Conservation of Human Microsatellites across 450 Million Years of Evolution
Conservation of Human Microsatellites across 450 Million Years of Evolution
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DOI：
10.1093/gbe/evq007
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发表时间：
2010-01-01
影响因子：
3.3
通讯作者：
Gemmell, Neil J.
中科院分区：
文献类型：
--
作者：
Buschiazzo, Emmanuel;Gemmell, Neil J.
脊椎动物基因组的测序和比较使得能够鉴定广泛保守的基因组元件。其中最主要的是基因和顺式调控区域，它们通常受到选择性限制，以促进它们在相关生物体中的保留。对缺乏功能或功能尚未确定的元素的守恒性的研究相对较少。特别是，微卫星是一类高度多态性重复序列，大多数人认为是中性进化的垃圾DNA，太不稳定而无法在遥远的物种中维持，尚未在比较基因组框架中进行全面研究。在这里，我们使用人类基因组与 11 种哺乳动物和 5 种非哺乳动物脊椎动物的 UCSC 比对来识别和检查脊椎动物基因组中人类微卫星的保守程度。在人类序列中发现的 696,016 个微卫星中，85.39% 在至少一种其他物种中保守，而 28.65% 和 5.98% 分别在至少一种和三种非灵长类物种中发现。随着进化时间的增加，微卫星保守性呈指数下降，人类基因组中保守微卫星与非保守微卫星的分布相当，以及微卫星保守性和整体序列保守性之间的正相关性，所有这些都表明，大多数微卫星只是偶然保留在基因组中，尽管在遥远的哺乳动物和其他脊椎动物中也发现了异常保守的人类微卫星。我们的研究结果首次对跨深层进化时间尺度（在本例中为 450 Myr 的脊椎动物进化）的微卫星保护进行了全面调查，并为识别功能性保守微卫星、开发跨物种微卫星标记以及研究物种水平以上的微卫星进化提供了新工具。
The sequencing and comparison of vertebrate genomes have enabled the identification of widely conserved genomic elements. Chief among these are genes and cis-regulatory regions, which are often under selective constraints that promote their retention in related organisms. The conservation of elements that either lack function or whose functions are yet to be ascribed has been relatively little investigated. In particular, microsatellites, a class of highly polymorphic repetitive sequences considered by most to be neutrally evolving junk DNA that is too labile to be maintained in distant species, have not been comprehensively studied in a comparative genomic framework. Here, we used the UCSC alignment of the human genome against those of 11 mammalian and five nonmammalian vertebrates to identify and examine the extent of conservation of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites found in human sequences, 85.39% were conserved in at least one other species, whereas 28.65% and 5.98% were found in at least one and three nonprimate species, respectively. An exponential decline of microsatellite conservation with increasing evolutionary time, a comparable distribution of conserved versus nonconserved microsatellites in the human genome, and a positive correlation between microsatellite conservation and overall sequence conservation, all suggest that most microsatellites are only maintained in genomes by chance, although exceptionally conserved human microsatellites were also found in distant mammals and other vertebrates. Our findings provide the first comprehensive survey of microsatellite conservation across deep evolutionary timescales, in this case 450 Myr of vertebrate evolution, and provide new tools for the identification of functional conserved microsatellites, the development of cross-species microsatellite markers and the study of microsatellite evolution above the species level.