家蚕MITE转座子的鉴定、进化和功能以及家蚕转座子的进化动力学研究
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摘要
微型反向重复转座子(MITE)是由Bureau和Wessler首次在玉米中发现并命名的。在随后的研究中发现MITE广泛分布于真核生物基因组中。家蚕作为鳞翅目昆虫的代表,全基因组测序已于2004年完成,并在2008年,由中日科学家合作完成了家蚕基因组精细图的组装。与此同时日本科学家Osanai-Futahashi等人在分析家蚕基因中转座子含量时,发现转座子序列约占整个家蚕基因组的40%。虽然他们发现家蚕基因组中含有丰富多样的转座子序列,但是对于MITE转座子的信息却一无所知。
转座子构成了高等生物基因组的大部分并且其在不同生物基因组中的含量有非常大的变化,因此,探明转座子的进化动力学对于理解高等生物基因组的进化有非常重要的意义。转座子的进化动力学在少数物种特别是在果蝇和拟南芥中已有较深入的研究。但是,所有已有的研究结果都是基于少数模式生物和相应自然群体获得的,对驯化物种中转座子的进化动力学研究仍然是一个空白。毫无疑问,这类研究无论对于理解驯化物种的驯化遗传学还是对于理解真核基因组的进化都有非常重要和普遍的理论意义。
MITE转座子广泛的分布在真核生物的基因组中。目前对于MITE转座子种类、含量、分布和转座机制都有深入的研究和清晰的认识。但是对MITE转座子在基因组中的功能研究同样处于空白状态。本文应用MUST软件以及一系列生物信息学方法和软件对家蚕基因组中的MITE转座子进行鉴定,分类,分布和进化分析；通过转座子显示技术、群体遗传学理论和方法以及生物信息学方法对家蚕转座子的进化动力学进行研究；借助转基因技术,细胞转染技术和常见的分子生物学手段探测家蚕BmMITE-2转座子对邻近基因表达的调控。主要研究结果如下：
1.家蚕基因组中MITE转座子的种类、含量和序列结构特征
应用MUST软件对家蚕全基因组进行扫描并经过一系列筛选程序,一共鉴定了17个MITE家族,命名为BmMITE-1到BmMITE-17,这些家族在家蚕基因组中一共含有5785个拷贝,约占整个家蚕基因组的0.4%。它们的TSD长度在2到9bp之间、TIR长度在8到59bp之间、序列全长在210到567bp之间。根据它们的TIR和TSD序列进行同源性注释发现,这17个家族中有3个(BmMITE-4,5,6)属于Tourist-like家族；3个(BmMITE-2,3,8)属于Stowaway-like家族；4个家族(BmMITE-13,14,15,16)属于Pegasus-like家族,剩下的7个家族(BmMITE-1,7,9,10,11,12,17)属于新的家族。
2.家蚕MITE转座子的扩增情况
为了估计这些MITE转座子在家蚕基因组中的扩增情况,我们分别对这些MITE转座子进行了插入时间估计、Network分析家族内部的序列分化度和滑窗分析各家族内全长序列不同区域的分化度。插入时间分析结果表明：不管是在家族间还是在家族内,家蚕MITE转座子插入时间都有很大的变化,它们的插入时间范围在0到4个百万年内,并且这17个MITE家族的插入时间主要发生在2个百万年内。一个有趣的结果是BmMITE-2转座子在0-1个百万年内可能发生过爆发式的扩增,并且在很短的时间内其拷贝数增加了2173个；Network的分析结果显示：家蚕的17个MITE家族中有8个家族(BmMITE-4、BmMITE-6、BmMITE-7、 BmMITE-1、BmMITE-14、BmMITE-15、BmMITE-16和BmMITE-17)可能是在很久以前发生的扩张,剩下的9个家族可能经历了最近的扩张,这一分析结果和插入时间估计的结果是一致的；滑窗分析的结果发现：除了6个MITE家族(BmMITE-4、BmMITE-5、BmMITE-9、BmMITE-12、BmMITE-14和BmMITE-15)只有一端的TIR比较保守,剩下的11个家族在序列两端的TIR区域都相对较保守。因为TIR是MITE转座过程中转座酶的识别位点,所以TIR的保守也反映出这些家族可能最近具有活性并发生了扩张。
3.家蚕MITE转座子在染色体和基因附近的分布情况
所有的MITE广泛分布于家蚕的28条染色体上,并且这些MITE在28条染色体上的分布并不是随机分布的(Chi-square=297, df=27, P<0.01),特别是在其中7个染色体上(2号、16号、20号、24号、26号、27号和28号染色体)实际观察值要显著的高于期望值。进一步探测这些MITE转座子在基因附近的分布情况时发现：5785个鉴定的MITE转座子中有3794个(66%)分布在基因的附近。其中有962个(25%)分布在基因的5’端侧翼区域(<5kb)、有60个(2%)分布在外显子区域、1427个(38%)分布在内含子区域和1343个(35%)分布在3’端侧翼区域(<5kb)。这一结果表明MITE在内含子和两个侧翼区域的分布要显著高于外显子区域。
4.主要家蚕转座子家族在家蚕群体和野桑蚕群体中的转座子显示数据和群体多态性
为了研究转座子在家蚕驯化过程中的进化动力学,我们不仅选择了两个代表性MITE(BmMITE-7和BmMITE-2)而且还选择了另外5个其它转座子家族(Bml, Pao、CR1、Jockey、Bmmar1、),应用转座子显示技术比较这些家族在4个家蚕群体(中系、日系、欧系和热带品系)和1个野桑蚕群体中的多态性分布情况。结果表明：(1)几乎所有转座子在家蚕群体中的平均的多态性条带频率(MPBF)、每个群体中每个个体的平均条带数(MTB)和群体内固定了的条带数(Sf)都显著高于野桑蚕群体中的相应数；(2)有11个家蚕群体中的每个个体的平均转座子条带数(MTB)显著的高于野蚕群体；(3)有23个在家蚕群体中固定的位点数(Sf)显著的高于野蚕群体。这就说明转座子在家蚕群体内发生了扩张和广泛的固定。
5.驱动转座子在家蚕群体和野桑蚕群体中多态性分布的因素
为了探究转座子在家蚕群体中扩增和固定的原因,我们分别进行了极大似然估计和应用考虑了瓶颈效应的溯祖模拟方法对这些转座子在家蚕群体和野桑蚕群体中受到的选择压情况进行了估计。极大似然法估计的结果显示：(1)有5个转座子家族(Bm1, Jockey, CR1, Bmmarl, BmMITE-2)在各群体中都受到了正选择的作用；(2)几乎所有的Nes值在家蚕群体中要显著的高于野桑蚕群体。这些结果表明大多数转座子在家蚕群体中受到了较强的正选择压力,而在野桑蚕群体中受到了相对较弱的正选择压力。但是需要注意的是上述方法并没有将瓶颈效应考虑进去。为了排除驯化过程瓶颈效应的影响,我们进一步采取了考虑瓶颈效应的溯祖模拟的方法来判断各个转座子家族在不同群体中受到的选择压情况。结果发现：这些家族大多数在家蚕群体中受到了正选择的作用,而在野桑蚕群体中是服从中性进化的。
6.BmMITE-2转座子对邻近基因的调控
BmMITE-2插入缺失品系中其邻近基因表达的差异调查,转基因、细胞转染和一些分子生物学手段均证实了BmMITE-2对邻近基因表达有调控作用：BmMITE-2插入到基因的5’端时会显著的增加下游基因的表达；当BmMITE-2插入到基因的3’端时会显著的降低上游基因的表达。
综上所述,我们可以得出如下结论：家蚕基因组中含有丰富的MITE转座子家族(17个家族),并且大多数在最近发生了爆发式扩增；大多数转座子在家蚕群体中受到了强的正选择的压力；BmMITE-2插入到基因的5’端会显著的增强下游基因的表达,BmMITE-2插入到基因的3’端会显著的降低上游基因的表达。我们的结果揭示了转座子的功能性并强调有必要重新评价转座子对动植物驯化的贡献和意义。
Miniature inverted-repeat transposable elements (MITEs) were originally discovered in maize genome by Bureau and Wessler. And they are widespread in the eukaryotic genomes. Silkworm, Bombyx mori, is a model insect for the order Lepidoptera. The draft genome sequences of silkworm were released by Mita et al. and Xia et al., respectively. Recently, a new assembly has been completed. Analyses of the silkworm genome sequence suggested that-40%of the genome is composed of the known TEs. Although silkworm (Bombyx mori) has a large amount of and a variety of transposable elements, the genome-wide information of the silkworm MITEs is unknown.
Transposable elements (TEs) constitute a substantial amount of eukaryotic organisms and content varied in different organisms. Thus knowledge of the evolutionary dynamics of TEs is very important for understanding the evolution of eukaryotic genomes. Previous studies revealed that transposition, natural selection, demography and mating system play significant roles in the TE evolutionary dynamics. However, all these lines of cognition mainly came from research on a few model organisms such as Drosophila and Arabidopsis and previous studies on the evolutionary dynamics of TEs focused exclusively on natural populations of individual model species. Yet there has been no study concerning the evolutionary dynamics of TEs in domesticated species. Howbeit, undoubtedly, this kind of research has very important implications for understanding both the genetics of domestication of higher organisms and the evolution of eukaryotic genomes.
MITEs are widespread in the eukaryotic genomes. At present types, contents, distribution and transpose mechanism of MITEs have been explored in depth. And we have a clear idea of these characters. However, the function of MITEs was remained unknown. In this study, identification, classification, distribution and evolution analysis of silkworm MITEs were performed using software of MUST with a series of methods and software of bioinformatics; Evolution dynamics of silkworm TEs were estimated by transposon display, theories and methods of population genetics and bioinformatics; Using transgene technology, technology of cell transfection and most basic techniques of molecular biology to detect whether BmMITE-2might regulate expression of its neighboring genes. The major results were as follow:
1. Types, contents and charaters of silkworm MITEs
MUST, a program designed to detect MITE elements, was first used to search the silkworm genome sequence. With MUST, we mined143333MITE candidates in the silkworm genome, which were grouped into1350families. Then, we filtered out pseudo-MITEs from predicted ones by Perl scripts. By this way, number of the MITE families reduced to17. These17families include5785intact MITEs and were designated as BmMITE-1to BmMITE-17, which constitute-1.86Mb (0.4%) of the silkworm genome. TSD lengths of all MITEs range from2to9bp, TIR lengths from8to59bp, and full lengths of complete MITEs from210to567bp. Based on the nucleotide composition of TSD,3MITE families (BmMITE-4,5,6) belong to Tourist-like family,3families (BmMITE-2,3,8) belong to Stowaway-like family, based on the nucleotide composition of TSD and TIR,4families (BmMITE-13,14,15,16) belong to Pegasus-like family, and the remaining7families (BmMITE-1,7,9,10,11,12,17) were novel.
2. Expansion of silkworm MITEs
To estimat expansion of silkworm MITEs, estimates of insertion date, network analysis and sliding window analysis were performed, respectivly. Results of insertion date showed that insertion date varies greatly among members of each family as well as among families, which ranges from0to4million years ago (mya). The major expansion events of17families might happen within2mya. Strikingly, BmMITE-2might be dramatically expanded during a period from0mya to1mya and accumulated up to2173copies during this short period; Results of network analysis indicated that8(BmMITE-4, BmMITE-6, BmMITE-7, BmMITE-11, BmMITE-14, BmMITE-15, BmMITE-16and BmMITE-17) of17MITE families presented the topologies that these MITE families might experience old population expansions. The topologies of rest9 families indicated that these families might undergo recent expansions. These observations are basically consistent with the insertion time estimates; Results of sliding window analysis suggested that regional variation pattern varies greatly among these17silkworm MITE families. Almost all families have highly conserved TIRs, however,6families (BmMITE-4, BmMITE-5, BmMITE-9, BmMITE-12. BmMITE-14, and BmMITE-15) have only one conserved TIR. Because TIRs must be first recognized by corresponding transposase for transposition, Thus these results could be reflected that most of these MITEs remianed actively and expansion in recently.
3. Distributions of MITEs on chromosomes and Estimation of MITE distance to the nearest gene
Results were as follow:all MITE families are widely distributed on all28silkworm chromosomes. Then, we examined whether MITEs were randomly distributed among28silkworm chromosomes using χ2test. The null hypothesis was rejected (P<0.01), suggesting that the distribution of MITEs is nonrandom in the silkworm genome. And observed values were significantly higher than expected ones in the7silkworm chromosomes (chromosome2,16,20,24,26-28). Furthermore, we examined whether insertion site of each MITE preferentially is in or close to genes. The results indicated that3794(66%) of the5785predicted MITEs inserted into gene regions. Of3794MiTEs inserted into gene regions,962(25%) were located in5'flanking regions of the closest genes,60(2%) in exons,1427(38%) in introns and1343(35%) in3'flanking regions of the closest genes, respectively. It appears that silkworm MITEs preferentially inserted into introns,3'-flanking regions and5'-flanking regions rather than exons.
4. TE-display data and population polymorphism of7major silkworm TEs in the domesticated silkworm and wild silkworm populations
We investigated the distribution and diversity of seven TE families (Bml, Pao, CR1, Jockey, Bmmarl, BmMITE-7and BmMITE-2) in the corresponding populations using TE-display technique. With these TE band data, we calculated six initial statistics (MPBF:mean polymorphic band frequency; var(f):variance of polymorphic band frequencies; S:the number of observed TE bands; Sx:the number of unique of TE bands in a pairwise comparison; MTB:mean TE bands in each individual of each population; Sf. the number of within-population fixed TE bands) for each TE in each silkworm population. Finally, results were as follow:(1) almost all the domestication silkworm populations have higher MPBF, MTB and Sf values than wild silkworm population;(2) there are eleven MTB values in the domesticated silkworm significant higher than those in wild silkworm;(3) there are twenty three Sf values in the domesticated silkworm significant higher than those in wild silkworm. These results suggested that these TE families experienced expansions and widely fixed in the domesticated silkworm.
5. Factors of TEs population polymorphism in the domesticated silkworm and wild silkworm populations
In order to detected reasons of TEs experienced expansions and widely fixed in the domesticated silkworm other than wild silkworm, maximum likelihood estimate and coalescent simulation were performed. Results of maximum likelihood estimate were as follow:(1) all95%credible intervals of Nes do not overlap zero and the Nes values of five TE families (Bml, Jockey, CR1, Bmmarl, BmMITE-2) in each population are positive;(2) Almost all of Nes values in the domesticated silkworm are significant higher than those in wild silkworm. These results indicated that these TEs experienced strong positive selection in the domesticated silkworm and these TEs experienced weak positive selection in the wild silkworm. However, it should be noted that the maximum likelihood approach does not take into account demographic history (Lockton et al.2008). To further detect whether there is positive selection on these TE families during silkworm domestication, the selection pressure of these TEs were estimated by coalescent simulation that take into account demographic history. And results showed that these TEs did experience positive selection in the domesticated silkworm population. However, they were under neutrality in the wild silkworm population.
6. BmMITE-2regulates expression of its neighboring genes
According to above results, BmMITE-2prefers to insert in silkworm gene regions and may experience positive selection during silkworm domestication. Whether BmMITE-2might regulate expression of its neighboring genes? To answer this question, we detected BmMITE-2effected on expression of its neighboring genes using transgene technology, technology of cell transfection and most basic techniques of molecular biology. Finally, the results indicated that BmMITE-2can up-regulate expression of its neighboring genes when BmMITE-2inserted into5'terminal of genes; In contrast, BmMITE-2can down-regulate expression of its neighboring genes when BmMITE-2inserted into3'terminal of genes.
According to the above results, we can conclude:There are abundent and varied MITEs in the silkworm genome, most these MITEs are experienced burst expantion; Most TEs are experienced strong positive selection in the domesticated silkworm popuplation; BmMITE-2can up-regulate expression of its neighboring genes when BmMITE-2inserted into5'terminal of genes, BmMITE-2can down-regulate expression of its neighboring genes when BmMITE-2inserted into3'terminal of genes.
转座子构成了高等生物基因组的大部分并且其在不同生物基因组中的含量有非常大的变化,因此,探明转座子的进化动力学对于理解高等生物基因组的进化有非常重要的意义。转座子的进化动力学在少数物种特别是在果蝇和拟南芥中已有较深入的研究。但是,所有已有的研究结果都是基于少数模式生物和相应自然群体获得的,对驯化物种中转座子的进化动力学研究仍然是一个空白。毫无疑问,这类研究无论对于理解驯化物种的驯化遗传学还是对于理解真核基因组的进化都有非常重要和普遍的理论意义。
MITE转座子广泛的分布在真核生物的基因组中。目前对于MITE转座子种类、含量、分布和转座机制都有深入的研究和清晰的认识。但是对MITE转座子在基因组中的功能研究同样处于空白状态。本文应用MUST软件以及一系列生物信息学方法和软件对家蚕基因组中的MITE转座子进行鉴定,分类,分布和进化分析；通过转座子显示技术、群体遗传学理论和方法以及生物信息学方法对家蚕转座子的进化动力学进行研究；借助转基因技术,细胞转染技术和常见的分子生物学手段探测家蚕BmMITE-2转座子对邻近基因表达的调控。主要研究结果如下：
1.家蚕基因组中MITE转座子的种类、含量和序列结构特征
应用MUST软件对家蚕全基因组进行扫描并经过一系列筛选程序,一共鉴定了17个MITE家族,命名为BmMITE-1到BmMITE-17,这些家族在家蚕基因组中一共含有5785个拷贝,约占整个家蚕基因组的0.4%。它们的TSD长度在2到9bp之间、TIR长度在8到59bp之间、序列全长在210到567bp之间。根据它们的TIR和TSD序列进行同源性注释发现,这17个家族中有3个(BmMITE-4,5,6)属于Tourist-like家族；3个(BmMITE-2,3,8)属于Stowaway-like家族；4个家族(BmMITE-13,14,15,16)属于Pegasus-like家族,剩下的7个家族(BmMITE-1,7,9,10,11,12,17)属于新的家族。
2.家蚕MITE转座子的扩增情况
为了估计这些MITE转座子在家蚕基因组中的扩增情况,我们分别对这些MITE转座子进行了插入时间估计、Network分析家族内部的序列分化度和滑窗分析各家族内全长序列不同区域的分化度。插入时间分析结果表明：不管是在家族间还是在家族内,家蚕MITE转座子插入时间都有很大的变化,它们的插入时间范围在0到4个百万年内,并且这17个MITE家族的插入时间主要发生在2个百万年内。一个有趣的结果是BmMITE-2转座子在0-1个百万年内可能发生过爆发式的扩增,并且在很短的时间内其拷贝数增加了2173个；Network的分析结果显示：家蚕的17个MITE家族中有8个家族(BmMITE-4、BmMITE-6、BmMITE-7、 BmMITE-1、BmMITE-14、BmMITE-15、BmMITE-16和BmMITE-17)可能是在很久以前发生的扩张,剩下的9个家族可能经历了最近的扩张,这一分析结果和插入时间估计的结果是一致的；滑窗分析的结果发现：除了6个MITE家族(BmMITE-4、BmMITE-5、BmMITE-9、BmMITE-12、BmMITE-14和BmMITE-15)只有一端的TIR比较保守,剩下的11个家族在序列两端的TIR区域都相对较保守。因为TIR是MITE转座过程中转座酶的识别位点,所以TIR的保守也反映出这些家族可能最近具有活性并发生了扩张。
3.家蚕MITE转座子在染色体和基因附近的分布情况
所有的MITE广泛分布于家蚕的28条染色体上,并且这些MITE在28条染色体上的分布并不是随机分布的(Chi-square=297, df=27, P<0.01),特别是在其中7个染色体上(2号、16号、20号、24号、26号、27号和28号染色体)实际观察值要显著的高于期望值。进一步探测这些MITE转座子在基因附近的分布情况时发现：5785个鉴定的MITE转座子中有3794个(66%)分布在基因的附近。其中有962个(25%)分布在基因的5’端侧翼区域(<5kb)、有60个(2%)分布在外显子区域、1427个(38%)分布在内含子区域和1343个(35%)分布在3’端侧翼区域(<5kb)。这一结果表明MITE在内含子和两个侧翼区域的分布要显著高于外显子区域。
4.主要家蚕转座子家族在家蚕群体和野桑蚕群体中的转座子显示数据和群体多态性
为了研究转座子在家蚕驯化过程中的进化动力学,我们不仅选择了两个代表性MITE(BmMITE-7和BmMITE-2)而且还选择了另外5个其它转座子家族(Bml, Pao、CR1、Jockey、Bmmar1、),应用转座子显示技术比较这些家族在4个家蚕群体(中系、日系、欧系和热带品系)和1个野桑蚕群体中的多态性分布情况。结果表明：(1)几乎所有转座子在家蚕群体中的平均的多态性条带频率(MPBF)、每个群体中每个个体的平均条带数(MTB)和群体内固定了的条带数(Sf)都显著高于野桑蚕群体中的相应数；(2)有11个家蚕群体中的每个个体的平均转座子条带数(MTB)显著的高于野蚕群体；(3)有23个在家蚕群体中固定的位点数(Sf)显著的高于野蚕群体。这就说明转座子在家蚕群体内发生了扩张和广泛的固定。
5.驱动转座子在家蚕群体和野桑蚕群体中多态性分布的因素
为了探究转座子在家蚕群体中扩增和固定的原因,我们分别进行了极大似然估计和应用考虑了瓶颈效应的溯祖模拟方法对这些转座子在家蚕群体和野桑蚕群体中受到的选择压情况进行了估计。极大似然法估计的结果显示：(1)有5个转座子家族(Bm1, Jockey, CR1, Bmmarl, BmMITE-2)在各群体中都受到了正选择的作用；(2)几乎所有的Nes值在家蚕群体中要显著的高于野桑蚕群体。这些结果表明大多数转座子在家蚕群体中受到了较强的正选择压力,而在野桑蚕群体中受到了相对较弱的正选择压力。但是需要注意的是上述方法并没有将瓶颈效应考虑进去。为了排除驯化过程瓶颈效应的影响,我们进一步采取了考虑瓶颈效应的溯祖模拟的方法来判断各个转座子家族在不同群体中受到的选择压情况。结果发现：这些家族大多数在家蚕群体中受到了正选择的作用,而在野桑蚕群体中是服从中性进化的。
6.BmMITE-2转座子对邻近基因的调控
BmMITE-2插入缺失品系中其邻近基因表达的差异调查,转基因、细胞转染和一些分子生物学手段均证实了BmMITE-2对邻近基因表达有调控作用：BmMITE-2插入到基因的5’端时会显著的增加下游基因的表达；当BmMITE-2插入到基因的3’端时会显著的降低上游基因的表达。
综上所述,我们可以得出如下结论：家蚕基因组中含有丰富的MITE转座子家族(17个家族),并且大多数在最近发生了爆发式扩增；大多数转座子在家蚕群体中受到了强的正选择的压力；BmMITE-2插入到基因的5’端会显著的增强下游基因的表达,BmMITE-2插入到基因的3’端会显著的降低上游基因的表达。我们的结果揭示了转座子的功能性并强调有必要重新评价转座子对动植物驯化的贡献和意义。
Miniature inverted-repeat transposable elements (MITEs) were originally discovered in maize genome by Bureau and Wessler. And they are widespread in the eukaryotic genomes. Silkworm, Bombyx mori, is a model insect for the order Lepidoptera. The draft genome sequences of silkworm were released by Mita et al. and Xia et al., respectively. Recently, a new assembly has been completed. Analyses of the silkworm genome sequence suggested that-40%of the genome is composed of the known TEs. Although silkworm (Bombyx mori) has a large amount of and a variety of transposable elements, the genome-wide information of the silkworm MITEs is unknown.
Transposable elements (TEs) constitute a substantial amount of eukaryotic organisms and content varied in different organisms. Thus knowledge of the evolutionary dynamics of TEs is very important for understanding the evolution of eukaryotic genomes. Previous studies revealed that transposition, natural selection, demography and mating system play significant roles in the TE evolutionary dynamics. However, all these lines of cognition mainly came from research on a few model organisms such as Drosophila and Arabidopsis and previous studies on the evolutionary dynamics of TEs focused exclusively on natural populations of individual model species. Yet there has been no study concerning the evolutionary dynamics of TEs in domesticated species. Howbeit, undoubtedly, this kind of research has very important implications for understanding both the genetics of domestication of higher organisms and the evolution of eukaryotic genomes.
MITEs are widespread in the eukaryotic genomes. At present types, contents, distribution and transpose mechanism of MITEs have been explored in depth. And we have a clear idea of these characters. However, the function of MITEs was remained unknown. In this study, identification, classification, distribution and evolution analysis of silkworm MITEs were performed using software of MUST with a series of methods and software of bioinformatics; Evolution dynamics of silkworm TEs were estimated by transposon display, theories and methods of population genetics and bioinformatics; Using transgene technology, technology of cell transfection and most basic techniques of molecular biology to detect whether BmMITE-2might regulate expression of its neighboring genes. The major results were as follow:
1. Types, contents and charaters of silkworm MITEs
MUST, a program designed to detect MITE elements, was first used to search the silkworm genome sequence. With MUST, we mined143333MITE candidates in the silkworm genome, which were grouped into1350families. Then, we filtered out pseudo-MITEs from predicted ones by Perl scripts. By this way, number of the MITE families reduced to17. These17families include5785intact MITEs and were designated as BmMITE-1to BmMITE-17, which constitute-1.86Mb (0.4%) of the silkworm genome. TSD lengths of all MITEs range from2to9bp, TIR lengths from8to59bp, and full lengths of complete MITEs from210to567bp. Based on the nucleotide composition of TSD,3MITE families (BmMITE-4,5,6) belong to Tourist-like family,3families (BmMITE-2,3,8) belong to Stowaway-like family, based on the nucleotide composition of TSD and TIR,4families (BmMITE-13,14,15,16) belong to Pegasus-like family, and the remaining7families (BmMITE-1,7,9,10,11,12,17) were novel.
2. Expansion of silkworm MITEs
To estimat expansion of silkworm MITEs, estimates of insertion date, network analysis and sliding window analysis were performed, respectivly. Results of insertion date showed that insertion date varies greatly among members of each family as well as among families, which ranges from0to4million years ago (mya). The major expansion events of17families might happen within2mya. Strikingly, BmMITE-2might be dramatically expanded during a period from0mya to1mya and accumulated up to2173copies during this short period; Results of network analysis indicated that8(BmMITE-4, BmMITE-6, BmMITE-7, BmMITE-11, BmMITE-14, BmMITE-15, BmMITE-16and BmMITE-17) of17MITE families presented the topologies that these MITE families might experience old population expansions. The topologies of rest9 families indicated that these families might undergo recent expansions. These observations are basically consistent with the insertion time estimates; Results of sliding window analysis suggested that regional variation pattern varies greatly among these17silkworm MITE families. Almost all families have highly conserved TIRs, however,6families (BmMITE-4, BmMITE-5, BmMITE-9, BmMITE-12. BmMITE-14, and BmMITE-15) have only one conserved TIR. Because TIRs must be first recognized by corresponding transposase for transposition, Thus these results could be reflected that most of these MITEs remianed actively and expansion in recently.
3. Distributions of MITEs on chromosomes and Estimation of MITE distance to the nearest gene
Results were as follow:all MITE families are widely distributed on all28silkworm chromosomes. Then, we examined whether MITEs were randomly distributed among28silkworm chromosomes using χ2test. The null hypothesis was rejected (P<0.01), suggesting that the distribution of MITEs is nonrandom in the silkworm genome. And observed values were significantly higher than expected ones in the7silkworm chromosomes (chromosome2,16,20,24,26-28). Furthermore, we examined whether insertion site of each MITE preferentially is in or close to genes. The results indicated that3794(66%) of the5785predicted MITEs inserted into gene regions. Of3794MiTEs inserted into gene regions,962(25%) were located in5'flanking regions of the closest genes,60(2%) in exons,1427(38%) in introns and1343(35%) in3'flanking regions of the closest genes, respectively. It appears that silkworm MITEs preferentially inserted into introns,3'-flanking regions and5'-flanking regions rather than exons.
4. TE-display data and population polymorphism of7major silkworm TEs in the domesticated silkworm and wild silkworm populations
We investigated the distribution and diversity of seven TE families (Bml, Pao, CR1, Jockey, Bmmarl, BmMITE-7and BmMITE-2) in the corresponding populations using TE-display technique. With these TE band data, we calculated six initial statistics (MPBF:mean polymorphic band frequency; var(f):variance of polymorphic band frequencies; S:the number of observed TE bands; Sx:the number of unique of TE bands in a pairwise comparison; MTB:mean TE bands in each individual of each population; Sf. the number of within-population fixed TE bands) for each TE in each silkworm population. Finally, results were as follow:(1) almost all the domestication silkworm populations have higher MPBF, MTB and Sf values than wild silkworm population;(2) there are eleven MTB values in the domesticated silkworm significant higher than those in wild silkworm;(3) there are twenty three Sf values in the domesticated silkworm significant higher than those in wild silkworm. These results suggested that these TE families experienced expansions and widely fixed in the domesticated silkworm.
5. Factors of TEs population polymorphism in the domesticated silkworm and wild silkworm populations
In order to detected reasons of TEs experienced expansions and widely fixed in the domesticated silkworm other than wild silkworm, maximum likelihood estimate and coalescent simulation were performed. Results of maximum likelihood estimate were as follow:(1) all95%credible intervals of Nes do not overlap zero and the Nes values of five TE families (Bml, Jockey, CR1, Bmmarl, BmMITE-2) in each population are positive;(2) Almost all of Nes values in the domesticated silkworm are significant higher than those in wild silkworm. These results indicated that these TEs experienced strong positive selection in the domesticated silkworm and these TEs experienced weak positive selection in the wild silkworm. However, it should be noted that the maximum likelihood approach does not take into account demographic history (Lockton et al.2008). To further detect whether there is positive selection on these TE families during silkworm domestication, the selection pressure of these TEs were estimated by coalescent simulation that take into account demographic history. And results showed that these TEs did experience positive selection in the domesticated silkworm population. However, they were under neutrality in the wild silkworm population.
6. BmMITE-2regulates expression of its neighboring genes
According to above results, BmMITE-2prefers to insert in silkworm gene regions and may experience positive selection during silkworm domestication. Whether BmMITE-2might regulate expression of its neighboring genes? To answer this question, we detected BmMITE-2effected on expression of its neighboring genes using transgene technology, technology of cell transfection and most basic techniques of molecular biology. Finally, the results indicated that BmMITE-2can up-regulate expression of its neighboring genes when BmMITE-2inserted into5'terminal of genes; In contrast, BmMITE-2can down-regulate expression of its neighboring genes when BmMITE-2inserted into3'terminal of genes.
According to the above results, we can conclude:There are abundent and varied MITEs in the silkworm genome, most these MITEs are experienced burst expantion; Most TEs are experienced strong positive selection in the domesticated silkworm popuplation; BmMITE-2can up-regulate expression of its neighboring genes when BmMITE-2inserted into5'terminal of genes, BmMITE-2can down-regulate expression of its neighboring genes when BmMITE-2inserted into3'terminal of genes.
引文
[1]Finnegan DJ. Eukaryotic transposable elements and genome evolution[J]. Trends Genet,1989, 5(4):103-7
[2]Mc CB. The origin and behavior of mutable loci in maize[J]. Proc Natl Acad Sci U S A,1950, 36(6):344-55
[3]Bennetzen JL, Ma J, Devos KM. Mechanisms of recent genome size variation in flowering plants[J]. Ann Bot,2005,95(1):127-32
[4]Biemont C, Vieira C. Genetics-Junk DNA as an evolutionary force[J]. Nature.2006, 443(7111):521-524
[5]Kidwell MG. Transposable elements and the evolution of genome size in eukaryotes[J]. Genetica, 2002,115(1):49-63
[6]Lonnig WE, Saedler H. Chromosome rearrangements and transposable elements[J]. Annu Rev Genet,2002,36:389-410
[7]Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen WZ, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J. Shah N. Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B. Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He RF, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin.JK, Dujmic Z. Kim W, Talag J, Zuccolo A, Fan C, Sebastian A. Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren LY, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, et al. The B73 Maize Genome:Complexity, Diversity, and Dynamics[J]. Science,2009,326(5956):1112-1115
[8]Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D. Wing RA. Transposable element distribution, abundance and role in genome size variation in the genus Oryza[J]. BMC Evol Biol,2007,7
[9]de Koning APJ, Gu WJ, Castoe TA, Batzer MA, Pollock DD. Repetitive Elements May Comprise Over Two-Thirds of the Human Genome[J]. PLoS Genet,2011,7(12)
[10]Lander ES, Consortium IHGS, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Roserti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, et al. Initial sequencing and analysis of the human genome[J], Nature,2001,409(6822):860-921
[11]Biemont C. A brief history of the status of transposable elements:from junk DNA to major players in evolution[J]. Genetics,2010,186(4):1085-93
[12]Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics[J]. Nat Rev Genet,2002,3(5):329-41
[13]Eichbush T, Craig NL, Craigie R, Gellert M. Origins and evolution of retrotransposons[J]. Mobile DNA II,2002, Washington D. C:Am. Soc. Microbiol. Press.:1111-1144
[14]Kumar A, Bennetzen JL. Plant retrotransposons[J]. Annu Rev Genet,1999,33:479-532
[15]Han JS, Boeke JD. LINE-1 retrotransposons:modulators of quantity and quality of mammalian gene expression?[J]. Bioessays,2005,27(8):775-84
[16]Sabot F, Schulman AH. Parasitism and the retrotransposon life cycle in plants:a hitchhiker's guide to the genome[J]. Heredity (Edinb),2006,97(6):381-8
[17]SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL. Nested retrotransposons in the intergenic regions of the maize genome[J]. Science,1996,274(5288):765-8
[18]Neumann P, Pozarkova D, Macas J. Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced[J]. Plant Mol Biol,2003,53(3):399-410
[19]Xiong Y, Burke WD, Eickbush TH. Pao, a Highly Divergent Retrotransposable Element from Bombyx-Mori Containing Long Terminal Repeats with Tandem Copies of the Putative-R Region[J]. Nucleic Acids Res,1993,21(9):2117-2123
[20]Frankel AD, Young JA. HIV-1:fifteen proteins and an RNA[J]. Annu Rev Biochem,1998, 67:1-25
[21]Seelamgari A, Maddukuri A, Berro R, de la Fuente C, Kehn K, Deng L, Dadgar S, Bottazzi ME, Ghedin E, Pumfery A, Kashanchi F. Role of viral regulatory and accessory proteins in HIV-1 replication[J]. Front Biosci,2004,9:2388-413
[22]Bucheton A. The Relationship between the Flamenco Gene and Gypsy in Drosophila-How to Tame a Retrovirus[J]. Trends in Genetics,1995, 11(9):349-353
[23]Cappello J, Handelsman K, Lodish HF. Sequence of Dictyostelium Dirs-1-an Apparent Retrotransposon with Inverted Terminal Repeats and an Internal Circle Junction Sequence[J]. Cell,1985,43(1):105-115
[24]Goodwin TJD, Poulter RTM. A new group of tyrosine recombinase-encoding retrotransposons[J]. Mol Biol Evol,2004,21(4):746-759
[25]Evgen'ev MB, Zelentsova H, Shostak N, Kozitsina M, Barskyi V, Lankenau DH, Corces VG. Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis[J]. Proc Natl Acad Sci U S A,1997,94(1):196-201
[26]Evgen'ev MB, Arkhipova IR. Penelope-like elements--a new class of retroelements: distribution, function and possible evolutionary significance[J]. Cytogenet Genome Res,2005, 110(1-4):510-21
[27]Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse Transcription of R2bm Rna Is Primed by a Nick at the Chromosomal Target Site-a Mechanism for Non-Ltr Retrotransposition[J]. Cell,1993,72(4):595-605
[28]Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail[J]. Cytogenet Genome Res,2005,110(1-4):475-90
[29]Weiner AM. An Abundant Cytoplasmic 7s Rna Is Complementary to the Dominant Interspersed Middle Repetitive DNA-Sequence Family in the Human Genome[J]. Cell,1980,22(1):209-218
[30]Ullu E, Tschudi C. Alu Sequences Are Processed 7sl Rna Genes[J]. Nature,1984, 312(5990):171-172
[31]Vassetzky NS, Ten OA, Kramerov DA. B1 and related SINEs in mammalian genomes[J]. Gene, 2003,319:149-160
[32]Kapitonov VV, Jurka J. A novel class of SINE elements derived from 5S rRNA[J]. Mol Biol Evol, 2003,20(5):694-702
[33]Nishihara H, Smit AF, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome[J]. Genome Res,2006,16(7):864-74
[34]Gogolevsky KP, Vassetzky NS, Kramerov DA.5S rRNA-derived and tRNA-derived SINEs in fruit bats[J]. Genomics,2009,93(5):494-500
[35]Lisch D. How important are transposons for plant evolution?[J]. Nat Rev Genet,2013, 14(1):49-61
[36]Shao HG, Tu ZJ. Expanding the diversity of the IS630-Tcl-mariner superfamily:Discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons[J]. Genetics,2001,159(3):1103-1115
[37]Kempken F, Windhofer F. The hATfamily:a versatile transposon group common to plants, fungi. animals, and man[J]. Chromosoma,2001,110(1):1-9
[38]Pritham ET, Feschotte C, Wessler SR. Unexpected diversity and differential success of DNA transposons in four species of Entamoeba protozoans[J]. Mol Biol Evol.2005,22(9):1751-1763
[39]Feschotte C. Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences[J]. Mol Biol Evol,2004, 21(9):1769-80
[40]Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons[J]. Plos Biology,2005,3(6):998-1011
[41]Sarkar A, Sim C, Hong YS, Hogan JR, Fraser MJ, Robertson HM, Collins FH. Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences[J]. Molecular Genetics and Genomics,2003,270(2):173-180
[42]Hammer SE, Strehl S, Hagemann S. Homologs of Drosophila P transposons were mobile in zebrafish but have been domesticated in a common ancestor of chicken and human[J]. Mol Biol Evol,2005,22(4):833-844
[43]Jurka J. Kapitonov W. PiFs meet Tourists and Harbingers:A superfamily reunion[J]. Proc Natl Acad Sci U S A,2001,98(22):12315-12316
[44]Wicker T, Guyot R, Yahiaoui N. Keller B. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements[J]. Plant Physiol,2003.132(1):52-63
[45]Bureau TE, Wessler SR. Tourist-a Large Family of Small Inverted Repeat Elements Frequently Associated with Maize Genes[J]. Plant Cell,1992,4(10):1283-1294
[46]Goodwin TJ, Butler MI, Poulter RT. Cryptons:a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi[J]. Microbiology,2003,149(Pt 11):3099-109
[47]Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes[J]. Proc Natl Acad Sci U S A, 2001,98(15):8714-9
[48]Feschotte C, Pritham EJ. Non-mammalian c-integrases are encoded by giant transposable elements[J]. Trends in Genetics,2005,21(10):551-552
[49]Kapitonov VV, Jurka J. Self-synthesizing DNA transposons in eukaryotes[J]. Proc Natl Acad Sci USA,2006,103(12):4540-4545
[50]Pritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses[J]. Gene,2007,390(1-2):3-17
[51]Tenaillon MI, Hollister JD, Gaut BS. A triptych of the evolution of plant transposable elements[J]. Trends Plant Sci,2010,15(8):471-8
[52]Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature,2000,408(6814):796-815
[53]The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon[J].Nature,2010,463(7282):763-8
[54]Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, et al. The B73 maize genome:complexity, diversity, and dynamics[J]. Science,2009,326(5956):1112-5
[55]Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N. A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats[J]. Plant Journal,2005, 41(2):184-194
[56]Feschotte C. Transposable elements and the evolution of regulatory networks[J]. Nat Rev Genet, 2008,9(5):397-405
[57]Britten RJ. Cases of ancient mobile element DNA insertions that now affect gene regulation[J]. Mol Phylogenet Evol,1996,5(1):13-17
[58]Brosius J. The contribution of RNAs and retroposition to evolutionary novelties[J]. Genetica, 2003,118(2-3):99-116
[59]Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK. Transposable elements donate lineage-specific regulatory sequences to host genomes[J]. Cytogenet Genome Res,2005, 110(1-4):333-341
[60]Jordan IK, Rogozin IB, Glazko GV, Koonin EV. Origin of a substantial fraction of human regulatory sequences from transposable elements[J]. Trends in Genetics,2003,19(2):68-72
[61]van de Lagemaat LN, Landry JR, Mager DL, Medstrand P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions[J]. Trends in Genetics,2003,19(10):530-536
[62]Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS. A de novo Alu insertion results in neurofibromatosis type 1[J]. Nature,1991,353(6347):864-6
[63]Girard L, Freeling M. Regulatory changes as a consequence of transposon insertion[J]. Developmental Genetics,1999,25(4):291-296
[64]Marino-Ramirez L, Jordan IK. Transposable element derived DNasel-hypersensitive sites in the human genome[J]. Biol Direct,2006,1
[65]Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes[J]. Proc Natl Acad Sci U S A,2007, 104(19):8005-10
[66]Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon[J]. Nature, 2006,441(7089):87-90
[67]Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, Rubinstein M. Ancient exaptation of a CORE-SINE Retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene[J]. PLoS Genet,2007,3(10):1813-1826
[68]Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay[J]. Genes Dev,2007,21(6):708-718
[69]Grewal SIS, Jia ST. Heterochromatin revisited[J]. Nature Reviews Genetics,2007,8(1):35-46
[70]Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome[J]. Nature Reviews Genetics,2007,8(4):272-285
[71]Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK. Transposable elements donate lineage-specific regulatory sequences to host genomes[J]. Cytogenet Genome Res,2005, 110(1-4):333-41
[72]Smalheiser NR, Torvik VI. Alu elements within human mRNAs are probable microRNA targets[J]. Trends in Genetics,2006,22(10):532-536
[73]Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK. Evaluating the protein coding potential of exonized transposable element sequences[J]. Biol Direct,2007,2:31
[74]Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit[J]. Science,2008, 319(5869):1527-30
[75]Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges[J]. Plant Cell,2012,24(3):1242-55
[76]Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color[J]. Science,2004,304(5673):982
[77]Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tbl[J]. Nat Genet,2011,43(11):1160-3
[78]Wang H, Chai Y, Chu X, Zhao Y, Wu Y, Zhao J, Ngezahayo F, Xu C, Liu B. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability[J]. BMC Plant Biol,2009,9:63
[79]Iida S, Morita Y, Choi JD, Park KI, Hoshino A. Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories[J]. Novel Developments on Genetic Recombination:DNA Double Strand Break and DNA End-Joining,2004,38:141-159
[80]Galimba KD. Tolkin TR, Sullivan AM, Melzer R, Theissen G, Di Stilio VS. Loss of deeply conserved C-class floral homeotic gene function and C-and E-class protein interaction in a double-flowered ranunculid mutant[J]. Proc Natl Acad Sci U S A,2012,109(34):E2267-75
[81]Dreger DL, Schmutz SM. A SINE insertion causes the black-and-tan and saddle tan phenotypes in domestic dogs[J]. J Hered,2011.102 Suppl 1:S11-8
[82]Morgan HD, Sutherland HGE, Martin DIK, Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse[J]. Nat Genet,1999,23(3):314-318
[83]Sakudoh T, Sezutsu H, Nakashima T, Kobayashi I, Fujimoto H, Uchino K, Banno Y, Iwano H, Maekawa H, Tamura T, Kataoka H, Tsuchida K. Carotenoid silk coloration is controlled by a carotenoid-binding protein, a product of the Yellow blood gene[J]. Proc Natl Acad Sci U S A, 2007,104(21):8941-8946
[84]Liu C, Yamamoto K, Cheng TC, Kadono-Okuda K, Narukawa J, Liu SP, Han Y, Futahashi R, Kidokoro K, Noda H, Kobayashi I, Tamura T, Ohnuma A, Banno Y, Dai FY, Xiang ZH, Goldsmith MR, Mita K, Xia QY. Repression of tyrosine hydroxylase is responsible for the sex-linked chocolate mutation of the silkworm, Bombyx mori[J]. Proc Natl Acad Sci U S A,2010, 107(29):12980-12985
[85]Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons:for better or worse, in sickness and in health[J]. Genome Res,2008,18(3):343-58
[86]Deininger PL, Batzer MA. Alu repeats and human disease[J]. Mol Genet Metab,1999, 67(3):183-93
[87]Chen J, Rattner A, Nathans J. Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation:lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements[J]. Hum Mol Genet,2006,15(13):2146-56
[88]Gu Y, Kodama H, Watanabe S, Kikuchi N, Ishitsuka I, Ozawa H, Fujisawa C, Shiga K. The first reported case of Menkes disease caused by an Alu insertion mutation[J]. Brain Dev,2007, 29(2):105-8
[89]Apoil PA, Kuhlein E, Robert A, Rubie H, Blancher A. HIGM syndrome caused by insertion of an AluYb8 element in exon 1 of the CD40LG gene[J]. Immunogenetics,2007,59(1):17-23
[90]Manco L, Relvas L, Silva Pinto C, Pereira J, Almeida AB, Ribeiro ML. Molecular characterization of five Portuguese patients with pyrimidine 5'-nucleotidase deficient hemolytic anemia showing three new P5'N-I mutations[J]. Haematologica,2006,91(2):266-7
[91]Chen JM, Masson E, Macek M, Jr., Raguenes O, Piskackova T, Fercot B, Fila L, Cooper DN, Audrezet MP, Ferec C. Detection of two Alu insertions in the CFTR gene[J]. J Cyst Fibros,2008, 7(1):37-43
[92]Okubo M, Horinishi A, Saito M, Ebara T, Endo Y, Kaku K, Murase T, Eto M. A novel complex deletion-insertion mutation mediated by Alu repetitive elements leads to lipoprotein lipase deficiency[J]. Mol Genet Metab,2007,92(3):229-33
[93]Udaka T, Okamoto N, Aramaki M, Torii C, Kosaki R, Hosokai N, Hayakawa T, Takahata N, Takahashi T, Kosaki K. An Alu retrotransposition-mediated deletion of CHD7 in a patient with CHARGE syndrome[J].Am J Med Genet A,2007,143(7):721-6
[94]Bouchet C, Vuillaumier-Barrot S, Gonzales M, Boukari S, Bizec CL, Fallet C, Delezoide AL, Moirot H, Laquerriere A, Encha-Razavi F, Durand G, Seta N. Detection of an Alu insertion in the POMT1 gene from three French Walker Warburg syndrome families[J]. Mol Genet Metab,2007, 90(1):93-6
[95]Hayakawa T, Satta Y, Gagneux P, Varki A, Takahata N. Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene[J]. Proc Nat1 Acad Sci U S A,2001, 98(20):11399-404
[96]Mine M, Chen JM, Brivet M, Desguerre I, Marchant D, de Lonlay P, Bernard A, Ferec C, Abitbol M, Ricquier D, Marsac C. A large genomic deletion in the PDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element[J]. Hum Mutat,2007, 28(2):137-42
[97]Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Su J, Wang X, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li D, Sun Y, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Ye J, Chen H, Zhou Y, Liu B, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Wong GK, Yang H. A draft sequence for the genome of the domesticated silkworm (Bombyx mori)[J]. Science,2004,306(5703):1937-40
[98]Osanai-Futahashi M, Suetsugu Y, Mita K, Fujiwara H. Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori[J]. Insect Biochem Mol Biol,2008,38(12):1046-1057
[99]Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi ZY, Megy K, Grabherr M, Ren QH, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu JS, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, deBruyn B, DeCaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao CH, Mauceli E, Menck CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, VanZee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng QD, Zhao Q, Zhao YM, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Genome sequence of Aedes aegypti, a major arbovirus vector[J]. Science,2007, 316(5832):1718-1723
[100]Bureau TE, Wessler SR. Tourist: a large family of small inverted repeat elements frequently associated with maize genes[J]. Plant Cell,1992,4(10):1283-94
[101]Bureau TE, Ronald PC, Wessler SR. A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes[J]. Proc Natl Acad Sci U SA,1996,93(16):8524-9
[102]Santiago N, Herraiz C, Goni JR, Messeguer X, Casacuberta JM. Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana[J]. Mol Biol Evol,2002,19(12):2285-93
[103]Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae:new functional implications for MITEs[J]. Genome Res,2009, 19(1):42-56
[104]Tu Z. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae[J]. Proc Natl Acad Sci U S A,2001,98(4):1699-704
[105]Smit AFA, Riggs AD. Tiggers and other DNA transposon fossils in the human genome[J]. Proc Natl Acad Sci U S A,1996,93(4):1443-1448
[106]Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR. Dramatic amplification of a rice transposable element during recent domestication[.T]. Proc Natl Acad Sci US A,2006,103(47):17620-5
[107]Yang G, Zhang F, Hancock CN, Wessler SR. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana[J]. Proc Natl Acad Sci U S A,2007, 104(26):10962-7
[108]Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. Tuned for transposition:molecular determinants underlying the hyperactivity of a Stowaway MITE[J]. Science,2009, 325(5946):1391-4
[109]Charlesworth B, Charlesworth D. The Population-Dynamics of Transposable Elements[J]. Genet Res,1983,42(I):1-27
[110]Charlesworth B, Langley CH. The Population-Genetics of Drosophila Transposable Elements[J]. Annu Rev Genet,1989,23:251-287
[111]Petrov DA, Fiston-Lavier AS, Lipatov M. Lenkov K, Gonzalez J. Population genomics of transposable elements in Drosophila melanogaster[J]. Mol Biol Evol,2011,28(5):1633-44
[112]Le Rouzic A, Deceliere G. Models of the population genetics of transposable elements[J]. Genet Res,2005,85(3):171-81
[113]Hollister JD, Gaut BS. Epigenetic silencing of transposable elements:A trade-off between reduced transposition and deleterious effects on neighboring gene expression[J]. Genome Res, 2009,19(8):1419-1428
[114]Almeida R, Allshire RC. RNA silencing and genome regulation[J]. Trends Cell Biol,2005, 15(5):251-258
[115]Zhang X, Shiu S, Cal A, Borevitz JO. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays[J]. PLoS Genet,2008, 4(3)
[116]Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, Voinnet O, Wincker P, Esteller M, Colot V. A Role for RNAi in the Selective Correction of DNA Methylation Defects[J]. Science,2009,323(5921):1600-1604
[117]Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control[J]. Nature,2004,430(6998):471-476
[118]Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription[J]. Nat Genet,2007,39(1):61-69
[119]Mcclintock B. The Significance of Responses of the Genome to Challenge[J]. Science,1984, 226(4676):792-801
[120]Charlesworth D, Charlesworth B. Transposable elements in inbreeding and outbreeding populations[J]. Genetics,1995,140(1):415-7
[121]Wright SI, Schoen DJ. Transposon dynamics and the breeding system[J]. Genetica,1999, 107(1-3):139-48
[122]Morgan MT. Transposable element number in mixed mating populations[J]. Genet Res (Camb), 2001,77(3):261-275
[123]Valizadeh P, Crease TJ. The association between breeding system and transposable element dynamics in Daphnia pulex[J]. J Mol Evol,2008,66(6):643-654
[124]Lockton S, Gaut BS. The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata[J]. BMC Evol Biol,2010,10
[125]Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N. Population bottlenecks as a potential major shaping force of human genome architecture[J]. PLoS Genet,2007,3(7):1223-1231
[126]Lockton S, Ross-Ibarra J, Gaut BS. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata[J]. Proc Nat1 Acad Sci USA,2008,105(37):13965-13970
[127]Xia QY, Wang J, Zhou ZY, Li RQ, Fan W, Cheng DJ, Cheng TC, Qin JJ, Duan J, Xu HF, Li QB, Li N, Wang MW, Dai FY, Liu C, Lin Y, Zhao P, Zhang HJ, Liu SP, Zha XF, Li CF, Zhao AC, Pan MH, Pan GQ, Shen YH, Gao ZH, Wang ZL, Wang GH, Wu ZL, Hou Y, Chai CL, Yu QY, He NJ, Zhang Z, Li SG, Yang HM, Lu C, Wang J, Xiang ZH, Mita K, Kasahara M, Nakatani Y, Yamamoto K, Abe H, Ahsan B, Dai-Mon T, Doi K, Fujii T, Fujiwara H, Fujiyama A, Futahashi R, Hashimoto SI, Ishibashi J, Iwami M, Kadono-Okuda K, Kanamori H, Kataoka H, Katsuma S, Kawaoka S, Kawasaki H, Kohara Y, Kozaki T, Kuroshu RM, Kuwazaki S, Matsushima K, Minami H, Nagayasu Y, Nakagawa T, Narukawa J, Nohata J, Ohishi K, Ono Y, Osanai-Futahashi M, Ozaki KH, Qu W, Roller L, Sasaki S, Sasaki T, Seino A, Shimomura M, Shimomura M, Shin-1 T, Shinoda T, Shiotsuki T, Suetsugu Y, Sugano S, Suwa M, Suzuki Y, Takiya SH, Tamura T, Tanaka H, Tanaka Y, Touhara K, Yamada T, Yamakawa M, Yamanaka N, Yoshikawa H, Zhong YS, Shima-Da T, Morishita S, et al. The genome of a lepidopteran model insect, the silkworm Bombyx mori[J]. Insect Biochem Mol Biol,2008,38(12):1036-1045
[128]Chen Y, Zhou F, Li G, Xu Y. MUST:a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi[J]. Gene,2009,436(1-2):1-7
[129]Xia X, Xie Z. DAMBE:software package for data analysis in molecular biology and evolution[J]. J Hered,2001,92(4):371-3
[130]Markham NR, Zuker M. UNAFold:software for nucleic acid folding and hybridization[J]. Methods Mol Biol,2008,453:3-31
[131]Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder:the reference centre for bacterial insertion sequences[J]. Nucleic Acids Res,2006,34(Database issue):D32-6
[132]Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements[J]. Cytogenet Genome Res,2005,110(1-4):462-7
[133]Thompson JD, Higgins DG, Gibson TJ. Clustal-W-Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice[J]. Nucleic Acids Res,1994,22(22):4673-4680
[134]Kimura M. A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide-Sequences[J]. J Mol Evol,1980,16(2):111-120
[135]Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol,1999,16(1):37-48
[136]Librado P, Rozas J. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics,2009,25(11):1451-1452
[137]Bureau TE, Wessler SR. Stowaway-a New Family of Inverted Repeat Elements Associated with the Genes of Both Monocotyledonous and Dicotyledonous Plants[J]. Plant Cell,1994, 6(6):907-916
[138]Besansky NJ, Mukabayire O, Bedell JA, Lusz H. Pegasus, a small terminal inverted repeat transposable element found in the white gene of Anopheles gambiae[J]. Genetica,1996, 98(2):119-129
[139]Zerjal T, Joets J, Alix K, Grandbastien MA, Tenaillon MI. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome[J]. Plant Mol Biol,2009,71(1-2):99-114
[140]Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome[J]. Genome Res,2009, 19(2):243-254
[141]Tu ZJ. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae[J]. Proc Natl Acad Sci U S A,2001,98(4):1699-1704
[142]Li C, Zhou A, Sang T. Rice domestication by reducing shattering[J]. Science,2006, 311(5769):1936-9
[143]Yoshitake N. Phylogenetic aspects on the origin of Japanese race of the silkworm. Bombyx mori L[J]. Journal of Sericological Sciences of Japan,1968,37:83-87
[144]Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y. Liu H, Zhao J. Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Yin X, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Xiang Z. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm(Bombyx)[J]. Science,2009,326(5951):433-6
[145]Petrov DA, Aminetzach YT, Davis JC, Bensasson D, Hirsh AE. Size matters:non-LTR retrotransposable elements and ectopic recombination in Drosophila[J]. Mol Biol Evol,2003, 20(6):880-92
[146]Lockton S, Ross-Ibarra J, Gaut BS. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata[J]. Proc Natl Acad Sci USA,2008,105(37):13965-70
[147]Kazazian HH. Mobile elements:Drivers of genome evolution[J]. Science,2004, 303(5664):1626-1632
[148]Naito K, Cho E, Yang GJ, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR. Dramatic amplification of a rice transposable element during recent domestication[J]. Proc Natl Acad Sci U S A,2006,103(47):17620-17625
[149]Feschotte C. Opinion-Transposable elements and the evolution of regulatory networks[J]. Nature Reviews Genetics,2008,9(5):397-405
[150]Bourque G. Transposable elements in gene regulation and in the evolution of vertebrate genomes[J]. Curr Opin Genet Dev,2009,19(6):607-612
[151]Le Rouzic A, Boutin TS, Capy P. Long-term evolution of transposable elements[J]. Proc Natl Acad Sci U S A,2007,104(49):19375-80
[152]Wright SI, Le QH, Schoen DJ, Bureau TE. Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis[J]. Genetics,2001,158(3):1279-88
[153]Boissinot S, Davis J, Entezam A, Petrov D, Furano AV. Fitness cost of LINE-1 (LI) activity in humans[J]. Proc Natl Acad Sci U S A,2006,103(25):9590-4
[154]Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D'Hauw M, Van Montagu M, Gerats T. Transposon Display identifies individual transposable elements in high copy number lines[J]. Plant J,1998,13(1):121-9
[155]Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR. The MITE family heartbreaker (Hbr):molecular markers in maize[J]. Proc Natl Acad Sci U S A,2000, 97(18):10083-9
[156]De Keukeleire P, Maes T, Sauer M, Zethof J, Van Montagu M, Gerats T. Analysis by Transposon Display of the behavior of the dTphl element family during ontogeny and inbreeding of Petunia hybrida[J]. Mol Genet Genomics,2001,265(1):72-81
[157]Bouck A, Peeler R, Arnold ML, Wessler SR. Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers[J]. Genetics,2005, 171(3):1289-1303
[158]Kwon SJ, Park KC, Kim JH, Lee JK, Kim NS. Rim 2/Hipa CACTA transposon display; A new genetic marker technique in Oryza species[J]. BMC Genet,2005,6
[159]Vitte C, Panaud O, Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.):recent burst amplifications followed by rapid DNA loss[J]. BMC Genomics,2007,8
[160]Cornman RS, Arnold ML. Phylogeography of Iris missouriensis (Iridaceae) based on nuclear and chloroplast markers[J]. Mol Ecol,2007,16(21):4585-4598
[161]Ma J, Devos KM, Bennetzen JL. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice[J]. Genome Res,2004,14(5):860-9
[162]Neafsey DE, Blumenstiel JP, Hartl DL. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies[J]. Mol Biol Evol,2004,21(12):2310-8
[163]Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T. A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica[J]. Genes Genet Syst,2008,83(4):321-9
[2]Mc CB. The origin and behavior of mutable loci in maize[J]. Proc Natl Acad Sci U S A,1950, 36(6):344-55
[3]Bennetzen JL, Ma J, Devos KM. Mechanisms of recent genome size variation in flowering plants[J]. Ann Bot,2005,95(1):127-32
[4]Biemont C, Vieira C. Genetics-Junk DNA as an evolutionary force[J]. Nature.2006, 443(7111):521-524
[5]Kidwell MG. Transposable elements and the evolution of genome size in eukaryotes[J]. Genetica, 2002,115(1):49-63
[6]Lonnig WE, Saedler H. Chromosome rearrangements and transposable elements[J]. Annu Rev Genet,2002,36:389-410
[7]Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen WZ, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J. Shah N. Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B. Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He RF, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin.JK, Dujmic Z. Kim W, Talag J, Zuccolo A, Fan C, Sebastian A. Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren LY, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, et al. The B73 Maize Genome:Complexity, Diversity, and Dynamics[J]. Science,2009,326(5956):1112-1115
[8]Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D. Wing RA. Transposable element distribution, abundance and role in genome size variation in the genus Oryza[J]. BMC Evol Biol,2007,7
[9]de Koning APJ, Gu WJ, Castoe TA, Batzer MA, Pollock DD. Repetitive Elements May Comprise Over Two-Thirds of the Human Genome[J]. PLoS Genet,2011,7(12)
[10]Lander ES, Consortium IHGS, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Roserti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, et al. Initial sequencing and analysis of the human genome[J], Nature,2001,409(6822):860-921
[11]Biemont C. A brief history of the status of transposable elements:from junk DNA to major players in evolution[J]. Genetics,2010,186(4):1085-93
[12]Feschotte C, Jiang N, Wessler SR. Plant transposable elements: where genetics meets genomics[J]. Nat Rev Genet,2002,3(5):329-41
[13]Eichbush T, Craig NL, Craigie R, Gellert M. Origins and evolution of retrotransposons[J]. Mobile DNA II,2002, Washington D. C:Am. Soc. Microbiol. Press.:1111-1144
[14]Kumar A, Bennetzen JL. Plant retrotransposons[J]. Annu Rev Genet,1999,33:479-532
[15]Han JS, Boeke JD. LINE-1 retrotransposons:modulators of quantity and quality of mammalian gene expression?[J]. Bioessays,2005,27(8):775-84
[16]Sabot F, Schulman AH. Parasitism and the retrotransposon life cycle in plants:a hitchhiker's guide to the genome[J]. Heredity (Edinb),2006,97(6):381-8
[17]SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL. Nested retrotransposons in the intergenic regions of the maize genome[J]. Science,1996,274(5288):765-8
[18]Neumann P, Pozarkova D, Macas J. Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced[J]. Plant Mol Biol,2003,53(3):399-410
[19]Xiong Y, Burke WD, Eickbush TH. Pao, a Highly Divergent Retrotransposable Element from Bombyx-Mori Containing Long Terminal Repeats with Tandem Copies of the Putative-R Region[J]. Nucleic Acids Res,1993,21(9):2117-2123
[20]Frankel AD, Young JA. HIV-1:fifteen proteins and an RNA[J]. Annu Rev Biochem,1998, 67:1-25
[21]Seelamgari A, Maddukuri A, Berro R, de la Fuente C, Kehn K, Deng L, Dadgar S, Bottazzi ME, Ghedin E, Pumfery A, Kashanchi F. Role of viral regulatory and accessory proteins in HIV-1 replication[J]. Front Biosci,2004,9:2388-413
[22]Bucheton A. The Relationship between the Flamenco Gene and Gypsy in Drosophila-How to Tame a Retrovirus[J]. Trends in Genetics,1995, 11(9):349-353
[23]Cappello J, Handelsman K, Lodish HF. Sequence of Dictyostelium Dirs-1-an Apparent Retrotransposon with Inverted Terminal Repeats and an Internal Circle Junction Sequence[J]. Cell,1985,43(1):105-115
[24]Goodwin TJD, Poulter RTM. A new group of tyrosine recombinase-encoding retrotransposons[J]. Mol Biol Evol,2004,21(4):746-759
[25]Evgen'ev MB, Zelentsova H, Shostak N, Kozitsina M, Barskyi V, Lankenau DH, Corces VG. Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis[J]. Proc Natl Acad Sci U S A,1997,94(1):196-201
[26]Evgen'ev MB, Arkhipova IR. Penelope-like elements--a new class of retroelements: distribution, function and possible evolutionary significance[J]. Cytogenet Genome Res,2005, 110(1-4):510-21
[27]Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse Transcription of R2bm Rna Is Primed by a Nick at the Chromosomal Target Site-a Mechanism for Non-Ltr Retrotransposition[J]. Cell,1993,72(4):595-605
[28]Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail[J]. Cytogenet Genome Res,2005,110(1-4):475-90
[29]Weiner AM. An Abundant Cytoplasmic 7s Rna Is Complementary to the Dominant Interspersed Middle Repetitive DNA-Sequence Family in the Human Genome[J]. Cell,1980,22(1):209-218
[30]Ullu E, Tschudi C. Alu Sequences Are Processed 7sl Rna Genes[J]. Nature,1984, 312(5990):171-172
[31]Vassetzky NS, Ten OA, Kramerov DA. B1 and related SINEs in mammalian genomes[J]. Gene, 2003,319:149-160
[32]Kapitonov VV, Jurka J. A novel class of SINE elements derived from 5S rRNA[J]. Mol Biol Evol, 2003,20(5):694-702
[33]Nishihara H, Smit AF, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome[J]. Genome Res,2006,16(7):864-74
[34]Gogolevsky KP, Vassetzky NS, Kramerov DA.5S rRNA-derived and tRNA-derived SINEs in fruit bats[J]. Genomics,2009,93(5):494-500
[35]Lisch D. How important are transposons for plant evolution?[J]. Nat Rev Genet,2013, 14(1):49-61
[36]Shao HG, Tu ZJ. Expanding the diversity of the IS630-Tcl-mariner superfamily:Discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons[J]. Genetics,2001,159(3):1103-1115
[37]Kempken F, Windhofer F. The hATfamily:a versatile transposon group common to plants, fungi. animals, and man[J]. Chromosoma,2001,110(1):1-9
[38]Pritham ET, Feschotte C, Wessler SR. Unexpected diversity and differential success of DNA transposons in four species of Entamoeba protozoans[J]. Mol Biol Evol.2005,22(9):1751-1763
[39]Feschotte C. Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences[J]. Mol Biol Evol,2004, 21(9):1769-80
[40]Kapitonov VV, Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons[J]. Plos Biology,2005,3(6):998-1011
[41]Sarkar A, Sim C, Hong YS, Hogan JR, Fraser MJ, Robertson HM, Collins FH. Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences[J]. Molecular Genetics and Genomics,2003,270(2):173-180
[42]Hammer SE, Strehl S, Hagemann S. Homologs of Drosophila P transposons were mobile in zebrafish but have been domesticated in a common ancestor of chicken and human[J]. Mol Biol Evol,2005,22(4):833-844
[43]Jurka J. Kapitonov W. PiFs meet Tourists and Harbingers:A superfamily reunion[J]. Proc Natl Acad Sci U S A,2001,98(22):12315-12316
[44]Wicker T, Guyot R, Yahiaoui N. Keller B. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements[J]. Plant Physiol,2003.132(1):52-63
[45]Bureau TE, Wessler SR. Tourist-a Large Family of Small Inverted Repeat Elements Frequently Associated with Maize Genes[J]. Plant Cell,1992,4(10):1283-1294
[46]Goodwin TJ, Butler MI, Poulter RT. Cryptons:a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi[J]. Microbiology,2003,149(Pt 11):3099-109
[47]Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes[J]. Proc Natl Acad Sci U S A, 2001,98(15):8714-9
[48]Feschotte C, Pritham EJ. Non-mammalian c-integrases are encoded by giant transposable elements[J]. Trends in Genetics,2005,21(10):551-552
[49]Kapitonov VV, Jurka J. Self-synthesizing DNA transposons in eukaryotes[J]. Proc Natl Acad Sci USA,2006,103(12):4540-4545
[50]Pritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses[J]. Gene,2007,390(1-2):3-17
[51]Tenaillon MI, Hollister JD, Gaut BS. A triptych of the evolution of plant transposable elements[J]. Trends Plant Sci,2010,15(8):471-8
[52]Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature,2000,408(6814):796-815
[53]The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon[J].Nature,2010,463(7282):763-8
[54]Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, et al. The B73 maize genome:complexity, diversity, and dynamics[J]. Science,2009,326(5956):1112-5
[55]Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N. A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats[J]. Plant Journal,2005, 41(2):184-194
[56]Feschotte C. Transposable elements and the evolution of regulatory networks[J]. Nat Rev Genet, 2008,9(5):397-405
[57]Britten RJ. Cases of ancient mobile element DNA insertions that now affect gene regulation[J]. Mol Phylogenet Evol,1996,5(1):13-17
[58]Brosius J. The contribution of RNAs and retroposition to evolutionary novelties[J]. Genetica, 2003,118(2-3):99-116
[59]Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK. Transposable elements donate lineage-specific regulatory sequences to host genomes[J]. Cytogenet Genome Res,2005, 110(1-4):333-341
[60]Jordan IK, Rogozin IB, Glazko GV, Koonin EV. Origin of a substantial fraction of human regulatory sequences from transposable elements[J]. Trends in Genetics,2003,19(2):68-72
[61]van de Lagemaat LN, Landry JR, Mager DL, Medstrand P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions[J]. Trends in Genetics,2003,19(10):530-536
[62]Wallace MR, Andersen LB, Saulino AM, Gregory PE, Glover TW, Collins FS. A de novo Alu insertion results in neurofibromatosis type 1[J]. Nature,1991,353(6347):864-6
[63]Girard L, Freeling M. Regulatory changes as a consequence of transposon insertion[J]. Developmental Genetics,1999,25(4):291-296
[64]Marino-Ramirez L, Jordan IK. Transposable element derived DNasel-hypersensitive sites in the human genome[J]. Biol Direct,2006,1
[65]Lowe CB, Bejerano G, Haussler D. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes[J]. Proc Natl Acad Sci U S A,2007, 104(19):8005-10
[66]Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon[J]. Nature, 2006,441(7089):87-90
[67]Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, Rubinstein M. Ancient exaptation of a CORE-SINE Retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene[J]. PLoS Genet,2007,3(10):1813-1826
[68]Ni JZ, Grate L, Donohue JP, Preston C, Nobida N, O'Brien G, Shiue L, Clark TA, Blume JE, Ares M. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay[J]. Genes Dev,2007,21(6):708-718
[69]Grewal SIS, Jia ST. Heterochromatin revisited[J]. Nature Reviews Genetics,2007,8(1):35-46
[70]Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome[J]. Nature Reviews Genetics,2007,8(4):272-285
[71]Marino-Ramirez L, Lewis KC, Landsman D, Jordan IK. Transposable elements donate lineage-specific regulatory sequences to host genomes[J]. Cytogenet Genome Res,2005, 110(1-4):333-41
[72]Smalheiser NR, Torvik VI. Alu elements within human mRNAs are probable microRNA targets[J]. Trends in Genetics,2006,22(10):532-536
[73]Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK. Evaluating the protein coding potential of exonized transposable element sequences[J]. Biol Direct,2007,2:31
[74]Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit[J]. Science,2008, 319(5869):1527-30
[75]Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges[J]. Plant Cell,2012,24(3):1242-55
[76]Kobayashi S, Goto-Yamamoto N, Hirochika H. Retrotransposon-induced mutations in grape skin color[J]. Science,2004,304(5673):982
[77]Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tbl[J]. Nat Genet,2011,43(11):1160-3
[78]Wang H, Chai Y, Chu X, Zhao Y, Wu Y, Zhao J, Ngezahayo F, Xu C, Liu B. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability[J]. BMC Plant Biol,2009,9:63
[79]Iida S, Morita Y, Choi JD, Park KI, Hoshino A. Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories[J]. Novel Developments on Genetic Recombination:DNA Double Strand Break and DNA End-Joining,2004,38:141-159
[80]Galimba KD. Tolkin TR, Sullivan AM, Melzer R, Theissen G, Di Stilio VS. Loss of deeply conserved C-class floral homeotic gene function and C-and E-class protein interaction in a double-flowered ranunculid mutant[J]. Proc Natl Acad Sci U S A,2012,109(34):E2267-75
[81]Dreger DL, Schmutz SM. A SINE insertion causes the black-and-tan and saddle tan phenotypes in domestic dogs[J]. J Hered,2011.102 Suppl 1:S11-8
[82]Morgan HD, Sutherland HGE, Martin DIK, Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse[J]. Nat Genet,1999,23(3):314-318
[83]Sakudoh T, Sezutsu H, Nakashima T, Kobayashi I, Fujimoto H, Uchino K, Banno Y, Iwano H, Maekawa H, Tamura T, Kataoka H, Tsuchida K. Carotenoid silk coloration is controlled by a carotenoid-binding protein, a product of the Yellow blood gene[J]. Proc Natl Acad Sci U S A, 2007,104(21):8941-8946
[84]Liu C, Yamamoto K, Cheng TC, Kadono-Okuda K, Narukawa J, Liu SP, Han Y, Futahashi R, Kidokoro K, Noda H, Kobayashi I, Tamura T, Ohnuma A, Banno Y, Dai FY, Xiang ZH, Goldsmith MR, Mita K, Xia QY. Repression of tyrosine hydroxylase is responsible for the sex-linked chocolate mutation of the silkworm, Bombyx mori[J]. Proc Natl Acad Sci U S A,2010, 107(29):12980-12985
[85]Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons:for better or worse, in sickness and in health[J]. Genome Res,2008,18(3):343-58
[86]Deininger PL, Batzer MA. Alu repeats and human disease[J]. Mol Genet Metab,1999, 67(3):183-93
[87]Chen J, Rattner A, Nathans J. Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation:lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements[J]. Hum Mol Genet,2006,15(13):2146-56
[88]Gu Y, Kodama H, Watanabe S, Kikuchi N, Ishitsuka I, Ozawa H, Fujisawa C, Shiga K. The first reported case of Menkes disease caused by an Alu insertion mutation[J]. Brain Dev,2007, 29(2):105-8
[89]Apoil PA, Kuhlein E, Robert A, Rubie H, Blancher A. HIGM syndrome caused by insertion of an AluYb8 element in exon 1 of the CD40LG gene[J]. Immunogenetics,2007,59(1):17-23
[90]Manco L, Relvas L, Silva Pinto C, Pereira J, Almeida AB, Ribeiro ML. Molecular characterization of five Portuguese patients with pyrimidine 5'-nucleotidase deficient hemolytic anemia showing three new P5'N-I mutations[J]. Haematologica,2006,91(2):266-7
[91]Chen JM, Masson E, Macek M, Jr., Raguenes O, Piskackova T, Fercot B, Fila L, Cooper DN, Audrezet MP, Ferec C. Detection of two Alu insertions in the CFTR gene[J]. J Cyst Fibros,2008, 7(1):37-43
[92]Okubo M, Horinishi A, Saito M, Ebara T, Endo Y, Kaku K, Murase T, Eto M. A novel complex deletion-insertion mutation mediated by Alu repetitive elements leads to lipoprotein lipase deficiency[J]. Mol Genet Metab,2007,92(3):229-33
[93]Udaka T, Okamoto N, Aramaki M, Torii C, Kosaki R, Hosokai N, Hayakawa T, Takahata N, Takahashi T, Kosaki K. An Alu retrotransposition-mediated deletion of CHD7 in a patient with CHARGE syndrome[J].Am J Med Genet A,2007,143(7):721-6
[94]Bouchet C, Vuillaumier-Barrot S, Gonzales M, Boukari S, Bizec CL, Fallet C, Delezoide AL, Moirot H, Laquerriere A, Encha-Razavi F, Durand G, Seta N. Detection of an Alu insertion in the POMT1 gene from three French Walker Warburg syndrome families[J]. Mol Genet Metab,2007, 90(1):93-6
[95]Hayakawa T, Satta Y, Gagneux P, Varki A, Takahata N. Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene[J]. Proc Nat1 Acad Sci U S A,2001, 98(20):11399-404
[96]Mine M, Chen JM, Brivet M, Desguerre I, Marchant D, de Lonlay P, Bernard A, Ferec C, Abitbol M, Ricquier D, Marsac C. A large genomic deletion in the PDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element[J]. Hum Mutat,2007, 28(2):137-42
[97]Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Su J, Wang X, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li D, Sun Y, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Ye J, Chen H, Zhou Y, Liu B, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Wong GK, Yang H. A draft sequence for the genome of the domesticated silkworm (Bombyx mori)[J]. Science,2004,306(5703):1937-40
[98]Osanai-Futahashi M, Suetsugu Y, Mita K, Fujiwara H. Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori[J]. Insect Biochem Mol Biol,2008,38(12):1046-1057
[99]Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi ZY, Megy K, Grabherr M, Ren QH, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu JS, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, deBruyn B, DeCaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, LaButti K, Lee E, Li S, Lovin DD, Mao CH, Mauceli E, Menck CFM, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'Leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JMC, VanZee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng QD, Zhao Q, Zhao YM, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Genome sequence of Aedes aegypti, a major arbovirus vector[J]. Science,2007, 316(5832):1718-1723
[100]Bureau TE, Wessler SR. Tourist: a large family of small inverted repeat elements frequently associated with maize genes[J]. Plant Cell,1992,4(10):1283-94
[101]Bureau TE, Ronald PC, Wessler SR. A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes[J]. Proc Natl Acad Sci U SA,1996,93(16):8524-9
[102]Santiago N, Herraiz C, Goni JR, Messeguer X, Casacuberta JM. Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana[J]. Mol Biol Evol,2002,19(12):2285-93
[103]Kuang H, Padmanabhan C, Li F, Kamei A, Bhaskar PB, Ouyang S, Jiang J, Buell CR, Baker B. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae:new functional implications for MITEs[J]. Genome Res,2009, 19(1):42-56
[104]Tu Z. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae[J]. Proc Natl Acad Sci U S A,2001,98(4):1699-704
[105]Smit AFA, Riggs AD. Tiggers and other DNA transposon fossils in the human genome[J]. Proc Natl Acad Sci U S A,1996,93(4):1443-1448
[106]Naito K, Cho E, Yang G, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR. Dramatic amplification of a rice transposable element during recent domestication[.T]. Proc Natl Acad Sci US A,2006,103(47):17620-5
[107]Yang G, Zhang F, Hancock CN, Wessler SR. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana[J]. Proc Natl Acad Sci U S A,2007, 104(26):10962-7
[108]Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. Tuned for transposition:molecular determinants underlying the hyperactivity of a Stowaway MITE[J]. Science,2009, 325(5946):1391-4
[109]Charlesworth B, Charlesworth D. The Population-Dynamics of Transposable Elements[J]. Genet Res,1983,42(I):1-27
[110]Charlesworth B, Langley CH. The Population-Genetics of Drosophila Transposable Elements[J]. Annu Rev Genet,1989,23:251-287
[111]Petrov DA, Fiston-Lavier AS, Lipatov M. Lenkov K, Gonzalez J. Population genomics of transposable elements in Drosophila melanogaster[J]. Mol Biol Evol,2011,28(5):1633-44
[112]Le Rouzic A, Deceliere G. Models of the population genetics of transposable elements[J]. Genet Res,2005,85(3):171-81
[113]Hollister JD, Gaut BS. Epigenetic silencing of transposable elements:A trade-off between reduced transposition and deleterious effects on neighboring gene expression[J]. Genome Res, 2009,19(8):1419-1428
[114]Almeida R, Allshire RC. RNA silencing and genome regulation[J]. Trends Cell Biol,2005, 15(5):251-258
[115]Zhang X, Shiu S, Cal A, Borevitz JO. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays[J]. PLoS Genet,2008, 4(3)
[116]Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, Voinnet O, Wincker P, Esteller M, Colot V. A Role for RNAi in the Selective Correction of DNA Methylation Defects[J]. Science,2009,323(5921):1600-1604
[117]Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control[J]. Nature,2004,430(6998):471-476
[118]Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription[J]. Nat Genet,2007,39(1):61-69
[119]Mcclintock B. The Significance of Responses of the Genome to Challenge[J]. Science,1984, 226(4676):792-801
[120]Charlesworth D, Charlesworth B. Transposable elements in inbreeding and outbreeding populations[J]. Genetics,1995,140(1):415-7
[121]Wright SI, Schoen DJ. Transposon dynamics and the breeding system[J]. Genetica,1999, 107(1-3):139-48
[122]Morgan MT. Transposable element number in mixed mating populations[J]. Genet Res (Camb), 2001,77(3):261-275
[123]Valizadeh P, Crease TJ. The association between breeding system and transposable element dynamics in Daphnia pulex[J]. J Mol Evol,2008,66(6):643-654
[124]Lockton S, Gaut BS. The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata[J]. BMC Evol Biol,2010,10
[125]Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N. Population bottlenecks as a potential major shaping force of human genome architecture[J]. PLoS Genet,2007,3(7):1223-1231
[126]Lockton S, Ross-Ibarra J, Gaut BS. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata[J]. Proc Nat1 Acad Sci USA,2008,105(37):13965-13970
[127]Xia QY, Wang J, Zhou ZY, Li RQ, Fan W, Cheng DJ, Cheng TC, Qin JJ, Duan J, Xu HF, Li QB, Li N, Wang MW, Dai FY, Liu C, Lin Y, Zhao P, Zhang HJ, Liu SP, Zha XF, Li CF, Zhao AC, Pan MH, Pan GQ, Shen YH, Gao ZH, Wang ZL, Wang GH, Wu ZL, Hou Y, Chai CL, Yu QY, He NJ, Zhang Z, Li SG, Yang HM, Lu C, Wang J, Xiang ZH, Mita K, Kasahara M, Nakatani Y, Yamamoto K, Abe H, Ahsan B, Dai-Mon T, Doi K, Fujii T, Fujiwara H, Fujiyama A, Futahashi R, Hashimoto SI, Ishibashi J, Iwami M, Kadono-Okuda K, Kanamori H, Kataoka H, Katsuma S, Kawaoka S, Kawasaki H, Kohara Y, Kozaki T, Kuroshu RM, Kuwazaki S, Matsushima K, Minami H, Nagayasu Y, Nakagawa T, Narukawa J, Nohata J, Ohishi K, Ono Y, Osanai-Futahashi M, Ozaki KH, Qu W, Roller L, Sasaki S, Sasaki T, Seino A, Shimomura M, Shimomura M, Shin-1 T, Shinoda T, Shiotsuki T, Suetsugu Y, Sugano S, Suwa M, Suzuki Y, Takiya SH, Tamura T, Tanaka H, Tanaka Y, Touhara K, Yamada T, Yamakawa M, Yamanaka N, Yoshikawa H, Zhong YS, Shima-Da T, Morishita S, et al. The genome of a lepidopteran model insect, the silkworm Bombyx mori[J]. Insect Biochem Mol Biol,2008,38(12):1036-1045
[128]Chen Y, Zhou F, Li G, Xu Y. MUST:a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyi[J]. Gene,2009,436(1-2):1-7
[129]Xia X, Xie Z. DAMBE:software package for data analysis in molecular biology and evolution[J]. J Hered,2001,92(4):371-3
[130]Markham NR, Zuker M. UNAFold:software for nucleic acid folding and hybridization[J]. Methods Mol Biol,2008,453:3-31
[131]Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder:the reference centre for bacterial insertion sequences[J]. Nucleic Acids Res,2006,34(Database issue):D32-6
[132]Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements[J]. Cytogenet Genome Res,2005,110(1-4):462-7
[133]Thompson JD, Higgins DG, Gibson TJ. Clustal-W-Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-Specific Gap Penalties and Weight Matrix Choice[J]. Nucleic Acids Res,1994,22(22):4673-4680
[134]Kimura M. A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide-Sequences[J]. J Mol Evol,1980,16(2):111-120
[135]Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol,1999,16(1):37-48
[136]Librado P, Rozas J. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics,2009,25(11):1451-1452
[137]Bureau TE, Wessler SR. Stowaway-a New Family of Inverted Repeat Elements Associated with the Genes of Both Monocotyledonous and Dicotyledonous Plants[J]. Plant Cell,1994, 6(6):907-916
[138]Besansky NJ, Mukabayire O, Bedell JA, Lusz H. Pegasus, a small terminal inverted repeat transposable element found in the white gene of Anopheles gambiae[J]. Genetica,1996, 98(2):119-129
[139]Zerjal T, Joets J, Alix K, Grandbastien MA, Tenaillon MI. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome[J]. Plant Mol Biol,2009,71(1-2):99-114
[140]Baucom RS, Estill JC, Leebens-Mack J, Bennetzen JL. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome[J]. Genome Res,2009, 19(2):243-254
[141]Tu ZJ. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae[J]. Proc Natl Acad Sci U S A,2001,98(4):1699-1704
[142]Li C, Zhou A, Sang T. Rice domestication by reducing shattering[J]. Science,2006, 311(5769):1936-9
[143]Yoshitake N. Phylogenetic aspects on the origin of Japanese race of the silkworm. Bombyx mori L[J]. Journal of Sericological Sciences of Japan,1968,37:83-87
[144]Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y. Liu H, Zhao J. Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Yin X, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Xiang Z. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm(Bombyx)[J]. Science,2009,326(5951):433-6
[145]Petrov DA, Aminetzach YT, Davis JC, Bensasson D, Hirsh AE. Size matters:non-LTR retrotransposable elements and ectopic recombination in Drosophila[J]. Mol Biol Evol,2003, 20(6):880-92
[146]Lockton S, Ross-Ibarra J, Gaut BS. Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata[J]. Proc Natl Acad Sci USA,2008,105(37):13965-70
[147]Kazazian HH. Mobile elements:Drivers of genome evolution[J]. Science,2004, 303(5664):1626-1632
[148]Naito K, Cho E, Yang GJ, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR. Dramatic amplification of a rice transposable element during recent domestication[J]. Proc Natl Acad Sci U S A,2006,103(47):17620-17625
[149]Feschotte C. Opinion-Transposable elements and the evolution of regulatory networks[J]. Nature Reviews Genetics,2008,9(5):397-405
[150]Bourque G. Transposable elements in gene regulation and in the evolution of vertebrate genomes[J]. Curr Opin Genet Dev,2009,19(6):607-612
[151]Le Rouzic A, Boutin TS, Capy P. Long-term evolution of transposable elements[J]. Proc Natl Acad Sci U S A,2007,104(49):19375-80
[152]Wright SI, Le QH, Schoen DJ, Bureau TE. Population dynamics of an Ac-like transposable element in self- and cross-pollinating arabidopsis[J]. Genetics,2001,158(3):1279-88
[153]Boissinot S, Davis J, Entezam A, Petrov D, Furano AV. Fitness cost of LINE-1 (LI) activity in humans[J]. Proc Natl Acad Sci U S A,2006,103(25):9590-4
[154]Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D'Hauw M, Van Montagu M, Gerats T. Transposon Display identifies individual transposable elements in high copy number lines[J]. Plant J,1998,13(1):121-9
[155]Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR. The MITE family heartbreaker (Hbr):molecular markers in maize[J]. Proc Natl Acad Sci U S A,2000, 97(18):10083-9
[156]De Keukeleire P, Maes T, Sauer M, Zethof J, Van Montagu M, Gerats T. Analysis by Transposon Display of the behavior of the dTphl element family during ontogeny and inbreeding of Petunia hybrida[J]. Mol Genet Genomics,2001,265(1):72-81
[157]Bouck A, Peeler R, Arnold ML, Wessler SR. Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers[J]. Genetics,2005, 171(3):1289-1303
[158]Kwon SJ, Park KC, Kim JH, Lee JK, Kim NS. Rim 2/Hipa CACTA transposon display; A new genetic marker technique in Oryza species[J]. BMC Genet,2005,6
[159]Vitte C, Panaud O, Quesneville H. LTR retrotransposons in rice (Oryza sativa, L.):recent burst amplifications followed by rapid DNA loss[J]. BMC Genomics,2007,8
[160]Cornman RS, Arnold ML. Phylogeography of Iris missouriensis (Iridaceae) based on nuclear and chloroplast markers[J]. Mol Ecol,2007,16(21):4585-4598
[161]Ma J, Devos KM, Bennetzen JL. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice[J]. Genome Res,2004,14(5):860-9
[162]Neafsey DE, Blumenstiel JP, Hartl DL. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies[J]. Mol Biol Evol,2004,21(12):2310-8
[163]Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T. A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica[J]. Genes Genet Syst,2008,83(4):321-9