Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data

Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.

石刁柏（Asparagus officinalis）是一种兼具重要经济与营养价值的蔬菜作物，被广泛栽培，同时作为研究植物性别决定与性染色体进化的模式雌雄异株物种得到广泛应用。为加深对其基因组组成的理解，尤其是针对占基因组绝大多数的转座因子（transposable elements, TEs），我们对雌雄石刁柏基因组开展了Illumina HiSeq2000测序，并随后进行了生物信息学分析。本研究共获得17吉碱基对（Gb）的测序数据，测序深度达12×，经组装得到163406个支架序列（scaffolds），总累积长度为400兆碱基对（Mbp），约占石刁柏全基因组的30%。总体而言，转座因子覆盖了该组装序列中约53%的区域。所鉴定出的转座因子绝大多数属于长末端重复序列反转录转座子（LTR retrotransposons），这类元件约占基因组DNA的28%；其中Ty1/copia型反转录转座子相较于Ty3/gypsy型，具有更高的多样性与拷贝数。相较于长末端重复序列反转录转座子，非长末端重复序列反转录转座子与DNA转座子的占比相对较低。此外，对雌雄基因组中转座因子类群的丰度比较显示，整体转座因子组成高度相似，仅少数类群的丰度存在细微差异，这与石刁柏性染色体起源时间较近的结论相符。本研究极大地提升了我们对石刁柏重复序列结构的认知，有助于筛选参与植物性染色体早期进化的转座因子，也为该雌雄异株植物的后续研究提供了有力支撑。