Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome.
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome.
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DOI：
10.1371/journal.pbio.0050101
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发表时间：
2007-04
期刊：
影响因子：
9.8
通讯作者：
Brenner S
中科院分区：
文献类型：
--
作者：
Venkatesh B;Kirkness EF;Loh YH;Halpern AL;Lee AP;Johnson J;Dandona N;Viswanathan LD;Tay A;Venter JC;Strausberg RL;Brenner S
由于其系统发育的位置，软骨鱼类（鲨鱼，射线，溜冰鞋，和银鲛）提供了一个重要的参考，为我们了解脊椎动物基因组的进化。相对较小的基因组的象鲨，Callorhinchus milii，嵌合体，使其成为一个有吸引力的模型软骨鱼类基因组的全基因组测序和比较分析。在这里，作者描述了对象鲨基因组的调查测序（1.4×覆盖率）和比较分析，这是第一个被测序到这个深度的软骨鱼类基因组之一。重复序列，主要是由一个新的家庭的短散布元件样和长散布元件样序列，占约28%的象鲨基因组。大约15，000个象鲨基因的片段揭示了在四足动物和硬骨鱼谱系进化过程中差异丢失的基因的具体例子。有趣的是，人类和象鲨基因组之间的保守同线性和保守序列的程度高于人类和硬骨鱼基因组之间。象鲨含有假定的四个Hox簇，表明与硬骨鱼基因组不同，象鲨基因组没有经历额外的全基因组复制。这些发现强调了象鲨作为人类和其他脊椎动物基因组比较分析的关键参考脊椎动物基因组的重要性。这项研究还表明，调查测序方法可以有效地应用于远亲脊椎动物基因组的比较分析。软骨鱼类（鲨鱼、鳐、鳐和银鲛）是在生殖学上最古老的有颚脊椎动物。它们也是了解人类和硬骨鱼等多骨脊椎动物进化的重要外群。我们进行了调查测序（1.4倍覆盖率）的嵌合体，象鲨（Callorhinchus milii）。象鲨的基因组，估计长约910 Mb，包含约28%的重复元件。对大约15，000个象鲨基因片段的比较分析揭示了在人类和硬骨鱼谱系进化过程中丢失的几个古老基因的例子。有趣的是，人类和象鲨的基因组比人类和硬骨鱼（斑马鱼和河豚）的基因组表现出更高程度的同线性和序列保守性，尽管人类与硬骨鱼的关系比象鲨更密切。与硬骨鱼的基因组不同，象鲨的基因组似乎没有经历额外一轮的全基因组复制。这些发现强调了象鲨作为了解脊椎动物基因组进化的有用的软骨鱼类基因组“模型”的重要性。软骨象鲨有一个基本的系统发育位置，有助于理解有颌脊椎动物的进化。其基因组的调查测序确定了四个Hox集群，这表明，不像硬骨鱼，没有额外的全基因组重复发生。
Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes. Cartilaginous fishes (sharks, rays, skates, and chimaeras) are the phylogenetically oldest group of living jawed vertebrates. They are also an important outgroup for understanding the evolution of bony vertebrates such as human and teleost fishes. We performed survey sequencing (1.4× coverage) of a chimaera, the elephant shark (Callorhinchus milii). The elephant shark genome, estimated to be about 910 Mb long, comprises about 28% repetitive elements. Comparative analysis of approximately 15,000 elephant shark gene fragments revealed examples of several ancient genes that have been lost differentially during the evolution of human and teleost fish lineages. Interestingly, the human and elephant shark genomes exhibit a higher degree of synteny and sequence conservation than human and teleost fish (zebrafish and fugu) genomes, even though humans are more closely related to teleost fishes than to the elephant shark. Unlike teleost fish genomes, the elephant shark genome does not seem to have experienced an additional round of whole-genome duplication. These findings underscore the importance of the elephant shark as a useful “model” cartilaginous fish genome for understanding vertebrate genome evolution. The cartilaginous elephant shark has a basal phylogenetic position useful for understanding jawed vertebrate evolution. Survey sequencing of its genome identified four Hox clusters, suggesting that, unlike for teleost fishes, no additional whole-genome duplication has occurred.
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影响因子：
7
作者：
Amores, A;Suzuki, T;Postlethwait, JH
通讯作者：
Postlethwait, JH
影响因子：
10.7
作者：
Brunet, Frederic G.;Roest Crollius, Hugues;Robinson-Rechavi, Marc
通讯作者：
Robinson-Rechavi, Marc
DOI：
10.1002/jez.b.00037
发表时间：
2003-10-15
影响因子：
2.2
作者：
Fried, C;Prohaska, SJ;Stadler, PF
通讯作者：
Stadler, PF
DOI：
10.1016/s0167-4781(99)00181-5
发表时间：
1999-10-28
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION
影响因子：
--
作者：
Hughes, DC;Barratt, CLR
通讯作者：
Barratt, CLR
DOI：
10.1152/ajpregu.00267.2002
发表时间：
2003-05-01
影响因子：
2.8
作者：
Hirata, T;Kaneko, T;Hirose, S
通讯作者：
Hirose, S