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 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation. With this data set, 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. In addition, 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之间的遗传分化程度存在显著变异，故而可为探究性染色体演化的完整谱系提供绝佳研究契机。本研究采用限制性酶切位点相关DNA测序（RAD-seq），针对具有显著异形ZW/ZZ性染色体的戈氏脂鲤（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），其在全基因组中的分布密度约为每100kb一个标记，用于检测与性别连锁的遗传变异。基于该数据集，我们共鉴定出26个雌性特异性RAD位点，推测其位于W染色体上；同时发现148个与性别相关的SNPs，在雌雄个体间呈现显著遗传分化（平均FST=0.144），这些位点所在区域的Z、W染色体分化时间相对较晚。此外，我们还检测到25个RAD位点，在雌性个体中呈现极端杂合子缺失现象，但在雄性个体中符合哈迪-温伯格平衡（Hardy–Weinberg equilibrium），这与W染色体的退化以及雌性的半合子状态相一致。我们在更大样本量的戈氏脂鲤群体中验证了7个雌性特异性标记与2个性别相关标记，其中3个定位至W染色体，可为野生样本的性别鉴定提供实用的分子标记工具。我们在脂鲤属（Characidium）的其他种群与物种中对已验证的标记进行了评估，该探索结果表明W染色体特异性重复序列存在快速的演化更替现象。综合来看，本研究的分析结果表明戈氏脂鲤的性染色体起源机制较为复杂，同时也凸显了RAD-seq在探究野生种群性染色体系统的组成与演化方面的应用价值。