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.现有系统发育采样结果表明，天门冬属（Asparagus）内的雌雄异株（dioecy）性状与XY染色体对仅演化出现过一次，亦可能存在两次独立起源。尽管该属中存在若干谱系特异性多倍化（polyploidization）事件，但其基础染色体数2n=2x=20仍相对保守。即便如此，雌雄异株物种的基因组大小（genome size）通常仍大于雌雄同株（hermaphroditic）物种。本研究旨在探究天门冬属雌雄异株物种的基因组扩张现象，是否与其内的多倍化事件、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属系统发育树上的4个雌雄同株物种与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普遍大于雌雄同株物种。通过系统发育组学（phylogenomic）分析方法，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，但确实找到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。我们基于随机全基因组鸟枪法测序（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组分进行了解析，并对常见重复序列元件进行了注释。在本次大范围系统发育采样范围内，尤以Ty1-Copia反转录转座子（Ty-1 Copia retroelements）在雌雄异株物种中出现了显著的增殖现象。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导致天门冬属雌雄异株物种基因组出现急剧扩张的最合理解释。