Genome-wide analysis of a recently active retrotransposon, Au SINE, in wheat: content, distribution within subgenomes and chromosomes, and gene associations.

ABSTRACT:

Key message

Here, we show that Au SINE elements have strong associations with protein-coding genes in wheat. Most importantly Au SINE insertion within introns causes allelic variation and might induce intron retention. The impact of transposable elements (TEs) on genome structure and function is intensively studied in eukaryotes, especially in plants where TEs can reach up to 90% of the genome in some cases, such as in wheat. Here, we have performed a genome-wide in-silico analysis using the updated publicly available genome draft of bread wheat (T. aestivum), in addition to the updated genome drafts of the diploid donor species, T. urartu and Ae. tauschii, to retrieve and analyze a non-LTR retrotransposon family, termed Au SINE, which was found to be widespread in plant species. T

SUBMITTER: Keidar D 

PROVIDER: S-EPMC5787218 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature