Abstract：
Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species\' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.
摘要：
Duskykob（Argylesomusjaponicus）是一种商业上重要的有翼鱼，南非土著，澳大利亚,和中国。以前的研究强调了遗传组成的差异，生活史,和不同地理区域的物种形态。为南非（SA）特异性生成了0.742Gb（N50=5.49Mb；BUSCO完整性=97.8％）的基因组序列草案和22,438个预测的蛋白质编码基因。与中国（CN）同源的比较显示，两个基因组中都有32,068个直系同源蛋白质簇的核心集合。与CN基因组中的1928个独特簇相比,SA基因组显示440个独特簇。运输和免疫反应过程在SA辅助基因组中被过度代表，而CN辅助基因组被富集用于免疫反应，DNA转座,和感官检测(FDR调整的p<0.01)。这些独特的簇可能代表了物种pangenome的适应性成分，可以解释由于环境专业化差异而导致的种群差异。此外，700个单拷贝直向同源物（SCO）显示了SA和CN基因组之间的阳性选择的证据，在全球范围内，这些基因组只有92%的相似性，表明它们可能是不同的物种。这些基因主要在新陈代谢和消化中发挥作用，说明了区分物种的进化途径。了解物种内部和物种之间的适应和进化的这些基因组机制提供了对kob生长和成熟的宝贵见解。与商业水产养殖特别相关的特征。
