Abstract
The sequence drafts of wild emmer and bread wheat facilitated high resolution, genome-wide analysis of transposable elements (TEs), which account for up to 90% of the wheat genome. Despite extensive studies, the role of TEs in reshaping nascent polyploid genomes remains to be fully understood. In this study, we retrieved miniature inverted-repeat transposable elements (MITEs) from the recently published genome drafts of Triticum aestivum, Triticum turgidum ssp. dicoccoides, Aegilops tauschii and the available genome draft of Triticum urartu. Overall, 239,126 MITE insertions were retrieved, including 3,874 insertions of a newly identified, wheat-unique MITE family that we named “Inbar”. The Stowaway superfamily accounts for ~80% of the retrieved MITE insertions, while Thalos is the most abundant family. MITE insertions are distributed in the seven homologous chromosomes of the wild emmer and bread wheat genomes. The remarkably high level of insertions in the B sub-genome (~59% of total retrieved MITE insertions in the wild emmer genome draft, and ~41% in the bread wheat genome draft), emphasize its highly repetitive nature. Nearly 52% of all MITE insertions were found within or close (less than 100bp) to coding genes, and ~400 MITE sequences were found in the bread wheat transcriptome, indicating that MITEs might have a strong impact on wheat genome expression. In addition, ~40% of MITE insertions were found within TE sequences, and remarkably, ~90% of Inbar insertions were located in retrotransposon sequences. Our data thus shed new light on the role of MITEs in the diversification of allopolyploid wheat species.
Highlights
The origin of wheat (Triticum-Aegilops group) dates back some 4 million years ago, with the divergence of three ancestral species from a common progenitor, namely Triticum urartu, an unknown Aegilops species from the sitopsis section and Aegilops tauschii [1]
Assessing miniature inverted-repeat transposable elements (MITEs) composition and chromosomal distribution in diploid and polyploid genomes In addition to the genome drafts of two diploid genome donors (A and D genomes), the updated genome drafts of the polyploid wild emmer wheat and bread wheat facilitated detailed analyses of the content, chromosome location and distribution of MITE families and allowed comparative analysis of MITE composition among Triticum and Aegilops species from different ploidy levels in the present study
The consensus sequences of all characterized MITE families in Triticum and Aegilops species were used as queries in MITE analysis kit (MAK) software to retrieve MITE insertions, together with flanking sequences (500 bp from each side), from the genome drafts of T. urartu, Ae. tauschii, T. turgidum ssp. dicoccoides and T. aestivum
Summary
The origin of wheat (Triticum-Aegilops group) dates back some 4 million years ago, with the divergence of three ancestral species from a common progenitor, namely Triticum urartu (donor of the A genome), an unknown Aegilops species from the sitopsis section (donor of the B genome) and Aegilops tauschii (donor of the D genome) [1]. The second event included hybridization between T. turgidum and Ae. tauschii, resulting in the formation of the hexaploid T. aestivum (bread wheat, genome ABD) around 10,000 years ago [1, 3]. Class I TEs, termed RNA elements or retrotransposons, move via a “copy and paste” mechanism involving an RNA intermediate. Class II TEs, termed DNA transposons, translocate via a “cut and paste” mechanism without the involvement of any intermediate molecules [4]. These TE classes can be sub-divided into superfamilies and families, with a given genome possibly consisting of hundreds or thousands of different families. Active TEs can affect genome structure and function [11,12,13]
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