Supporting data for "Exploring the cobia (<i>Rachycentron canadum</i>) genome: Unveiling putative male heterogametic regions and identification sex-specific markers".

Cobia (<i>Rachycentron canadum</i>) is the only member of the <i>Rachycentridae</i> family and exhibits considerable sexual dimorphism in growth rate. Sex determination in teleosts has been a long-standing basic biological question, and the molecular mechanisms of sex determination/differentiation in cobia species are completely unknown. <br>Here, we reported two high-quality, chromosome-level annotated male and female cobia genomes with assembly sizes of 586.51 Mb (contig/scaffold N50: 86.0 kb/24.3 Mb) and 583.88 Mb (79.9 kb/22.5 Mb), respectively. Synteny inference among perciform genomes revealed that cobia and the remora <i>Echeneis<em> </em>naucrates</i><em> </em>were sister groups. Further, whole genome resequencing of 31 males and 60 females, genome-wide association study (GWAS) and sequencing depth analysis identified three short male-specific regions within a 10.7 kb continuous genomic region on male chromosome 18, which hinted at an undifferentiated sex chromosome system with an XX/XY mode of sex determination in cobia. Importantly, the two only genes within/between the male-specific regions, epoxide hydrolase 1 (<i>ephx1</i>, renamed <i>cephx1y</i>), and transcription factor 24 (<i>tcf24</i>, renamed <i>ctcf24y</i>), showed testis-specific/biased gene expression, whereas their counterparts <i>cephx1x</i> and<em> </em><i>ctf24x</i>, located in female chromosome 18, were similarly expressed in both sexes. In addition, male-specific PCR targeting the <i>cephx1y</i> gene revealed that this genomic feature is conserved in cobia populations from Panama, Brazil, Australia, and Japan. <br>The first comprehensive genomic survey presented here is a valuable resource for future studies on cobia population structure and dynamics, conservation, and evolutionary history. Furthermore, it establishes evidence of male heterogametic regions with two genes playing a potential role in the sex determination of the species, and provides further support for the rapid evolution of sex-determining mechanisms in teleost fish.

军曹鱼（<i>Rachycentron canadum</i>）是军曹鱼科（<i>Rachycentridae</i>）的唯一物种，其生长速率存在显著的性别二态性。硬骨鱼的性别决定始终是基础生物学领域长期存在的核心问题，而军曹鱼的性别决定/分化分子机制迄今仍完全未知。
本研究报道了两个高质量的染色体级注释的雌雄军曹鱼基因组，组装大小分别为586.51 Mb（重叠群/支架N50：86.0 kb/24.3 Mb）和583.88 Mb（79.9 kb/22.5 Mb）。通过对鲈形目鱼类基因组开展共线性分析，结果显示军曹鱼与䲟鱼（<i>Echeneis naucrates</i>）互为姊妹群。进一步对31尾雄性和60尾雌性个体开展全基因组重测序，结合全基因组关联分析（Genome-Wide Association Study, GWAS）与测序深度分析，在雄性18号染色体的10.7 kb连续基因组区域内鉴定出3处短小的雄性特异性区域，提示军曹鱼的性别决定系统为未完全分化的XX/XY型性别决定系统。值得注意的是，雄性特异性区域内/区间仅有的两个基因——环氧化物水解酶1（<i>ephx1</i>，后重命名为<i>cephx1y</i>）与转录因子24（<i>tcf24</i>，后重命名为<i>ctcf24y</i>）——呈现睾丸特异性/偏向性表达；而位于雌性18号染色体上的同源基因<i>cephx1x</i>与<i>ctf24x</i>则在雌雄个体中均表现出相似的表达水平。此外，针对<i>cephx1y</i>基因的雄性特异性PCR检测证实，该基因组特征在巴拿马、巴西、澳大利亚及日本的军曹鱼种群中均保守存在。
本研究首次完成军曹鱼的综合性基因组调研，其结果将为后续军曹鱼种群结构与动态、物种保护及演化历史的相关研究提供宝贵的资源。同时，本研究证实军曹鱼存在雄性异配性别区域，且其中的两个基因可能参与该物种的性别决定过程，为硬骨鱼性别决定机制的快速演化提供了新的实验支撑。