Data from: Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants

Species with separate sexes (dioecy) are a minority among flowering
plants, but dioecy has evolved multiple times independently in their
history. The sex determination system and sex-linked genomic regions are
currently identified in a limited number of dioecious plants only. Here,
we study the sex-determination system in a genus of dioecious plants that
lack heteromorphic sex chromosomes and are not amenable to controlled
breeding: Nepenthes pitcher plants. We genotyped wild populations of
flowering males and females of three Nepenthes taxa using ddRAD-seq, and
sequenced a male inflorescence transcriptome. We developed a statistical
tool (privacy rarefaction) to distinguish true sex-specificity from
stochastic noise in read coverage of sequencing data from wild populations
and identified male-specific loci and XY-patterned SNPs in all three
Nepenthes taxa, suggesting the presence of homomorphic XY sex chromosomes.
The male-specific region of the Y chromosome showed little conservation
among the three taxa, except for the essential pollen development gene
DYT1 which was confirmed as male-specific by PCR in additional Nepenthes
taxa. Hence, dioecy and part of the male-specific region of the Nepenthes
Y-chromosomes likely have a single evolutionary origin.

雌雄异株（dioecy）物种在被子植物中占比甚少，但在其演化历史中，雌雄异株已独立起源多次。目前，仅在少数雌雄异株植物中鉴定出性别决定系统与性连锁基因组区域。本研究聚焦于一类缺乏异形性染色体且难以开展受控繁育的雌雄异株植物属——猪笼草属（Nepenthes）的性别决定系统。我们采用ddRAD测序（ddRAD-seq）对3个猪笼草类群的野生开花种群（包含雄性与雌性个体）进行了基因分型，并对雄性花序转录组进行了测序。我们开发了一款名为隐私稀疏化（privacy rarefaction）的统计工具，用于从野生种群测序数据的reads覆盖度中区分真实的性别特异性信号与随机噪声，并在3个猪笼草类群中均鉴定出雄性特异性位点及XY型单核苷酸多态性（SNPs），提示存在同形XY性染色体。Y染色体的雄性特异性区域在3个类群间保守性极低，唯有花粉发育必需基因DYT1例外；该基因在额外猪笼草类群中经聚合酶链式反应（PCR）验证为雄性特异性。综上，雌雄异株及猪笼草Y染色体部分雄性特异性区域可能起源于单次演化事件。