Abstract
Key messageHere, we show thatAuSINE elements have strong associations with protein-coding genes in wheat. Most importantlyAuSINE 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. 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 SINE-containing 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 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.
Highlights
Transposable elements (TEs) make up a large fraction of plant genomes (Kidwell 2002), as they can reach up to 90%Communicated by Mark C
The updated genome draft sequence of T. aestivum was published for each chromosome separately, which allowed the analysis of Au Short INterspersed Nuclear Elements (SINEs) content in each one of the three subgenomes (A, B and D), and analysis of the distribution of Au SINE in the seven homoeologous chromosomes
The copy number of Au SINE in the allohexaploid T. aestivum genome was ~ tenfold its copy number in the diploid genomes, T. urartu and Ae. tauschii, indicating the massive retrotransposition burst of Au SINE following allopolyploidization events; most probably, the retrotransposition burst occurred following allotetraploidization because a similar content of Au SINE was found in the genome draft of Triticum turgidum ssp. dicoccoides
Summary
Transposable elements (TEs) make up a large fraction of plant genomes (Kidwell 2002), as they can reach up to 90%Communicated by Mark C. Transposable elements (TEs) make up a large fraction of plant genomes (Kidwell 2002), as they can reach up to 90%. Several SINE families have been discovered in plants, such as in Brassica napus (Deragon et al 1994) Oryza sativa (Hirano et al 1994), Nicotiana tabacum (Yoshioka et al 1993), Myotis daubentonii (Borodulina and Kramerov 1999) and others (Deragon and Zhang 2006; Wenke et al 2011). The impact of SINEs on plant genomes is poorly studied, while it has been well studied in mammalians, e.g., MIR and Alu elements (Deininger and Batzer 1999; Lev-Maor et al 2003; Makalowski 2003; Schmid 1998; Schmitz and Brosius 2011; Smit 1996, 1999)
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