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Dynamique et évolution de deux lignées remarquables de rétrotransposons à LTR dans le genre Coffea (famille des Rubiacées)

Abstract : Transposable elements (TEs) are DNA fragments that are able to move and to increase their copy numbers. Two transposition mechanisms corresponding to the two main TE classes are found in almost all organisms. LTR retrotransposons (Long Terminal Repeats, LTR-RTs), belonging to Class 1, are the main components of plant genomes. Genome organisation, size variation, evolution and gene activity can be strongly impacted by their proliferation.Worldwide consumed and produced by South countries, coffee is obtained from two African cultivated species: Coffea arabica and C. canephora. The Coffea genus includes 139 species occurring in diverse habitats in Africa, Madagascar, Mascarene Islands, Comoros, India, Southeast and Tropical Asia and North Australia. All the species are diploids, except the noteworthy allotetraploid C. arabica, originated from a recent inter-specific hybridisation between two diploids: C. canephora and C. eugenioides. However, genome size of diploid species can vary for up to two folds. Today, the numerous genomic data available for Coffea allows the study of LTR- RTs, constituting at least 42% of C. canephora genome, the sequenced species available in public databases.In this work, two notable LTR-RT lineages, Bianca and SIRE, have been studied by bioinformatics approaches. Bianca s.s., is present only in Monocots and it is represented in Dicots by the Divo family, poorly studied nowadays. The recent activation of Divo, without leading to its own structuring, is closely associated to the genetic differentiation of C. canephora. However, this activation seems sporadic as being present in all the coffee-trees species studied here. On the opposite, SIRE elements, which are the only Copia LTR-RTs carrying an envelope-like gene as retroviruses, show an important structuring variation between accessions among C. arabica progenitors, and in parallel to the genus evolution.Our work shows that understanding the LTR-RTs dynamics in a genus allows a better perception of its evolutionary history, with the possibility of different evolutionary timing given by different LTR-RTs families. Our results also indicate that both the biogeographic clades (coffee molecular phylogeny) and also some diploid accessions have peculiar histories, probably related to the colonisation of new ecological niches and to the LTR- RTs dynamics.
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Submitted on : Wednesday, February 21, 2018 - 12:05:11 PM
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Mathilde Dupeyron. Dynamique et évolution de deux lignées remarquables de rétrotransposons à LTR dans le genre Coffea (famille des Rubiacées). Biologie végétale. Université Montpellier, 2017. Français. ⟨NNT : 2017MONTT128⟩. ⟨tel-01714153⟩

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