Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that non-recombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole genome scans that the sex-associated region in P. trichocarpa is small and much younger than the age of the genus. This indicates that sex-determination is highly labile in poplar, consistent with recent evidence of "turnover" of sex determination regions in animals. We performed whole genome resequencing of 52 Populus trichocarpa (black cottonwood) and 34 P. balsamifera (balsam poplar) individuals of known sex. Genome-wide association studies (GWAS) in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 Kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex associated SNPs revealed this to be an XY sex determining system. Estimated divergence times of X and Y haplotype sequences (6-7 MYA) are much more recent than the divergence of P. trichocarpa (poplar) and P. tremuloides (aspen). Consistent with this, in P. tremuloides we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.杨属（Populus）的所有物种均为雌雄异株，该性状的起源被认为十分古老。尽管存在部分实证反例，但理论预测不发生重组的性连锁区域会快速扩散，最终演化出异型性染色体。与之相反，本研究通过全基因组扫描发现，三角叶杨（P. trichocarpa）的性相关区域规模极小，且其演化时间远晚于杨属的起源时间。这表明杨树的性别决定机制具有高度不稳定性，这与近期动物界性决定区域发生"turnover"的研究证据相符。本研究对52株已知性别的三角叶杨（P. trichocarpa，美洲黑杨）以及34株已知性别的香脂杨（P. balsamifera）个体进行了全基因组重测序。对这些无群体结构的种群进行全基因组关联分析（GWAS），共鉴定出650个与性别显著相关的单核苷酸多态性位点（SNP）。本研究估算性连锁区域的大小约为100千碱基对（Kbp）。尽管在参考基因组2.2版本中，这些与性别显著相关的单核苷酸多态性位点被定位到6条不同染色体（外加3个未定位的支架序列（scaffold））上，但它们均处于高度连锁不平衡状态。本研究证实，该现象极有可能源于基因组组装错误。与性别相关的单核苷酸多态性位点的分离模式表明，该物种的性别决定系统为XY型。X与Y单倍型序列的估算分化时间（600万至700万年前）远晚于三角叶杨（P. trichocarpa）与美洲山杨（P. tremuloides，颤杨）的分化时间。与此一致，本研究在美洲山杨中未发现三角叶杨性决定区域内存在XY单倍型分化。因此这两个物种的性别决定基因组架构存在差异，暗示其在近期至少发生过一次性决定区域的更替事件。