The Arabidopsis thaliana mobilome and its impact at the species level.

Leandro Quadrana,Robert A Martienssen,Chantal Leblanc,Vincent Colot,Amanda Bortolini Silveira,George F Mayhew,Jeffrey A Jeddeloh

doi:10.7554/elife.15716

Abstract

Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.

Highlights

Transposable elements (TEs) are sequences that move and replicate around the genome
To limit the problem posed by the presence of TEs in multiple copies across the genome, with varying degrees of similarity to each other, we performed an aggregated CNV analysis based on the 11,851 annotated Col-0 TE sequences longer than 300 bp
CNVs were detected for 263 TE families (Figure 1A and B; Figure 1—source data 1; see ‘Materials and methods’), in keeping with the results of a previous study indicating that the vast majority of the TE sequences annotated in the Col-0 reference genome are absent from that of at least one of 80 accessions analyzed (Cao et al, 2011)

Summary

Introduction

Transposable elements (TEs) are sequences that move and replicate around the genome Depending on whether their mobilization relies on a RNA or DNA intermediate, they are classified as retrotransposons (class I) or DNA transposons (class II), respectively (Slotkin and Martienssen, 2007). TEs are further subdivided into distinct families, the prevalence of which differs between organisms because of a complex array of factors, including variable transposition activity and diverse selection pressures (Barron et al, 2014). Given their mobile nature, TEs pose multiple threats to the physical and functional integrity of genomes. A major control is through epigenetic silencing mechanisms, including DNA methylation and these mechanisms can in turn have ’epimutagenic’ effects on adjacent

Methods

Results

Conclusion