Supporting data for "De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish <i>Megaleporinus macrocephalus</i>"

<i>Megaleporinus macrocephalus</i> (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for <i>M. macrocephalus</i>. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes of <i>M. macrocephalus</i> sex determination. <br>The <i>M. macrocephalus</i> reference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst, and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF- family (<i>amhr2, bmp7</i>) and Wnt/-catenin pathway (<i>wnt4, wnt7a</i>), and some of them were differentially expressed. <br>The chromosome-level genome of piauçu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, <i>amhr2</i> and <i>bmp7</i> are potential candidate genes for sex determination in <i>M. macrocephalus</i>.巨首巨脂鲤（*Megaleporinus macrocephalus*，俗称piauçu）是隶属于脂鲤亚目（Characoidei）的新热带鱼类，其拥有成熟明确的异形型ZZ/ZW性别决定系统，因此是研究鱼类W、Z染色体的理想模型。本研究采用PacBio测序读段与Hi-C技术，组装获得了该物种的染色体级参考基因组。我们通过家系分离信息构建了遗传图谱，对雌雄个体开展混池测序（pool-seq）以解析其性别决定系统，并通过RNA测序（RNA-seq）筛选巨首巨脂鲤性别决定相关候选基因。 巨首巨脂鲤的参考基因组总长为1,282,030,339 bp，重叠群N50（contig N50）与支架序列N50（scaffold N50）分别为5.0 Mb与45.03 Mb。基于重组抑制模式、测序覆盖度、群体分化指数（Fst）以及性别特异性单核苷酸多态性（SNPs），我们在性染色体上鉴定出三个主要功能区域：W特异性区域（高度分化）、Z特异性区域（处于退化进程中）以及拟常染色体区域（PAR）。性染色体编码的基因集包含转化生长因子-β（TGF-β）家族基因（*amhr2*、*bmp7*）以及Wnt/β-连环蛋白通路基因（*wnt4*、*wnt7a*），其中部分基因存在显著差异表达。 该染色体级别的巨首巨脂鲤基因组具有较高质量，为该类群的相关研究提供了宝贵的资源。本研究的发现为解析鱼类Z、W性染色体的进化动态提供了新的视角，揭示了持续进行的染色体退化进程，并表明特定基因组区域内Z与W序列间存在复杂的相互作用。值得注意的是，*amhr2*与*bmp7*是巨首巨脂鲤性别决定的潜在候选基因。