Flatheads are valuable commercial fish species endemic to the Indo-West Pacific. Due to their economic value and unique biological traits, such as metamorphosis and camouflage, they serve as ideal marine organisms for studies on demersal adaptation and evolution. The brown-spotted flathead (Platycephalus sp.1) is the most widely distributed in the northwestern Pacific. Despite the lack of a valid scientific name, it has been long recognized and exploited in the marine fisheries of China, Japan, and Korea. In the current study, we applied Illumina, PacBio, and Hi-C sequencing to assemble a chromosome-scale genome for this species. The assembled genome was 660.63 Mb long with a scaffold N50 of 28.65 Mb and 100% of the contigs were anchored onto 24 chromosomes. We predicted 22 743 protein-coding genes, 94.8% of which were functionally annotated. Comparative genomic analyses suggested that Platycephalus sp.1 diverged from its common ancestor with Gasterosteus aculeatus ~88.4 million years ago. The expanded gene families were significantly enriched in immune, biosynthetic, and metabolic pathways. Furthermore, three shared Gene Ontology terms and 377 common positively selected genes were identified between flathead and flatfish species, suggesting that these genes may contribute to demersal adaptation in flatheads. The assembled genomic data provide a valuable molecular resource for further research on the biological and adaptive evolution of flathead species.
鲬科鱼类是印度-西太平洋特有的海洋鱼类，独特的生物学特征（如变态发育和伪装）及较高的经济价值使其成为研究海洋底栖适应和进化的理想物种。褐斑鲬（Platycephalus sp.1）为西北太平洋海域分布最广泛的鲬科鱼类。尽管缺乏有效学名，褐斑鲬早已成为中、日、韩等国海洋渔业重要的渔获种类。该研究利用PacBio、Illumina和Hi-C测序技术组装了褐斑鲬染色体水平基因组序列。组装的基因组大小为660.63 Mb，其Scaffold N50 为28.65 Mb，同时所有contigs均锚定到24条染色体上。基因组内共预测到22 743个蛋白质编码基因，其中功能注释的基因占94.8%。系统发育分析结果表明褐斑鲬与三刺鱼的分化时间大约在88.4百万年前。扩张的基因家族主要在免疫、生物合成和代谢通路显著富集。此外，我们还识别出褐斑鲬和比目鱼间共有的3个GO功能集和377个正选择基因，这些共有基因可能与褐斑鲬底栖适应有关。组装的褐斑鲬基因组数据可为后续鲬科鱼类生物适应进化研究提供宝贵的分子遗传学资源。.
Keywords: Chromosome-scale genome assembly; Comparative genomics; Demersal adaptation; Platycephalidae.