance, underdominance and additivity was observedin the gene action modes of Jiyan-1. The functional annotation of enriched DTs indicated the metabolism was more activated in Jiyan-1. In addition, therewere35KEGG pathways affiliated by more than3DTs. Among them, thexenobiotics and drug metabolism pathways mediated by cytochrome P450andthe metabolism pathway of carbohydrate, amino acid and triglyceridepotentially gave rise to the high tolerance of hostile environment and fastgrowth rate. The identified novel transcript isoforms in Jiyan-1were likelyinvolved in a variety of biological processes including signal transduction,metabolism, transmembrane transportation and so on, which also underlinedthat heterosis was not originated from one single mechanism, but by theaccumulation of disparities from multiple pathways.
本研究使用菊黄东方鲀基因组DNA构建了三个不同插入片段长度的Mate-Pair文库，文库使用SOLiD4测序，得到测序总长度76.0Gb，平均测序深度超过190。利用辅助拼接策略对基因组进行组装，共得到50，947条scaffolds， scaffold N50为305,741bp。菊黄东方鲀基因组平均GC含量为45.2%，重复序列总长占全基因组的6.87%。结构特征分析表明菊黄东方鲀基因组在GC含量和重复序列等多方面与红鳍东方鲀基因组相似，同样为小而紧密的基因组。通过基因组序列对比发现菊黄东方鲀基因组序列与红鳍东方鲀基因组序列存在明显的共线性关系。
菊黄东方鲀基因组中共含有1,253个非编码RNA基因。其中包括659个tRNA基因，可编码50种反密码子。而miRNA基因的种类数和拷贝数均多于已知河鲀miRNA基因，表明miRNA的基因扩张在物种分化后仍在进行。菊黄东方鲀基因组中共有30,285个蛋白编码基因，蛋白平均长度为519.9个氨基酸，平均每个基因含7.2个内含子，75%的内含子长度小于543bp。菊黄东方鲀中有11,142个蛋白簇与红鳍东方鲀中蛋白序列相似，有8,819个蛋白簇与斑点绿河鲀中蛋白序列相似。利用全蛋白组序列进行系统进化分析，证明菊黄东方鲀与红鳍东方鲀分化时间较晚，为近缘物种。对菊黄东方鲀进行蛋白质功能注释，鉴定负责黑色、黄色和红色等色素颗粒的合成的相关基因共16个，微管运输相关基因116个，Brinker编码基因42个，基因拷贝数远超过红鳍东方鲀。另外，菊黄东方鲀中脂联素受体编码基因和去甲肾上腺素转运蛋白编码基因也具有较多的拷贝数。
对冀研一号、红鳍东方鲀、菊黄东方鲀进行全转录组测序，测序总长度为12,189Mb，共覆盖44,305个转录本。冀研一号68.7%的差异转录本表达水平显著高于两亲本，19.8%的差异转录本表达水平与亲本中的一方相接近，4.6%的差异转录本表达水平与两亲本表达水平的平均值相近。表明在冀研一号中，超显性效应、显性效应和累加效应共同存在。另外共鉴定14,148个差异表达转录本，仅存在于冀研一号与两亲本之间的差异表达转录本为2,024个。对该部分转录本进行富集分析和功能注释，多数具有新陈代谢相关功能，表明冀研一号活跃的代谢活性可能与其较快的生长速度等杂交优势表征相关。对潜在的杂交优势相关基因进行KEGG通路富集，共得到80条通路，其中含有三个以上差异表达转录本的通路35条。细胞色素P450介导的外源性化学物代谢通路和碳水化合物、氨基酸、脂类代谢通路所含差异表达转录本多数为上调表达，其活跃的代谢活性可能与冀研一号的高抗逆性和快速生长速度有关。而对新转录剪接体的鉴定，表明冀研一号中存在大量未知的转录可变剪接形式。对新转录剪接体进行功能预测，其功能涵盖信号转导、新陈代谢和物质跨膜运输等多个生物过程，也提示杂交优势并非起源于单一机制，而是由多通路多层次差异的积累而形成。
本研究对亲本菊黄东方鲀进行基因组草图的搭建和分析，完善了亲本的遗传背景信息，也为进行转录组水平的研究提供了数据支持；对冀研一号及亲本进行转录组对比分析，证明杂交优势为超显性、显性和累加多种效应共存的结果，并由多个基因、多条通路共同参与调控。
Heterosis refers to the improved biological qualities in the hybrid offspringof two distinct species, which has been used to increase yields and vigor inagricultural production for thousands of years. The mechanism study ofheterosis has been processding since1900’s, however there is stillcontroversy. Jiyan-1is the hybrid offspring of Takifugu rubripes and Takifuguflavidus, which exhibits obvious heterosis in the fields of growth performance,flavor and stress tolerance. In the present study, the genome of T. flavidus wassequenced and assembled, and the characteristic features were also analyzed.In addition, the transcriptomes of Jiyan-1and both parental species werecomparatively studied. The potential mechanisms of heterosis were discussedin the fields of gene action modes, function annotation of differentiallyexpressed transcripts and prediction of novel transcript isoforms.
Firstly, three Mate-Pair libraries with different insert sizes were constructedfrom genomic DNA of T. flavidus, and sequenced using SOLiD4platform. Thecombined sequencing length was76.0Gb, and the average sequencing depthwas more than190-fold. The genome was assembled with assisted-assemblywhich generated50,947scaffolds with N50value of305.7kb. The average GCcontent was45.2%, and the proportion of repetive sequences was6.87%ofthe genome, which indicated the genome of T. flavidus was as compact as thegenome of T. rubripes. Sequence comparison of scaffolds showed obvioussynteny between the genomes of T. flavidus and T. rubripes.
There were1,253non-coding RNA genes, including649tRNA genes whichwere capable of encoding50anticodons for all species of amino acids. Thenumbers of species and copies of miRNA genes were more than that in the genomes of T. rubripes and T. nigroviridus, indicating the gene expression wasunder more rigorous monitor and the gene expasion had been ongoing afterthe speciation of T. flavidus. There were30,285protein-encoding genes whoseprotein products had an average length of519.9aa. There were average7.2introns per gene, and75%of introns were with length less than543bp. Thelengths of introns in T. flavidus were greater than that of T. rubripes, while nosignificant difference was found for the number of protein-encoding genes andintrons, the sequences of proteins and the length distribution of proteinsbetween T. flavidus and T. rubripes. The phylogenetic analysis of wholeproteomes indicated T. flavidus and T. rubripes were closely allied species.
There were16genes related to the biosynthesis of pigment granules and116genes evolved in the microtubule-dependent transport system. The copynumbers of these genes were much more that in the T. rubripes, indicating themicrotubule-dependent transport system might play a role in the color patternvariation during the growth. The T. flavidus genome contained42genesencoding Brinker which was an importance suppressor for Dpp signalingpathway. Besides, the more copy numbers of adiponectin receptor gene andnoradrenaline transporter gene suggested the activities of lipid mobilizationand metabolism were up-regulated in T. flavidus. The genomic level analysiscontributed to better understanding of the relationship between the genotypeand phenotype, and also provided valuable data resource for heterosis studyin transcriptomic level.
Whole transcriptomes of Jiyan-1, T. rubripes and T. flavidus weresequenced by SOLiD4platform. The combined sequencing length was12.2Gb. A total of44,305transcripts were identified, among which there were14,148differentially expressed transcripts (DTs). In Jiyan-1,68.7%DTs wereclassified as “above high parent”,19.8%DTs were classified as “low parent” or“high parent”, and4.6%DTs were classified as “mid parent”. The coexistenceof overdominance, dominance, underdominance and additivity was observedin the gene action modes of Jiyan-1. The functional annotation of enriched DTs indicated the metabolism was more activated in Jiyan-1. In addition, therewere35KEGG pathways affiliated by more than3DTs. Among them, thexenobiotics and drug metabolism pathways mediated by cytochrome P450andthe metabolism pathway of carbohydrate, amino acid and triglyceridepotentially gave rise to the high tolerance of hostile environment and fastgrowth rate. The identified novel transcript isoforms in Jiyan-1were likelyinvolved in a variety of biological processes including signal transduction,metabolism, transmembrane transportation and so on, which also underlinedthat heterosis was not originated from one single mechanism, but by theaccumulation of disparities from multiple pathways.
引文
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