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 Taraxacum officinale and compare it between five accessions from the same apomictic lineage. The main objective of this study is to evaluate extent of within-lineage divergence attributed to TE content and activity. We examined 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. All TE families are transcribed with low-abundant genomic clusters exhibiting higher level of transcription. Using bisulfite reduced representation sequencing, we detected 18.9% of CG 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 differentially transcribed and methylated within the apomictic lineage including 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. Indeed, this additional genetic diversity could be needed in clonally reproducing species facing environmental heterogeneity. We speculate that accession-specific TE families both transcriptionally and epigenetically variable are more prone to trigger changes in expression on nearby coding sequences. These findings are of tremendous interest to further look at the importance of TE-induced mutations on functional genes during asexual genome evolution.