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31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu INRA Clermont Auvergne University

UMR GDEC

Joint Research Unit 1095 Genetics, Diversity and Ecophysiology of Cereals

3. Evolutionary dynamics of transposable elements

Aim: Understanding the impact of TEs on the wheat genome dynamics

Transposable elements (TEs) have encountered an amazing evolutionary success in the Triticeae. Our knowledge about TEs, especially in bread wheat, have been limited for a while by the challenge of accessing large contiguous genomic sequences (Mb-sized).

transposableElements

Therefore, the availability of the high quality sequence of chromosome 3B allowed us to study the TE landscape in wheat and the impact of TEs on the organization and recent evolution of the wheat genome at a scale never reached so far. 

In the PhD thesis of J. Daron (defended in Jan-2015; Daron et al. Genom Biol 2015), we have established a new strategy to annotate TEs in complex genomes, in collaboration with Quesneville's lab at URGI (INRA Versailles), which is based on the development of:

  • CLARI-TE-Rep: a curated library of wheat TEs classified by family
  • CLARI-TE: a bioinformatic tool for automated modeling in TEs in genomic sequences that enables the reconstruction of nested TE clusters (see Figure).

We have identified around 250,000 TEs along the 3B sequence, belonging to 485 families and representing 86% of the sequence. Retrotransposons represent 67% of the genome, confirming their major impact on genome size increase in Triticeae. We also revealed that 16% of this sequence is composed of CACTAs (classe II transposons), 3 times more than previously mentioned. We have estimated the date of the insertion events of around 21,000 LTR-retrotransposons along chromosome 3B in order to get better insights into the dynamics of TE amplification/deletion. It revealed that TEs have been massively amplified by successive bursts between 1 and 3 million years ago but have been mainly silenced since then, suggesting that polyploidization was not followed by massive reactivation of transposition. 

dendrogram of the Fatima family

The distribution of TEs is uneven along the 3B chromosome. The proportion of TEs is lower in the chromosomal extremities. However, this distribution is quite variable depending on the TE families. For example, 22 CACTA families are overrepresented in these extremities, suggesting a role of CACTAs in gene duplications. Indeed, a preferential association between CACTAs and genes originating from recent inter- or intra- duplication has been observed, together with 140 events of TE-mediated gene capture.

We have recently developed a strategy to estimate the level of polymorphism involving structural variations of TEs. Based on this approach, our group is currently estimating more precisely the impact of such TE polymorphisms on gene expression and genome evolution by integrating data from genomics, transcriptomics, epigenomics, and polymorphism.