DOI: 10.5061/dryad.f2j00
title: Data from: Recent and dynamic transposable elements contribute to genomic divergence under asexuality

description: 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.
description: ContigsMacra3Taraxacum officinale microspecies Macranthoides accession 3 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.ContigsMacra8Taraxacum officinale microspecies Macranthoides accession 8 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.ContigsMacra11Taraxacum officinale microspecies Macranthoides accession 11 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.ContigsMacra12Taraxacum officinale microspecies Macranthoides accession 12 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.ContigsMacra13Taraxacum officinale microspecies Macranthoides accession 13 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.Histograms of pairwise percentage identity scores of the most abundant transposable element families for all five studied T. officinale accessionsMethods are detailed in the manuscript.Histograms_TE_clusters.zip