The contribution of transposable elements to size variations between four teleost genomes.
The contribution of transposable elements to size variations between four teleost genomes.
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转座元件对四种硬骨鱼基因组大小变化的贡献
DOI：
10.1186/s13100-016-0059-7
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发表时间：
2016
期刊：
影响因子：
4.9
通讯作者：
Song C
中科院分区：
文献类型：
--
作者：
Gao B;Shen D;Xue S;Chen C;Cui H;Song C
硬骨鱼是脊椎动物中唯一的，在非常接近的谱系中具有广泛的单倍体基因组大小，从河豚的不到400兆碱基对（Mb）到鲑鱼的超过3000 Mb不等。基因组大小差异的原因在很大程度上仍然无法解释。在这项研究中，我们揭示了转座因子（TE）的差异成功与四个代表性的硬骨鱼物种（斑马鱼，青，棘鱼，和tetraodon）的基因组大小的变化相关。与较小的基因组相比，较大的基因组代表了每个分支（超家族）和家族内较高的多样性和更大丰度的TE;斑马鱼，代表最大的基因组，在其基因组中显示出最高的TE多样性和丰度，其次是青鳉和棘鱼;而四齿鱼，代表最紧凑的基因组，在其基因组中显示出最低的TE多样性和密度。I类（反转录转座子）和II类（DNA转座子）TE都对硬骨鱼基因组TE积累的差异有贡献，然而，II类TE是所分析的较大硬骨鱼基因组的主要组成部分，并且是硬骨鱼谱系中基因组大小变异的最重要贡献者。hAT和Tc 1/Mariner超家族是所有四种研究的硬骨鱼的主要DNA转座子。发散分布揭示了反转录转座子的分支之间和物种之间的对比增殖动态。在斑马鱼和青鳉较大的基因组内的TE代表相对较强的活动，在进化历史的一个延长的时间段，在较小的刺鱼基因组中的非常年轻的活动，或在tetraodon基因组中的活性非常低的水平相比。总的来说，我们的数据表明，硬骨鱼代表对比配置文件的mobilomes与差异密度，多样性和活动的TE。TE积累的差异，占主导地位的DNA转座子，解释了主要的基因组大小的变化，在所调查的硬骨鱼类物种，和物种差异的多样性和活性的TE的积累的变化，在四个硬骨鱼类。TE在硬骨鱼基因组进化中起着重要作用。本文的在线版本（doi：10.1186/s13100-016-0059-7）包含补充材料，可供授权用户使用。
Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained. In this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome. Overall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution. The online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.