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）性状与XY染色体对仅演化过一次，亦存在演化两次的可能性。尽管该属中存在若干谱系特异性多倍化（polyploidization）事件，但天门冬属的基数染色体数2n=2x=20仍相对保守。无论如何，雌雄异株物种的基因组大小（genome size）往往大于雌雄同体（hermaphroditic）物种。本研究旨在探究天门冬属雌雄异株物种的基因组大小扩张，是否与其多倍化、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中的4个雌雄同体物种与4个雌雄异株物种的基因组大小进行估算，或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。通过系统基因组学（phylogenomic）分析方法，我们未发现古多倍化事件对所采样的雌雄异株物种基因组大小扩张存在贡献的证据，但却找到了支持天门冬属分化前曾发生一次古老全基因组复制（whole genome duplication）事件的依据。我们基于随机抽样的全基因组鸟枪法测序（whole genome shotgun sequencing）数据，对上述4个雌雄同体物种与4个雌雄异株物种的重复DNA含量进行了表征，并注释了常见的重复序列元件。在我们覆盖广泛的系统发育采样范围内，尤以Ty-1 Copia型反转录转座子（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。