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

分子遗传学和基因组学的最新进展使我们能够确定家畜和作物中许多重要农艺性状的染色体区域。然后，这些基因组信息可以用于比传统方法更有效的选择。由于基因组序列是基因座鉴定的有力资源，目前已完成了主要家畜和农作物的全基因组测序计划。与家畜和农作物的物种数量相对有限相比，对水产养殖重要的鱼类物种数量超过10种。因此，目前生成所有这些鱼类的序列草案仍不切实际。了解水产养殖鱼类基因组结构的另一种方法可能是通过比较模式鱼如河豚和青鳉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，我之前曾预测过一代人 ...更多信息 利用东方鲀和青鳉的基因组信息，可以很好地保存鱼的某些结构。本研究对模式鱼类的基因组结构进行了全面的比较，以推断主要养殖鱼类的基因组结构。结果如下：86%的河豚基因组序列锚定在高密度的河豚遗传图谱上。该图谱的质量（覆盖率）在5种模式鱼类（青鳉、河豚、河豚、斑马鱼、刺鱼）中排名第二。利用本研究所获得的河豚高密度图谱，推测了河豚和河豚最后共同祖先的基因组结构。结果表明，这些鱼类在分化过程中发生了一些基因组重排事件。鉴于主要养殖鱼类如真鲷和黄尾鱼的系统发育关系，本研究中发现的保守基因组区域在这些鱼类中也应该是保守的。少

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