Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha
Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha
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DOI：
10.1186/s13100-016-0057-9
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发表时间：
2016-01-25
期刊：
影响因子：
4.9
通讯作者：
Landweber, Laura F.
中科院分区：
文献类型：
--
作者：
Chen, Xiao;Landweber, Laura F.
背景：转座因子是遗传变异和塑造基因组进化的主要因素。多个独立的转座子驯化事件发生在纤毛虫中，招募转座子在细胞过程中发挥关键作用。在纤毛虫三叶草（Oxytricha trifallax）中，端粒承载元件（TBE），一种Tc1/mariner转座子，占据生殖系基因组的很大一部分，并参与程序性基因组重排，在发育过程中从生殖系细胞核的拷贝产生转录活跃的体细胞核。结果：在这里，我们提供了一个全面的表征分布和TBE转座子的序列在Oxytricha种系基因组。我们注释了超过10,000个完整和24,000个部分TBE序列。TBEs集群分为四个主要家族，并表现出插入保留在体细胞基因组中的DNA片段或维持在这些位点的偏好。所有4个家族的3个tbe编码基因的dN/dS比都远低于1，表明存在全基因组纯化选择。我们还在其他纤毛虫物种中鉴定了be同源物进行系统基因组分析。结论：本文提供了一类主要纤毛虫转座子的全基因组特征。系统基因组分析揭示了转座子编码基因的选择性约束，揭示了这些转座子的进化和驯化功能。
Background: Transposable elements are a major player contributing to genetic variation and shaping genome evolution. Multiple independent transposon domestication events have occurred in ciliates, recruiting transposases to key roles in cellular processes. In the ciliate Oxytricha trifallax, the telomere-bearing elements (TBE), a Tc1/mariner transposon, occupy a significant portion of the germline genome and are involved in programmed genome rearrangements that produce a transcriptionally active somatic nucleus from a copy of the germline nucleus during development.Results: Here we provide a thorough characterization of the distribution and sequences of TBE transposons in the Oxytricha germline genome. We annotate more than 10,000 complete and 24,000 partial TBE sequences. TBEs cluster into four major families and display a preference for either insertion into DNA segments that are retained in the somatic genome or their maintenance at such sites. The three TBE-encoded genes in all four families display dN/dS ratios much lower than 1, suggesting genome-wide purifying selection. We also identify TBE homologs in other ciliate species for phylogenomic analysis.Conclusions: This paper provides genome-wide characterization of a major class of ciliate transposons. Phylogenomic analysis reveals selective constraints on transposon-encoded genes, shedding light on the evolution and domesticated functions of these transposons.