Gap-free telomere-to-telomere genome assembly of marbled flounder (Pseudopleuronectes yokohamae)

Here, we reported the first gap-free T2T genome in flatfish (marbled flounder), with length of 582.73 Mb combing short reads, PacBio HiFi long reads, ONT ultra-long reads, and Hi-C data. All of the genome sequences were assembled onto 24 chromosomes, and 48 telomeres were identified on both ends of all chromosomes. 99.29% complete BUSCOs were identified, demonstrating a high level of completeness. The average mapping ratio of short reads, PacBio HiFi reads, and ONT ultra-long reads aligned to the genome assembly was more than 99.89%. Moreover, 121.02 Mb repeating elements and 22,778 protein-coding genes were identified in the genome assembly. These results provide valuable resources for the evolutionary genomics research and the identification of key candidate genes for economic traits in marbled flounder.

本研究首次报道了花斑比目鱼（marbled flounder）的首个无间隙端粒到端粒（Telomere-to-Telomere, T2T）基因组，其组装总长为582.73 Mb，整合了短读长测序数据、PacBio HiFi长读长测序数据、ONT超长读长测序数据以及Hi-C染色质构象捕获数据。所有基因组序列均被锚定至24条染色体，且所有染色体的两端共鉴定出48个端粒。本研究共鉴定出99.29%的完整BUSCO（Benchmarking Universal Single-Copy Orthologs），表明该基因组组装具有极高的完整性。比对至该基因组组装序列的短读长、PacBio HiFi长读长以及ONT超长读长的平均比对率均超过99.89%。此外，该基因组组装中共鉴定出121.02 Mb的重复元件以及22778个蛋白质编码基因。上述研究结果为花斑比目鱼的进化基因组学研究以及经济性状关键候选基因的筛选提供了宝贵的基因组资源。