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Inferring the genomic structure of major cultured fishes by using high-density genetic map of tiger pufferfish

利用虎河豚高密度遗传图谱推断主要养殖鱼类基因组结构

基本信息

批准号：
18580175
负责人：
KIKUCHI Kiyoshi
金额：
$ 2.49万
依托单位：
The University of Tokyo
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2006
资助国家：
日本
起止时间：
2006 至 2007
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18580175/
关键词：
genome linkage map the tiger pufferfish medaka synteny aquaculture フグ比較ゲノム魚類進化育種ゲノム構造

项目摘要

Recent advance in molecular genetics and genomics have enabled us to identify chromosomal regions underlying many agronomically important traits in domestic animals and crops. This genomic information can then be used for more effective selection than achieved by traditional methods. As genome sequences are powerful resource for the identification of loci, whole genome sequencing project for the major domestic animals and crops has been done. In contrast to the domestic animals and crops of which the number of species is relatively limited, the number of fish species important for aquaculture is more than dozen. Therefore, it would be still unpractical to generate draft sequence of all these fishes at the moment. An alternative way to understand, genomic structure of aquaculture fishes might be accomplished by precise inferring of the genome structure of "not yet sequenced genomes" by comparing genomes of model fishes such as fugu and medaka. Indeed, I previously predicted that the gen … More ome structure of fished belonging to Acanthopterygii should be well conserved by using genomic information from fugu and medaka. In this study I have done comprehensive comparison of the genome structure of model fishes, in order to infer the genome structure of major aquaculture fishes. The results are summarized as follows.86% of the genome sequences of fugu were anchored to a high-density genetic map of fugu. This quality (coverage) of the map is ranked second among five model fishes (medaka, fugu, Tetraodon, zebrafish, stickleback).By using the high-density map of fugu generated in this study, I inferred genome structure of the last common ancestor of fugu and Tetraodon. The result suggests that these fish experienced a few rearrangement events in genome since they diverged.I comprehensively identified conserved genomic structure between fugu and medaka. Given the phylogenetic relationship of the major aquaculture fishes such as sea bream and yellowtail, the conserved genomic regions identified in this study should be also conserved among these fishes. Less

分子遗传学和基因组学的最新进展使我们能够识别家畜和作物中许多重要农艺性状的染色体区域。这些基因组信息可以用于比传统方法更有效的选择。由于基因组序列是鉴定基因座的有力资源，主要家畜和农作物的全基因组测序项目已经开展。家畜和农作物的物种数量相对有限，而对水产养殖重要的鱼类有十几种。因此，目前生成所有这些鱼类的吃水序列仍然是不现实的。另一种了解水产养殖鱼类基因组结构的方法可能是通过比较河豚和medaka等模式鱼的基因组来精确推断“尚未测序的基因组”的基因组结构。事实上，我曾利用河豚和medaka的基因组信息，预测棘鳍鱼科鱼类的gen . More some结构应该得到很好的保存。在本研究中，我对模式鱼的基因组结构进行了全面的比较，以推断主要水产养殖鱼类的基因组结构。结果总结如下：86%的河豚基因组序列被锚定在一个高密度的河豚遗传图谱上。该地图的质量（覆盖率）在五种模型鱼类（medaka, fugu, Tetraodon，斑马鱼，棘鱼）中排名第二。利用本研究生成的河豚高密度图谱，推测了河豚与四齿兽最后共同祖先的基因组结构。结果表明，这些鱼在分化后经历了一些基因组重排事件。全面鉴定了河豚和medaka之间保守的基因组结构。鉴于鲷鱼和黄尾鱼等主要水产养殖鱼类的系统发育关系，本研究确定的基因组保守区域也应在这些鱼类中保守。少