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研究显示，天门冬属（Asparagus）中的雌雄异株（dioecy）性状与XY性染色体对仅演化过一次，亦有可能演化过两次。尽管该属中存在若干谱系特异性多倍化（polyploidization）事件，但天门冬属的基础染色体数2n=2x=20整体相对保守。即便如此，雌雄异株物种的基因组尺寸往往大于雌雄同株（hermaphroditic）物种。本研究旨在探究天门冬属雌雄异株物种的基因组尺寸扩张，是否与该类群中的多倍化事件、后续染色体融合或反转录转座子（retrotransposon）增殖存在关联。我们首先对分布于该系统发育树不同分支的4个雌雄同株物种与4个雌雄异株物种的基因组尺寸进行估算，或直接采用已发表的相关数据，结果再次证实雌雄异株物种的基因组尺寸普遍大于雌雄同株物种。通过系统发育基因组学（phylogenomic）分析方法，我们未发现采样的雌雄异株物种存在可解释其基因组尺寸扩张的古老多倍化事件证据，但确实发现了支持天门冬属物种分化前存在一次古老全基因组复制（whole genome duplication）事件的证据。我们基于随机采样的全基因组鸟枪测序（whole genome shotgun sequencing）数据，对上述4个雌雄同株与4个雌雄异株物种的重复DNA组分进行了表征，并对常见重复序列元件完成了注释。在本次大范围系统发育采样范围内，尤以Ty-1 Copia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尺寸急剧扩张的最合理解释。