State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
Fisheries Research Institute of Fujian, Xiamen 361000, China.
Gene. 2023 Jan 15;849:146910. doi: 10.1016/j.gene.2022.146910. Epub 2022 Sep 24.
Takifugu genus has been brought to the fore in scientific and practical research due to its compact genome, explosive speciation progress and economic value. Here we updated the chromosome-level genome of Takifugu bimaculatus by an ultra-high-density linkage map, a classic and accurate way of chromosome assembly. The map constituted a robust assembly frame, with 92.2% (372.77 Mb) of the draft genome cumulatively placed. With intraspecies and interspecies comparative genomic analysis, we developed a criterion to quantify the differences between assemblies and established a novel way to integrate information from multiple assemblies. The integrated assembly rectified potential mis-assemblies, greatly improving the genome contiguity and correctness. Our results rendered profound information on the genetic recombination of T. bimaculatus and provided new insights into effective genome assembly. The consolidated assembly will be a contributory tool of T. bimaculatus and broadly across the Takifugu by providing a convincing reference for genomic research.
由于其紧凑的基因组、爆发式的物种形成进展和经济价值，Takifugu 属在科学和实际研究中备受关注。在这里，我们通过超高密度连锁图谱（经典且准确的染色体组装方法）更新了双斑东方鲀的染色体水平基因组。该图谱构成了一个强大的组装框架，累计放置了 92.2%（372.77Mb）的草图基因组。通过种内和种间比较基因组分析，我们开发了一种量化组装差异的标准，并建立了一种整合来自多个组装信息的新方法。整合的组装纠正了潜在的错误组装，极大地提高了基因组的连续性和正确性。我们的结果提供了关于双斑东方鲀遗传重组的深刻信息，并为有效的基因组组装提供了新的见解。综合组装将为双斑东方鲀乃至整个 Takifugu 属提供有价值的工具，为基因组研究提供令人信服的参考。
