Data from: Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex-linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co-opted for sex determination among amphibians. The most efficient mapping strategy was a three-step hierarchical approach, where R. arvalis reads were first mapped to a low-coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex-diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.本研究以沼泽蛙（Rana arvalis）为研究对象，基于野生捕获个体的无创采样策略，开发了一种测序基因分型（genotyping-by-sequencing）方法，用于鉴定其同形性染色体及其在远缘参考基因组中的同源染色体。研究采集同一种群的30只雄性与21只雌性的口腔拭子，构建了双酶切限制性位点相关DNA测序（double-digest RADseq）文库。针对未过滤数据集（共411446个RAD标签）开展性别限制性标记筛选，在筛选杂合度或等位基因频率存在性别差异的标记时，其效果优于过滤后数据集（共33073个RAD标签）的筛选结果。本研究共获得292个推定的性别连锁RAD位点，其中98%的位点指向雄性异配性别决定模式。我们可将其中15个位点比对到热带爪蟾（Xenopus tropicalis）基因组，除1个位点外，其余均定位于1号染色体对——该染色体在两栖动物的性别决定过程中似乎常被共利用。最优的比对策略采用三步分层法：首先将沼泽蛙的测序读段（reads）比对到欧洲林蛙（Rana temporaria）的低覆盖度基因组（分化时长约17百万年），随后将欧洲林蛙的基因组支架（scaffolds）比对到帕克倭蛙（Nanorana parkeri）基因组（分化时长约90百万年），最终将帕克倭蛙的基因组支架比对到热带爪蟾基因组（分化时长约210百万年）。我们通过扩增候选性别决定基因双性和 mab-3 相关转录因子1（Dmrt1，定位于1号染色体）部分序列的聚合酶链式反应（PCR）引物验证了研究结论：所有30只雄性均携带性别诊断性等位基因，而21只雌性均未携带该等位基因。本方法在生物样本和/或基因组资源有限的诸多研究场景中均具备良好的应用潜力。