Data from: Evolution and conservation of Characidium sex chromosomes

Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used Restriction site Associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9,863 SNPs, corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this dataset, we identified 26 female-specific RAD loci, putatively located on the W chromosome, as well as 148 sex-associated SNPs showing significant differentiation (average FST = 0.144) between males and females, and therefore in regions of more recent divergence between the Z and W chromosomes. Additionally, we detected 25 RAD loci showing extreme heterozygote deficiency in females but which were in Hardy-Weinberg equilibrium in males, consistent with degeneration of the W chromosome and therefore female hemizygosity. We validated seven female-specific and two sex-associated markers in a larger sample of C. gomesi, of which three localised to the W chromosome, thereby providing useful markers for sexing wild samples. Validated markers were evaluated in other populations and species of the genus Characidium, this exploration suggesting a rapid turnover of W-specific repetitive elements. Together, our analyses point to a complex origin for the sex chromosome of C. gomesi and highlight the utility of RAD-seq for studying the composition and evolution of sex chromosomes systems in wild populations.

鱼类物种的性染色体对间遗传分化程度存在显著变异，故而可为性染色体演化完整历程的研究提供绝佳契机。本研究采用限制性酶切位点相关DNA测序（Restriction site Associated DNA sequencing, RAD-seq）技术，对具有典型异型ZW/ZZ性染色体的格氏脂鲤（Characidium gomesi）的性染色体展开研究。我们筛选了9863个单核苷酸多态性位点（Single Nucleotide Polymorphisms, SNPs），全基因组范围内平均每100kb分布1个标记，用于检测性连锁变异。基于该数据集，我们共鉴定出26个雌性特异性RAD位点，推测其定位于W染色体；同时发现148个性相关SNPs，在雌雄个体间呈现显著遗传分化（平均固定指数FST=0.144），对应Z与W染色体间较晚发生分化的区域。此外，我们还检测到25个RAD位点，在雌性个体中表现出极端杂合子缺失，而在雄性个体中符合哈迪-温伯格平衡（Hardy-Weinberg equilibrium），这与W染色体退化、雌性为半合子的现象一致。我们在更大规模的格氏脂鲤样本中验证了7个雌性特异性标记与2个性相关标记，其中3个位点定位于W染色体，可为野生样本的性别鉴定提供实用工具。我们进一步在脂鲤属（Characidium）的其他种群与物种中对已验证的标记进行评估，结果显示W染色体特异性重复序列存在快速周转现象。综合来看，本研究的分析结果表明格氏脂鲤的性染色体起源具有复杂性，同时凸显了RAD-seq技术在研究野生种群性染色体系统的组成与演化方面的应用价值。