Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements.
Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements.
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DOI：
10.1093/gbe/evw208
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发表时间：
2016-10-05
影响因子：
3.3
通讯作者：
Lunt DH
中科院分区：
文献类型：
--
作者：
Szitenberg A;Cha S;Opperman CH;Bird DM;Blaxter ML;Lunt DH
转座元件(TES)是生命各分支基因组变异的主要来源。虽然TES可能在宿主的基因组中起到适应作用，但它们往往是有害的，而净化选择是控制其基因组负载的重要因素。相反，生活史、交配系统、GC含量和RNAi途径被认为可以解释不同物种TE负荷的差异。以前对真菌、植物和动物基因组的研究报告了关于这些基因组特征驱动TE进化的方向的相互矛盾的结果。然而，其中许多研究的力量有限，因为它们研究的是分类学上狭窄的系统，只比较了有限数量的系统发育上独立的对比，并没有解决对TE进化的长期影响。在这里，我们通过比较42个线虫基因组来测试TE进化的长期决定因素，这些基因组跨越了5亿年的多样化。这一分析包括生活史状态和RNAi途径之间的许多转变，并评估这些作用力是否足够持久，以影响真核基因组中TE负载的长期进化。尽管我们展示了检测选择的统计能力，但我们没有发现这些因素的变化会在较长时间内影响基因组TE负载的证据。相反，遗传漂移的影响似乎持续存在，并控制着物种间的TE变异。我们认为，测试因素的变化在很大程度上与观察到的基因组之间TE含量的巨大差异无关，只有通过这些大规模的比较，我们才能区分长期和持久的影响与瞬时或随机的变化。
Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here, we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.
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影响因子：
2.9
作者：
Butler, MA;King, AA
通讯作者：
King, AA
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
14.9
作者：
Benson, G
通讯作者：
Benson, G
影响因子：
3.3
作者：
Bennettt, EA;Coleman, LE;Devine, SE
通讯作者：
Devine, SE
影响因子：
10.7
作者：
Campos JL;Halligan DL;Haddrill PR;Charlesworth B
通讯作者：
Charlesworth B