Data from: Retrotransposon proliferation coincident with the evolution of dioecy in asparagus

Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or retrotransposon proliferation in dioecious species. We first estimate genome sizes or use published values for four hermaphrodites and four dioecious species distributed across the phylogeny and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements in particular have undergone a marked proliferation in dioecious species. In the absence of a detectable whole genome duplication event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.当前的系统发育采样（phylogenetic sampling）研究表明，天门冬属（Asparagus）中的雌雄异株（dioecy）与XY染色体对（XY sex chromosome pair）仅演化过一次，或至多演化两次。尽管该属存在若干谱系特异性多倍化（polyploidization）事件，但其染色体基数整体相对保守，为2n=2x=20。尽管如此，雌雄异株物种的基因组大小（genome size）往往高于雌雄同体（hermaphroditic）物种。本研究旨在检验：天门冬属雌雄异株物种的基因组扩张现象，是否与其体内发生的多倍化及后续染色体融合，或反转录转座子（retrotransposon）增殖存在关联。我们首先对覆盖该属系统发育分支的4个雌雄同体物种与4个雌雄异株物种进行基因组大小估算，或直接采用已发表的相关数据，结果证实雌雄异株物种的基因组大小通常大于雌雄同体物种。借助系统基因组学方法（phylogenomic approach）开展分析，我们未发现古老多倍化事件会导致所采样的雌雄异株物种基因组增大的证据；但我们找到了支持天门冬属分化前便存在一次古老全基因组复制（whole genome duplication）事件的依据。我们通过随机抽样的全基因组鸟枪测序（whole genome shotgun sequencing）技术，对上述4个雌雄同体物种与4个雌雄异株物种的重复DNA组分进行了表征，并对常见重复序列完成了注释。在我们覆盖范围广泛的系统发育采样中，尤其是Ty-1 Copia类反转录转座子（Ty-1 Copia retroelements）在雌雄异株物种中发生了显著增殖。在未检测到全基因组复制事件的前提下，反转录转座子增殖是解释天门冬属雌雄异株物种基因组大小急剧扩张的最合理解释。