Data from: Transposon proliferation in an asexual parasitoid

The widespread occurrence of sex is one of the most elusive problems in evolutionary biology. Theory predicts that asexual lineages can be driven to extinction by uncontrolled proliferation of vertically transmitted transposable elements (TEs), which accumulate because of the inefficiency of purifying selection in the absense of sex and recombination. To test this prediction, we compared genome-wide TE load between a sexual lineage of the parasitoid wasp Leptopilina clavipes and a lineage of the same species that is rendered asexual by Wolbachia-induced parthenogenesis. We sequenced the entire genomes of both the sexual and the asexual lineages using next-generation sequencing. We identified transposons of most major classes (including DNA transposons, LTR and LINE-like retrotransposable elements) in both lineages. Quantification of TE abundance using coverage depth showed that copy numbers in the asexual lineage exceeded those in the sexual lineage for DNA transposons, but not LTR and LINE-like elements. However, one or a small number of gypsy-like LTR elements exhibited a four-fold higher coverage in the asexual lineage. Quantitative PCR showed that high loads of this gypsy-like TE were characteristic for 11 genetically distinct asexual wasp lineages when compared to sexual lineages. Bisulfite sequencing revealed no DNA cytosine methylation of the gypsy-like TE in either lineage. We found no evidence for an overall increase in copy number for all TE types in asexuals as predicted by theory. Instead, we suggest that our results are best explained as side-effects of (epi)genetic manipulations of the host genome by Wolbachia. Asexuality is achieved in a myriad of ways in nature, many of which could create similar problems with TE proliferation.

有性生殖的广泛存在，是进化生物学领域最令人困惑的核心问题之一。理论预测，无性繁殖谱系可能因垂直传播的转座因子（Transposable Elements, TEs）不受控地增殖而走向灭绝；由于缺乏有性生殖与重组，纯化选择效率低下，转座因子会不断积累。为验证该理论预测，本研究对棒翅细蜂（Leptopilina clavipes）的有性繁殖谱系，以及被沃尔巴克氏体（Wolbachia）诱导产生孤雌生殖的同种无性繁殖谱系的全基因组转座因子负载量进行了比较。本研究采用下一代测序（next-generation sequencing）技术，对这两个谱系的全基因组进行了测序。本研究在两个谱系中均鉴定出了绝大多数主要类别的转座子，包括DNA转座子（DNA transposons）、长末端重复序列（Long Terminal Repeat, LTR）反转录转座子以及类长散在核元件（Long Interspersed Nuclear Elements, LINE）反转录转座子。通过测序覆盖深度对转座因子丰度进行定量分析的结果显示：无性繁殖谱系中DNA转座子的拷贝数显著高于有性繁殖谱系，但长末端重复序列反转录转座子与类LINE反转录转座子并无此差异。然而，有一类或少数几种类gypsy的LTR反转录转座子在无性繁殖谱系中的覆盖度是有性繁殖谱系的4倍。定量PCR实验结果表明，相较于有性繁殖谱系，11个遗传背景各异的无性寄生蜂谱系均表现出该类gypsy样转座因子的高负载量特征。亚硫酸氢盐测序结果显示，两个谱系中该类gypsy样转座因子均未发生DNA胞嘧啶甲基化修饰。本研究未发现如理论预测的那样，无性繁殖谱系中所有类型转座因子的拷贝数均出现整体上升的证据。据此，本研究认为，研究结果更适合用沃尔巴克氏体对宿主基因组进行（表观）遗传操纵所产生的副效应来解释。自然界中无性生殖的实现途径多种多样，其中许多途径都可能引发转座因子增殖的类似问题。