Data from: Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Background: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage. The main objective of this study is to evaluate the extent of within-lineage divergence attributed to TE content and activity. We examined the repetitive genomic contribution, diversity, transcription and methylation changes to characterize accession-specific TEs. Results: Using low-coverage genomic sequencing, we report a highly heterogeneous TE compartment in the triploid apomict T. officinale representing up to 38.6 % of the homoploid genome. The repetitive compartment is dominated by LTR retrotransposon families accompanied by few non-LTR retrotransposons and DNA transposons. Up to half of the repeat clusters are biased towards very high read identity, indicating recent and potentially ongoing activity of these TE families. Interestingly, the five accessions are divided into two main clades based on their TE composition. Clade 2 is more dynamic than clade 1 with higher abundance of Gypsy Chromovirus sequences and transposons. Furthermore, a few low-abundant genomic TE clusters exhibit high level of transcription in two of the accessions analysed. Using reduced representation bisulfite sequencing, we detected 18.9 % of loci differentially methylated, of which 25.4 and 40.7 % are annotated as TEs or functional genes, respectively. Additionally, we show clear evidence for accession-specific TE families that are differentially transcribed and differentially methylated within the apomictic lineage, including one Copia Ale II LTR element and a PIF-Harbinger DNA transposon. Conclusion: We report here a very young and dynamic repetitive compartment that enhances divergence within one asexual lineage of T. officinale. We speculate that accession-specific TE families that are both transcriptionally and epigenetically variable are more prone to trigger changes in expression on nearby coding sequences. These findings emphasize the potential of TE-induced mutations on functional genes during asexual genome evolution.

研究背景：转座因子（Transposable elements, TEs）是可移动的遗传信息片段，对宿主基因组具有较高的诱变潜力。转座作用通常呈中性或有害性，但也可能产生具有潜在适应性的遗传变异。这类额外的变异来源在进行无性繁殖的非重组物种中尤为关键。然而，目前仍缺乏相关证据，用以明确转座因子在植物无性基因组进化中的作用及其相关效应。
本研究对普通蒲公英（Taraxacum officinale）基因组的重复序列组分进行了表征，并对来自同一无融合生殖谱系的5个种质开展比较分析。本研究的核心目标是评估由转座因子含量与活性所导致的谱系内分化程度。我们通过分析重复基因组的组分贡献、序列多样性、转录活性及甲基化修饰变化，来表征种质特异性的转座因子。

研究结果：通过低覆盖度基因组测序，我们在三倍体无融合生殖物种普通蒲公英中发现了高度异质性的转座因子组分区段，其占同倍体基因组的比例最高可达38.6%。该重复序列组分以长末端重复序列（LTR）反转录转座子家族为主，同时伴随少量非长末端重复序列（non-LTR）反转录转座子与DNA转座子。近半数的重复序列簇呈现极高的读段一致性，表明这些转座因子家族近期且可能仍处于活跃状态。
值得注意的是，基于转座因子组成，这5个种质可划分为两个主要进化枝。进化枝2相较于进化枝1更为活跃，其Gypsy Chromovirus序列与转座子的丰度更高。此外，在所分析的2个种质中，少量低丰度基因组转座因子簇呈现出高水平的转录活性。
通过简化代表性亚硫酸氢盐测序（reduced representation bisulfite sequencing），我们检测到18.9%的位点存在差异甲基化，其中分别有25.4%和40.7%的位点被注释为转座因子或功能基因。此外，我们还找到了明确证据，证明该无融合生殖谱系中存在种质特异性的转座因子家族，其转录与甲基化水平均存在差异，包括1个Copia Ale II型LTR转座元件与1个PIF-Harbinger型DNA转座子。

研究结论：本研究揭示了一个极为年轻且具有动态性的重复序列组分，该组分可加剧普通蒲公英单个无性谱系内的分化。我们推测，同时在转录与表观遗传层面存在变异的种质特异性转座因子家族，更易引发邻近编码序列的表达变化。上述研究结果凸显了在无性基因组进化过程中，转座因子诱导的功能基因突变所具备的潜在价值。