10.5061/DRYAD.F2J00
Ferreira de Carvalho, Julie
Nederlands Instituut voor Ecologie
de Jager, Victor
Nederlands Instituut voor Ecologie
van Gurp, Thomas P.
Nederlands Instituut voor Ecologie
Wagemaker, Niels C.A.M.
Radboud University Nijmegen
Verhoeven, Koen J.F.
Nederlands Instituut voor Ecologie
Data from: Recent and dynamic transposable elements contribute to genomic
divergence under asexuality
Dryad
dataset
2017
Asexuality
Apomixis
Taraxacum officinale
Methylation
Genome evolution
Dandelion
Transposable elements
2017-09-02T00:00:00Z
2017-09-02T00:00:00Z
en
https://doi.org/10.1186/s12864-016-3234-9
438916445 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
Europe