来自数百个物种的串联重复序列的比较分析揭示了对着丝粒进化的独特见解
Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution
摘要：
着丝粒对于染色体分离是必不可少的，然而它们的DNA序列进化得很快。在大多数已被研究的动物和植物中，着丝粒含有兆碱基规模的串联重复序列。尽管它们的重要性，很少有人知道的程度，着丝粒串联重复序列之间的不同物种跨越不同的门共享共同的属性。我们使用生物信息学的方法来识别高拷贝串联重复序列从282种使用公开的基因组序列和我们自己的数据。最丰富的串联重复序列是着丝粒DNA的假设对于大多数物种都是正确的，这些物种的着丝粒先前已经被表征，这表明这是基因组的一般性质。我们的方法与目前所有的测序技术兼容。长的Pacific Biosciences序列读数使我们能够找到高达1，419 bp的串联重复单体。高拷贝着丝粒串联重复序列存在于几乎所有的动植物基因组中，但重复单体的序列组成和长度变化很大。此外，序列同源性的系统发育分析显示，在5000万年的分歧之后，几乎没有序列保守性的证据。我们发现，尽管总体上缺乏序列保守性，但不同物种的着丝粒串联重复序列显示出相似的进化模式，包括出现高阶重复结构，其中几个多态性单体组成一个较大的重复单元。虽然大多数真核生物中的着丝粒位置是由表观遗传学决定的，但我们的研究结果表明，串联重复序列在动物和植物的着丝粒中非常普遍。这表明这种重复的功能作用，也许在促进跨染色体的着丝粒DNA的协同进化。
英文摘要：
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution, including the appearance of higher order repeat structures in which several polymorphic monomers make up a larger repeating unit. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animals and plants. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.
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