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20种果蝇物种中LTR反转录转座子的进化史。

Evolutionary history of LTR-retrotransposons among 20 Drosophila species.

作者信息

Bargues Nicolas, Lerat Emmanuelle

机构信息

CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France.

出版信息

Mob DNA. 2017 Apr 27;8:7. doi: 10.1186/s13100-017-0090-3. eCollection 2017.

DOI:10.1186/s13100-017-0090-3
PMID:28465726
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5408442/
Abstract

BACKGROUND

The presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, and . However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus and revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content. The identification of some consensus sequences of TEs from the various sequenced species allowed to get an idea concerning their variety in term of diversity of superfamilies but the used classification remains very elusive and ambiguous.

RESULTS

We choose to focus on LTR-retrotransposons because they represent the most widely represented class of TEs in the genomes. In this work, we describe for the first time the phylogenetic relationship of each LTR-retrotransposon family described in 20 Drosophila species, compute their proportion in their respective genomes and identify several new cases of horizontal transfers.

CONCLUSION

All these results allow us to have a clearer view on the evolutionary history of LTR retrotransposons among that seems to be mainly driven by vertical transmissions although the implications of horizontal transfers, losses and intra-specific diversification are clearly also at play.

摘要

背景

基因组中存在转座元件（TEs），这在一定程度上解释了真核生物基因组大小的差异。即使在亲缘关系密切的物种中，TE数量的变化也可能很显著，例如在两个近缘物种 和 之间。然而，关于其他果蝇物种的TE含量和动态变化，我们了解得并不多。对几个果蝇基因组的测序，涵盖了两个亚属 和 ，揭示了这些物种之间重复序列含量的巨大差异，但关于它们精确的TE含量，我们所知甚少。从各种已测序的 物种中鉴定出一些TE的共有序列，使我们对它们在超家族多样性方面的种类有了一定的了解，但所采用的分类仍然非常难以捉摸且模糊不清。

结果

我们选择专注于LTR反转录转座子，因为它们是果蝇基因组中最广泛存在的TE类别。在这项工作中，我们首次描述了20种果蝇中所描述的每个LTR反转录转座子家族的系统发育关系，计算了它们在各自基因组中的比例，并鉴定出几个新的水平转移案例。

结论

所有这些结果使我们能够更清楚地了解果蝇中LTR反转录转座子的进化历史，其似乎主要由垂直传递驱动，尽管水平转移、丢失和种内多样化的影响显然也在起作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/d2e8daeb570a/13100_2017_90_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/69189a7c504a/13100_2017_90_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/12f400da6f16/13100_2017_90_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/fb4785dd40f0/13100_2017_90_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/3d0cf24a0d68/13100_2017_90_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/7cc8c3e7267a/13100_2017_90_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/d2e8daeb570a/13100_2017_90_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/69189a7c504a/13100_2017_90_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/12f400da6f16/13100_2017_90_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/fb4785dd40f0/13100_2017_90_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/3d0cf24a0d68/13100_2017_90_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/7cc8c3e7267a/13100_2017_90_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92f9/5408442/d2e8daeb570a/13100_2017_90_Fig6_HTML.jpg

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