Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.
Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.
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DOI：
10.1371/journal.pbio.0050167
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发表时间：
2007-07
期刊：
影响因子：
9.8
通讯作者：
Waterston RH
中科院分区：
文献类型：
--
作者：
Hillier LW;Miller RD;Baird SE;Chinwalla A;Fulton LA;Koboldt DC;Waterston RH
为了确定秀丽隐杆线虫染色体组织的独特特征是否与布氏秀丽隐杆线虫基因组相同，我们构建了一个基于单核苷酸多态性的遗传图谱，以便沿着布氏秀丽隐杆线虫的六条染色体对全基因组鸟枪法组装进行排序和定向。尽管这两个物种属于同一属，但它们最近的共同祖先存在于8000 - 1.1亿年前，因此它们在进化上的距离比例如人类和小鼠之间的距离更远。我们发现，与秀丽隐杆线虫的染色体一样，布氏秀丽隐杆线虫的染色体在臂上表现出高水平的重组，并且与染色体中心相比，具有更高的重复密度、更高比例的内含子序列和更低比例的外显子序列。尽管染色体内发生了大量重排，但一对一的直系同源基因往往保留在染色体的同一区域，并且与臂相比，染色体中心的直系同源基因共线区块往往更长。更引人注目的是，这两个物种显示出几乎完全的同线性保守，在一个物种的单条染色体上存在的一对一直系同源基因在另一个物种的单条染色体上也能找到。这两个远缘物种之间染色体组织和同线性的保守性表明，染色体组织在生物体适应性中的作用目前还知之甚少。
染色体组织在一个物种适应性中的重要性目前还了解甚少。1998年秀丽隐杆线虫基因组序列的公布揭示了更高层次组织的特征，表明其染色体被组织成不同的区域。染色体臂比染色体中心积累变化的速度更快。在本文中，我们比较了布氏秀丽隐杆线虫基因组与秀丽隐杆线虫基因组的组织。通过基于布氏秀丽隐杆线虫两个品系之间的DNA变异构建遗传图谱，并利用该图谱对2003年公布的布氏秀丽隐杆线虫基因组草图序列进行组织，我们发现了以下几点：（1）染色体内重排在臂内甚至臂间频繁发生，但在中心区域内以及臂和中心之间不太常见。（2）基因绝大多数保留在相同的染色体上。（3）区分秀丽隐杆线虫臂和中心的独特特征在布氏秀丽隐杆线虫的染色体上也能看到。尽管这两个物种自它们最近的共同祖先以来大约已经过了1亿年，但这些特征在这两个物种之间的保守性为染色体区域结构的选择优势提供了明确的证据。基因在相同染色体上的持续关联表明这可能也是有利的。
两个远缘物种之间染色体组织和同线性的保守性表明染色体组织在生物体适应性中具有作用。
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently. The importance of chromosomal organization in the fitness of a species is only poorly understood. The publication of the C. elegans genome sequence in 1998 revealed features of higher level organization that suggested its chromosomes were organized into distinct domains. Chromosome arms were accumulating changes more rapidly than the centers of chromosomes. In this paper, we have compared the organization of the nematode C. briggsae genome with that of C. elegans. By building a genetic map based on DNA variations between two strains of C. briggsae, and by using that map to organize the draft genome sequence of C. briggsae published in 2003, we found the following: (1) Intrachromosomal rearrangements are frequent within and even between arms but are less common within central regions and between arms and centers. (2) Genes have remained overwhelmingly on the same chromosomes. (3) The distinctive features that distinguish C. elegans arms from centers also are seen in C. briggsae chromosomes. The conservation of these features between these two species, despite the approximately 100 million years since their most recent common ancestor, provides clear evidence of the selective advantages of the domain architecture of chromosomes. The continuing association of genes on the same chromosomes suggests that this may also be advantageous. The conservation of both chromosomal organization and synteny between two distantly related species suggests roles for chromosome organization in the fitness of an organism.
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影响因子：
14.9
作者：
Lee, KZ;Eizinger, A;Sommer, RJ
通讯作者：
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3.4
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2.5
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作者：
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