10.5061/DRYAD.6P2N6
Ferreira de Carvalho, Julie
Nederlands Instituut voor Ecologie
Oplaat, Carla
Nederlands Instituut voor Ecologie
Pappas, Nikolaos
Wageningen University & Research
Derks, Martijn
Wageningen University & Research
de Ridder, Dick
Wageningen University & Research
Verhoeven, Koen J. F.
Nederlands Instituut voor Ecologie
Data from: Heritable gene expression differences between apomictic clone
members in Taraxacum officinale: insights into early stages of
evolutionary divergence in asexual plants
Dryad
dataset
2017
Apomixis
Transposable elements
Taraxacum officinale
Functional Divergence
Dandelion
2017-02-10T00:00:00Z
2017-02-10T00:00:00Z
en
https://doi.org/10.1186/s12864-016-2524-6
150849321 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: Asexual reproduction has the potential to enhance deleterious
mutation accumulation and to constrain adaptive evolution. One source of
mutations that can be especially relevant in recent asexuals is activity
of transposable elements (TEs), which may have experienced selection for
high transposition rates in sexual ancestor populations. Predictions of
genomic divergence under asexual reproduction therefore likely include a
large contribution of transposable elements but limited adaptive
divergence. For plants empirical insight into genome divergence under
asexual reproduction remains limited. Here, we characterize expression
divergence between clone members of a single apomictic lineage of the
common dandelion (Taraxacum officinale) to contribute to our knowledge of
genome evolution under asexuality. Results: Using RNA-Seq, we show that
about one third of heritable divergence within the apomictic lineage is
driven by TEs and TE-related gene activity. In addition, we identify
non-random transcriptional differences in pathways related to acyl-lipid
and abscisic acid metabolisms which might reflect functional divergence
within the apomictic lineage. We analyze SNPs in the transcriptome to
assess genetic divergence between the apomictic clone members and reveal
that heritable expression differences between the accessions are not
explained simply by genome-wide genetic divergence. Conclusion: The
present study depicts a first effort towards a more complete understanding
of apomictic plant genome evolution. We identify abundant TE activity and
ecologically relevant functional genes and pathways affecting heritable
within-lineage expression divergence. These findings offer valuable
resources for future work looking at epigenetic silencing and
Cis-regulation of gene expression with particular emphasis on the effects
of TE activity on asexual species’ genome.
de novo transcriptome assembly of dandelion leaf tissueIllumina sequencing
Trinity assemblyTrinity.fastaField experiment raw count tableraw count of
reads mapping the reference transcriptome using RSEM (semi-natural field
experiment)F_Trinity_genes.counts.matrixGreenhouse experiment raw count
tableraw count of reads mapping the reference transcriptome using RSEM
(greenhouse experiment)GH_Trinity_genes.counts.matrix
Europe