Evolutionary Dynamics Of Transposable Elements In The Hexaploid Wheat Genome

We have undertaken the complete sequencing of the wheat chromosome 3B which accounts for nearly 1 Gb. It was assembled into less than 5000 scaffolds and the construction of a pseudomolecule is underway, providing an opportunity to study the dynamics of transposable elements (TEs) at a scale never reached so far in a giant and polyploid genome. To provide a high quality annotation of the TE content we first developed new resources to accurately predict TE models, and automatically reconstruct the structure of nested TE clusters that are numerous in the wheat genome. (1) A manually curated library of 4929 previously identified TEs was produced as a basis for similarity-based search. (2) The clariTE program was developed to postprocess similarity search outputs. ClariTE was evaluated on 1Mb of manually curated sample sequences. It significantly improved the sensitivity and specificity of automated TE predictions compared to RepeatMasker. The 1000 Mb of the 3B chromosome were annotated using clariTE and analyzed in terms of TE composition and organization. Novel results concerning the distribution of TE families along wheat chromosomes, association with genes, and their impact on adjacent gene expression and on genome evolution will be presented.