Transposable elements are important contributors to standing variation in gene expression inCapsella grandiflora

Abstract

Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect phenotypic variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterised TE insertion polymorphisms and their effects on gene expression in 124 wholegenome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of rare single nucleotide polymorphisms (SNPs). The frequency of insertions was negatively correlated with distance to genes, as well as density of conserved non-coding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up-and down-regulation, but have a weaker effect than TEs. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are more likely than rare SNPs to cause extreme changes in gene expression.

The impact of transposable elements on tomato diversity

“…Despite a relatively narrow genetic diversity, the more than 25,000 cultivars grown around the world today exhibit an extraordinary phenotypic diversity, and the underlying allelic variants are being progressively identified, thanks to the advent of high-throughput genome sequencing. Here, we show that TIPs, which to date have been ignored from population genomic studies in tomato, are an important diversifying force to consider, as has been proposed for other plant species 27,33,34,[50][51][52][53][54][55] . For instance, GWAS in rice for grain length and width using respectively structural variants and TIPs uncovered associations that could not be detected using SNP data 8,9 .…”

The impact of transposable elements on tomato diversity

“…Despite a relatively narrow genetic diversity, the 25,000 cultivars grown around the world today exhibit an extraordinary phenotypic diversity and the underlying allelic variants are being progressively identified thanks to the advent of high-throughput genome sequencing. In this context, we show that TIPs, which to date have been ignored from population genomic studies in tomato, are an important diversifying force to consider, as has been proposed for other plant species 27,33,34,[52][53][54][55][56][57] . In particular, most TE insertions are low frequency variants, they are typically not tagged by SNPs, representing a previously uncharacterized source of phenotypic variation.…”

“…In many organisms, including plants and animals, TIPs have been associated with large transcriptomic changes 14,27,[32][33][34] . To assess the impact of TIPs on gene expression in tomato we used RNA-seq data obtained from breaker fruits for 400 accessions 35 .…”

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

“…A vast majority of the genes in the A. setaceus genome were functionally annotated. Repetitive sequences, mainly consisting of TEs, constitute a major fraction of eukaryotic genomes and play vital roles in genome evolution 27,28 , chromosome rearrangement 29 , and gene regulation 30 . Repetitive sequences occupied 65.59% of the A. setaceus genome assembly; this percentage is very similar to that in the A. officinalis genome (69%).…”