Recent and dynamic transposable elements contribute to genomic divergence under asexuality

Abstract

BackgroundTransposable 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.ResultsUsing 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3234-9) contains supplementary material, which is available to authorized users.

Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing

“…Relative cluster age was approximated using the among-read divergence profile of each cluster, as previously used for Fritillaria ( Kelly et al 2015 ) and dandelion ( Ferreira de Carvalho et al 2016 ). Briefly, an all-versus-all BLASTn ( Altschul et al 1990 ; Boratyn et al 2013 ) was conducted on a cluster-by-cluster basis using the same BLAST parameters implemented in RepeatExplorer.…”

“…A histogram of pairwise percent identity was generated for each cluster and the trend (i.e., biased toward high-identity, “young” or lower-identity, “older” element reads) was described for each via regression models using R. Specifically, two regression models were used to describe the data as either linear ( Y = a + bX ) or quadratic ( Y = a + bX + cX 2 ), and the model with the highest confidence was determined using the Bayesian Information Criterion ( Schwarz 1978 ). The read similarity profile for each cluster was automatically evaluated for each histogram to determine if the reads trend toward highly similar “young” or more divergent “older” reads, as previously characterized ( Ferreira de Carvalho et al 2016 ) but with an additional category. These categories include the following: 1) positive linear regression; 2) absence of linear regression; 3) negative linear regression; 4) positive quadratic vertical parabola, trend described by right side of vertex; 4b) positive quadratic vertical parabola, trend described by left side of vertex; 5) negative quadratic vertical parabola, trend described by right side of vertex; and 6) negative quadratic vertical parabola, trend described by left side of vertex and vertex at > 99% pairwise-identity ( supplementary fig.…”

Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features

“…The proportion of reads in each cluster is in theory directly related to the genome proportion of repetitive DNA families of the analyzed accession. In all eight runs, the pairwise differences in read abundances for all clusters above a threshold of 0.2% were obtained (Appendix S3); the threshold was adopted from a study on closely related Taraxacum (Ferreira de Carvalho et al., ). The magnitude of intra– and interspecific differences between accessions was assessed statistically by summarizing the absolute differences in proportions of reads across clusters, which were subsequently used in a linear regression mode.…”

Rice siR109944 suppresses plant immunity to sheath blight and impacts multiple agronomic traits by affecting auxin homeostasis

“…Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for host genomes (Lippman et al , ; Ferreira de Carvalho et al , ). Miniature inverted ‐ repeat transposable elements (MITEs) are a class of short non ‐ autonomous DNA transposons derived from full ‐ length DNA transposons that are widespread and abundant in plant genomes (Juretic et al , ; Zhang et al , ).…”

“…Miniature inverted ‐ repeat transposable elements (MITEs) are a class of short non ‐ autonomous DNA transposons derived from full ‐ length DNA transposons that are widespread and abundant in plant genomes (Juretic et al , ; Zhang et al , ). Tourist ‐ like and Stowaway elements are two predominant MITE families that appear to play an essential role in gene and genome evolution, as they are abundant and preferentially inserted into genes (Naito et al , ; Ferreira de Carvalho et al , ; Cho, ). Plants produce 24 ‐ nt siRNAs from repetitive sequences and TEs that trigger DNA methylation at all CG, CHG, and CHH (where H = A, T, or C) sites, resulting in H3K9me2 modification and histone H3K4 demethylation (Piriyapongsa and Jordan, ; Ou‐Yang et al , ; Wei et al , ).…”