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 582.95 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, 56.54 Mb repeating elements and 22,778 protein-coding genes were identified in the genome assembly. These results provide valuable resources for the genetic research and the development of molecular breeding technologies in marbled flounder.

本研究首次报道了比目鱼（斑鲆，marbled flounder）的首个无间隙端粒到端粒（Telomere-to-Telomere, T2T）基因组，组装总长度为582.95 Mb，整合了短读长测序数据（short reads）、PacBio HiFi长读长测序数据（PacBio HiFi long reads）、ONT超长长读长测序数据（ONT ultra-long reads）以及Hi-C测序数据（Hi-C data）。所有基因组序列均被组装至24条染色体上，且在所有染色体的两端共鉴定到48个端粒。经BUSCO（Benchmarking Universal Single-Copy Orthologs）评估，该基因组的完整单拷贝同源基因检出率达99.29%，表明其组装完整性极高。比对至该基因组组装版本的短读长测序数据、PacBio HiFi长读长测序数据以及ONT超长长读长测序数据的平均比对率均超过99.89%。此外，该基因组组装中共鉴定到56.54 Mb的重复序列元件以及22778个蛋白质编码基因。上述研究结果为斑鲆（marbled flounder）的遗传学研究与分子育种技术开发提供了宝贵的遗传资源。