Abstract
Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they might have occurred via unequal intra-strand recombination or double-strand break (DSB) events. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.
Highlights
Introduction ofDNA fragments of unidentified origin into the wheat genome
1,761 full length Fatima insertions were retrieved from the wild emmer genome and 1,741 full length Fatima insertions were retrieved from the bread wheat genome
268 Fatima insertions were retrieved from chromosome 3B and 274 Fatima insertions were retrieved from chromosome 5B, while in bread wheat, 274 Fatima insertions were retrieved from chromosome 3B and 277 Fatima insertions were retrieved from chromosome 5B
Summary
Introduction ofDNA fragments of unidentified origin into the wheat genome. The indel in chromosome 5B locus 5B5 (Table 1) was revealed based on sequence alignment of the flanking sequences of a wild emmer-specific Fatima insertion into bread wheat chromosome 5B. The third PCR amplification used a forward primer based on the 11 kb bread wheat-specific sequence and the same reverse primer based on sequence located downstream to the indel, as used in the previously described reaction This third PCR resulted in amplification of both of the examined bread wheat accessions, yet no amplification was observed for wild emmer (Fig 2J). The 11 kb sequence insertion found in locus 5B5 in the bread wheat genome was not identified within the wild emmer or Ae. tauschii (the donor of the D sub-genome) genomes based on sequence alignment. This phenomenon might be caused by an introgression of a novel sequence into the wheat genome. The second allopolyploidization event that occurred ~10,000 years ago included hybridization of the domesticated emmer and Aegilops tauschii (donor of the D genome) and led to the generation of the bread wheat T. aestivum (genome AABBDD) [3,6].
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