Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates.
Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates.
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DOI：
10.1093/gbe/evv005
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发表时间：
2015-01-09
影响因子：
3.3
通讯作者：
Volff JN
中科院分区：
文献类型：
--
作者：
Chalopin D;Naville M;Plard F;Galiana D;Volff JN
转座因子是脊椎动物基因组的主要组成部分，在基因组的构建和进化中起着重要作用。为了表征TE含量和TE进化中的共同模式和谱系特异性差异，我们比较了23种脊椎动物基因组的mobilomes，包括10种actinopterygian鱼类，11种sarcoprophans和2种非骨脊椎动物。我们发现TE含量的重要变化（从6%的河豚鱼tetraodon的55%，在斑马鱼），与更重要的相对贡献TE的基因组大小在鱼类比哺乳动物。一些TE超家族被发现在脊椎动物中广泛存在，但大多数元素显示出更不规则的分布，表明多个事件的损失或获得。有趣的是，在sarcopterygian谱系的进化过程中观察到主要TE家族的损失，鸟类和哺乳动物的TE多样性特别强烈。TE的组成和活动的系统发育趋势进行了检测：硬骨鱼基因组主要由DNA转座子，并包含一些古老的TE副本，而哺乳动物基因组已主要由非长末端重复反转录转座子，沿着的持久性较老的序列。在谱系内也发现了差异：青鳉鱼基因组比相关的比目鱼经历了更近的TE扩增，正如在小鼠中观察到的LINE反转录转座子与人类基因组相比。这项研究允许的TE水平转移的推定案件的鉴定，并初步推断的祖先脊椎动物mobilome组成。两者合计，所获得的结果突出了TE在脊椎动物基因组的结构和进化中的重要性，并证明了它们对谱系之间和谱系内的基因组多样性的重大影响。
Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
4.5
作者：
de Koning AP;Gu W;Castoe TA;Batzer MA;Pollock DD
通讯作者：
Pollock DD
影响因子：
64.8
作者：
Agrawal, A;Eastman, QM;Schatz, DG
通讯作者：
Schatz, DG
影响因子：
10.7
作者：
Boehne, Astrid;Zhou, Qingchun;Volff, Jean-Nicolas
通讯作者：
Volff, Jean-Nicolas
DOI：
10.1002/jez.b.22521
发表时间：
2014-09-01
影响因子：
2.2
作者：
Chalopin, Domitille;Fan, Shaohua;Volff, Jean-Nicolas
通讯作者：
Volff, Jean-Nicolas