Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants

Abstract

BackgroundAsexual 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.ResultsUsing 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2524-6) contains supplementary material, which is available to authorized users.

Recent and dynamic transposable elements contribute to genomic divergence under asexuality

“…Macranthoides is a geographically widespread apomictic dandelion lineage, also referred to as a microspecies, that can be identified by expert taxonomist and whose unique clonal nature was confirmed by identical multi-locus microsatellite genotypes [25]. The same five accessions were previously screened for heritable divergence in gene expression using RNA-Seq [26]. The accessions were identified by Taraxacum taxonomists and sampled in Germany and Czech Republic from 3 different field locations (maximum distance 300 km) during spring 2012 (Additional file 1).…”

“…From a previous study, we developed Illumina transcriptomic resources for these same T. officinale Macranthoides accessions [26]. For each accession, contigs assembled through the RepeatExplorer pipeline were used as a new TE database to which genomic and transcriptomic Illumina reads were mapped.…”

“…This process has led to numerous widespread apomictic lineages [25]. We observed previously that active TE and TE-related genes are an important component of transcriptomic divergence within such apomictic lineages [26]. We hypothesized that recent and dynamic TEs are triggering most of the genomic differences observed within apomictic lineages.…”

Epigenetic inheritance in apomictic dandelions : stress-induced and heritable modifications in DNA methylation and small RNA

“…All reads with length <18nt and >30nt were filtered out. Reads were aligned with BWA (Li & Durbin 2009) to: i) a dandelion transcriptome (Ferreira de Carvalho et al 2016) and ii) a small subset of dandelion genomic reference from BAC sequences, only considering perfect matches. Multiple mapping sRNA reads were assigned a random mapping location.…”

“…All consensus BAC sequences were pooled together and sequences were searched for repeats using Repeatmasker version 2.2.27 (with query species Arabidopsis), which resulted in 244 sequences consisting of 178 (6.7%) retroelements and 35 (0.4%) DNA transposons. The transcriptome was assembled de novo from RNAseq data (Ferreira de Carvalho et al 2016), which resulted in a total of 123,232 transcripts of which 39,685 transcripts were annotated to TAIR genes (using BLASTn). The relative number of different sRNA length classes was calculated and compared between groups of grandparental control and stress treatment (drought or SA).…”