Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Shizuoka, Japan.
Genome Biol Evol. 2011;3:424-42. doi: 10.1093/gbe/evr041. Epub 2011 Jun 1.
The compact genome of fugu (Takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.fugu-sg.org/). The integrated genome map revealed a higher recombination rate in fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of fugu. We used the extended assembly to explore recent rearrangement events in the lineages of fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ~25 species of Takifugu that evolved within the last 5 My.
河豚（Takifugu rubripes）的紧凑基因组被广泛用作理解脊椎动物基因组进化的参考基因组。然而，河豚基因组组装的碎片化限制了其在脊椎动物基因组结构比较中的应用。为了将组装的连续性扩展到染色体水平，我们生成了河豚的综合遗传图谱，并将组装的支架锚定到河豚的 22 条染色体上。该图谱由 1220 个微卫星标记组成，为覆盖基因组组装 86%的 697 个支架提供了锚点（http://www.fugu-sg.org/）。整合的基因组图谱显示，与其他脊椎动物相比，河豚的重组率更高，而且雌雄之间以及河豚染色体之间的重组率差异很大。我们利用扩展的组装来探索河豚、东方鲀和青鳉的进化谱系中的近期重排事件，并将其与三个哺乳动物（人类、小鼠和负鼠）谱系中的重排进行比较。在这两种河豚鱼中，河豚经历的染色体重排比东方鲀少。由于在脊椎动物中染色体间重排的速率较低，因此三个硬骨鱼的基因顺序比哺乳动物更高度保守。这些结果为硬骨鱼和哺乳动物之间不同的基因组进化模式提供了新的见解。整合的基因组图谱和河豚的遗传图谱是脊椎动物比较基因组学和阐明约 25 种 Takifugu 物种表型多样性遗传基础的宝贵资源，这些物种在过去 500 万年中进化而来。
