Séminaire IBIP
Les séminaires ont lieu sur le Campus Montpellier SupAgro/INRA de La Gaillarde (2, place P. Viala Montpellier)

Jeudi 15 mai 2014
Amphi 206 (Cœur d’Ecole) à 14h

Evolution et impact des élements transposables chez les Brassicaceae

Hadi Quesneville
UR INRA 1164 Génomique-Info, Versailles

Little is known about the evolution of the nature and impact of repeated sequences over long periods of times. The genome of several A. thaliana relatives that diverged approx. 5-40 MYA have been sequenced: Arabidopsis lyrata, Capsella rubella, Arabis alpina, Brassica rapa, Thellungiellasalsuginea (formerly Thellungiella halophila), and Schrenkiella parvulum (formerly Thellungiella parvula). As well, the genomes from four other A. thaliana ecotypes have been assembled (Ler-1, Kro-0, Bur-0, and C24). For all these genomes, we have generated a library of consensus repeat sequences that we appended to the Col-0 library ( the reference A. thalina genome) in order to compile a “Brassicaceae” library that was used to annotate the Col-0 genome. Our Brassicaceae TE annotations cover over 31.8 Mb of the A. thaliana genome and appear to achieve highly sensitive detection. We found that most of the copies are detected with better scores by sequences fetched from other Brassicaceae species. When measuring the coverage of TE annotations attributed to consensus sequences from each species, we found that while Col-0 contributes the largest part (36.8%), A. lyrata and B. rapa contribute as much as 17.5 and 25.8%, respectively, with modest (below 6.5%) contributions from other species and the pool of non-Col-0 A. thaliana ecotypes. The fact that most A. thalianacopies can be detected more accurately by consensus sequences built in foreign species is presumably most parsimoniously explainable by differential selective bursts among the Brassicaceae which would rule out the accelerated divergence hypothesis and indicate the long decay of these copies in A. thaliana. The present analysis therefore provides independent evidences supporting the ancient origin of the A. thaliana repeats as well as the chromosome-level distribution of old versus young copies in this species. We found that the majority of the repeats found in the A. thaliana genome are rather ancient and likely to derive from the retention of fragments deposited by ancestral bursts that occurred early during the Brassicaceae evolution. We illustrate the way repeated sequences are composed by mutations towards genomic dark matter over time. We present results illustrating that the repeated sequences evolve in a bimodal fashion with mutation rates first dominated by the deamination of methylcytosines and then by the basal endogenous rates of transitions and transversions. Our results further suggest that the deleterious impact of repeats on gene expression as well as their regulation through small RNA-mediated pathways can last over prolonged periods. We show that a substantial pool of small RNAs corresponds to old repeats suggesting that repeat sequence divergence is accompanied by a diversifying population of small RNAs. We show that repeats have prolonged effects on the expression levels of proximal genes.

Contact : Françoise Gosti

Contacts IBIP :
Sabine Zimmermann
Philippe Nacry
Christine Granier
Chantal Baracco