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

<p>Danielle Keidar Friedman, Chen Doron and Khalil Kashkush</p>

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

Danielle Keidar Friedman, Chen Doron and Khalil Kashkush

Ben Gurion University, Israel

: J Plant Physiol Pathol

Abstract

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. 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 (Short Interspersed Nuclear Elements), which was found to be widespread in plant species. Then, we have performed site-specific PCR and realtime RT-PCR analyses to assess the possible impact of Au SINE on gene structure and function. To this end, we retrieved 133, 180 and 1886 intact Au SINE insertions from T. urartu, Ae. tauschii and T. aestivum genome drafts, respectively. The 1886 Au SINE insertions were distributed in the seven homoeologous chromosomes of T. aestivum, while ~67% of the insertions were associated with genes. Detailed analysis of 40 genes harboring Au SINE revealed allelic variation of those genes in the Triticum-Aegilops genus. In addition, expression analysis revealed that both regular transcripts and alternative Au SINEcontaining transcripts were simultaneously amplified in the same tissue, indicating retention of Au SINE-containing introns. Analysis of the wheat transcriptome revealed that hundreds of protein-coding genes that harbor Au SINE in at least one of their mature splice variants. Au SINE might play a prominent role in speciation by creating transcriptome variation.

Biography

Danielle Keidar Friedman is a PhD Candidate at Ben Gurion University, Israel. Her study focuses on transposable elements dynamics in allopolyploid wheat species. She is studying SINE (Short Interspersed Nuclear Elements) and MITE (Miniature Inverted-repeat Transposable Elements) proliferation following polyploidization events, their possible impact on gene expression and regulation and their mode of transposition.