Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution
Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution
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DOI：
10.1139/gen-2015-0124
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发表时间：
2016-05-01
期刊：
影响因子：
3.1
通讯作者：
Castoe, Todd A.
中科院分区：
文献类型：
--
作者：
Adams, Richard H.;Blackmon, Heath;Castoe, Todd A.
脊椎动物生命树上的简单序列重复(SSR或微卫星)的进化动力学在很大程度上仍然没有文献记载，也知之甚少。在这项研究中，我们分析了71个脊椎动物基因组的基因组微卫星丰度和进化模式。最高丰度的微卫星存在于鳍鱼、有鳞爬行动物和哺乳动物的基因组中，而鳄鱼、海龟和鸟类的基因组则表现出较少的微卫星景观。我们使用比较的方法来推断脊椎动物微卫星丰度的进化速率，并强调经历了基因组微卫星丰度异常高或低速率变化的特定谱系。总体而言，在爬行动物的主要谱系中观察到的微卫星含量、丰度和进化速度的差异最大，但我们发现几个高度分化的支系(即鳞状爬行动物和哺乳动物)包含相对相似的基因组微卫星组成。始祖龙爬行动物(海龟、鳄鱼和鸟类)的基因组微卫星含量减少，微卫星进化速度最慢，而鳞状爬行动物基因组的微卫星进化速度最高。灵长类、单孔动物、啮齿动物、蛇和鱼类中SSR含量的显著分支特异性变化也很明显。总体而言，我们的结果支持脊椎动物之间微卫星基因组格局的多个重大变化。
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.