Zhang Xinhui, Chen Jieming, Zhou Wenchuan, Wen Jiufu, Shi Qiong
Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen, 518081, China.
Sci Data. 2025 Aug 21;12(1):1457. doi: 10.1038/s41597-025-05735-w.
As a protandrous hermaphroditic fish species with natural sex change from male to female, Asian seabass (Lates calcarifer) represents an attractive model for studying sequential hermaphroditism. In this study, we constructed the first telomere-to-telomere (T2T) gap-free genome assembly of Asian seabass, by integration of MGI short-read, PacBio HiFi long-read, ONT ultra-long and Hi-C sequencing technologies. The haplotypic 614.19 Mb genome sequences were successfully anchored onto 24 chromosomes, demonstrating exceptional contiguity with a contig N50 of 26.57 Mb. Comprehensive annotation revealed precise localization of telomeric repeats and centromeric regions across various chromosomes. Good results from Merqury (QV: 57.8), CRAQ (99.45%) and BUSCO (100%) indicate a high level of accuracy for the assembled genome. ONT ultra-long and PacBio HiFi sequencing data were aligned with the assembly using minimap2, resulting in a mapping rate over 98%. Repetitive elements accounted for 18.18% (111.64 Mb) of the entire genome, and a total of 25,093 protein-coding genes were annotated. This high-quality T2T genome assembly provides a valuable genetic resource for in-depth comparative genomics, population genetics, molecular breeding, and functional studies of this economically important marine species. This reference assembly also facilitates investigations into the detailed molecular mechanisms underlying its unique reproductive strategy of the protandrous hermaphrodite Asian seabass.
亚洲海鲈（尖吻鲈）是一种具有从雄性自然转变为雌性的雄性先熟雌雄同体鱼类，是研究序列雌雄同体现象的一个有吸引力的模型。在本研究中，我们通过整合MGI短读长、PacBio HiFi长读长、ONT超长读长和Hi-C测序技术，构建了首个亚洲海鲈的端粒到端粒（T2T）无间隙基因组组装。614.19 Mb的单倍型基因组序列成功锚定到24条染色体上，显示出卓越的连续性，重叠群N50为26.57 Mb。全面注释揭示了端粒重复序列和着丝粒区域在各条染色体上的精确定位。Merqury（QV：57.8）、CRAQ（99.45%）和BUSCO（100%）的良好结果表明组装基因组具有较高的准确性。ONT超长读长和PacBio HiFi测序数据使用minimap2与组装序列比对，比对率超过98%。重复元件占整个基因组的18.18%（111.6 Mb），共注释了25,093个蛋白质编码基因。这种高质量的T2T基因组组装为深入开展这种经济重要性海洋物种的比较基因组学、群体遗传学、分子育种和功能研究提供了宝贵的遗传资源。这个参考组装也有助于深入研究雄性先熟雌雄同体亚洲海鲈独特繁殖策略背后的详细分子机制。
