Abstract
BackgroundThe 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far.ResultsWe develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation.ConclusionAccurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0546-4) contains supplementary material, which is available to authorized users.
Highlights
The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization
An improved procedure for predicting transposable element models and their nested pattern in a complex genome Predicting TE features in complex genomes where repeated elements represent more than 80% of the sequence remains a computational challenge, and obtaining a high quality annotation still requires manual curation
There are incongruencies in the classification of the TEs; most of the TEs were assigned a family name based on their best BLAST hit, which can lead to an overestimation of the family numbers [44]
Summary
The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of TEs on the complex wheat genome structure and evolution at a resolution and scale not reached so far. First discovered in maize [1], transposable elements (TEs) are ubiquitous components of almost every eukaryotic genome investigated so far and their impact on genome structure and evolution is well established (reviewed in [2]). No evidence for a direct relationship between genetic recombination rate and DNA transposon abundance has been provided so far in plant genomes [18], whereas it was observed in Caenorhabditis elegans [19]. A key aspect of DNA transposons is their interaction with host genes [20]. In rice, 2,809 Pack-Mutator-like elements (Pack-MULEs) containing host gene fragments were identified [23]
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