Abstract
BackgroundTransposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes.ResultsThe overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.ConclusionsEven though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.
Highlights
Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution
TE content and distribution along the 21 bread wheat chromosomes Building from a decade-long effort from the wheat genomics community, we used the accumulated knowledge about TEs to precisely delineate the TE repertoire of the 21 chromosomes based on a similarity search with a high-quality TE databank: ClariTeRep [17] which includes TREP [19]
This represents 3050 manually annotated and curated TEs carried by the three subgenomes and mainly identified on bacterial artificial chromosome (BAC) sequences obtained during map-based cloning or survey sequencing projects, especially on chromosome 3B [20]
Summary
Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. Transposable elements (TEs) are ubiquitous components of genomes and one of the major forces driving genome evolution [1]. They are classified into two classes: retrotransposons (class 1), transposing via reverse transcription of their messenger RNA (mRNA), and DNA transposons (class 2), representing all other types of elements [2]. At the whole genome level, Makarevitch et al have shown that four to nine maize TE families, including all major class I superfamilies (Gypsy, Copia, long interspersed nuclear elements (LINEs)), and DNA transposons, are enriched (more than twofold) in promoters of genes being up-regulated in response to different abiotic stresses [15]. This study suggested that TEs are a major source of allelic variations explaining differential response to stress between accessions
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