The zebrafish gene map defines ancestral vertebrate chromosomes
The zebrafish gene map defines ancestral vertebrate chromosomes
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DOI：
10.1101/gr.4134305
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发表时间：
2005-09-01
期刊：
影响因子：
7
通讯作者：
Talbot, WS
中科院分区：
文献类型：
--
作者：
Woods, IG;Wilson, C;Talbot, WS
斑马鱼（Danio rerio）的基因筛选已经确定了定义数百种基本脊椎动物基因作用的突变。遗传图谱可以通过提供突变候选基因和多态性遗传标记，将突变表型与基因序列联系起来。在这里，我们报告了一个包含4073个多态性标记的斑马鱼遗传图谱，其编码序列的数量是以前报道的斑马鱼遗传图谱的两倍多。我们在比较研究中使用该图谱来确定斑马鱼、四齿兽和人类基因组中保守的许多共效区域。此外，我们使用我们的图谱来分析斑马鱼和四齿兽基因组中的基因复制。目前的证据表明，在硬骨鱼从四足动物谱系中分离出来后，硬骨鱼谱系中发生了全基因组复制，而现代硬骨鱼基因组中只保留了复制的一部分。有人提出，重复基因的差异保留可能促进了硬骨鱼在大量辐射期间形成的新生物种的分离。我们发现在斑马鱼和四齿兽中保留了不同的重复基因，尽管在两个基因组中都保留了相似数量的重复基因。最后，我们使用比较制图数据来解决脊椎动物共同祖先具有由12条染色体组成的基因组的提议。在斑马鱼、四齿兽和人类基因组的三方比较中，我们的分析描绘了这12条拟议祖先染色体中的11条的基因含量。
Genetic screens in zebrafish (Danio rerio) have identified mutations that define the roles of hundreds of essential vertebrate genes. Genetic maps can link mutant phenotype with gene sequence by providing candidate genes for mutations and polymorphic genetic markers useful in positional cloning projects. Here we report a zebrafish genetic map comprising 4073 polymorphic markers, with more than twice the number of coding sequences localized in previously reported zebrafish genetic maps. We use this map in comparative studies to identify numerous regions of synteny conserved among the genomes of zebrafish, Tetraodon, and human. In addition, we use our map to analyze gene duplication in the zebrafish and Tetraodon genomes. Current evidence suggests that a whole-genome duplication occurred in the teleost lineage after it split from the tetrapod lineage, and that only a subset of the duplicates have been retained in modern teleost genomes. It has been proposed that differential retention of duplicate genes may have facilitated the isolation of nascent species formed during the vast radiation of teleosts. We find that different duplicated genes have been retained in zebrafish and Tetraodon, although similar numbers of duplicates remain in both genomes. Finally, we use comparative mapping data to address the proposal that the common ancestor of vertebrates had a genome consisting of 12 chromosomes. In a three-way comparison between the genomes of zebrafish, Tetraodon, and human, our analysis delineates the gene content for 11 of these 12 proposed ancestral chromosomes.