Publications des scientifiques de l'IRD

Guyot Romain, Darre T., Dupeyron M., Kochko Alexandre de, Hamon Serge, Couturon Emmanuel, Crouzillat D., Rigoreau M., Rakotomalala J. J., Raharimalala N. E., Akaffou S. D., Hamon Perla. (2016). Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories. Molecular Genetics and Genomics, 291 (5), p. 1979-1990. ISSN 1617-4615.

Titre du document
Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories
Année de publication
2016
Type de document
Article référencé dans le Web of Science WOS:000382145100014
Auteurs
Guyot Romain, Darre T., Dupeyron M., Kochko Alexandre de, Hamon Serge, Couturon Emmanuel, Crouzillat D., Rigoreau M., Rakotomalala J. J., Raharimalala N. E., Akaffou S. D., Hamon Perla
Source
Molecular Genetics and Genomics, 2016, 291 (5), p. 1979-1990 ISSN 1617-4615
The Coffea genus, 124 described species, has a natural distribution spreading from inter-tropical Africa, to Western Indian Ocean Islands, India, Asia and up to Australasia. Two cultivated species, C. arabica and C. canephora, are intensively studied while, the breeding potential and the genome composition of all the wild species remained poorly uncharacterized. Here, we report the characterization and comparison of the highly repeated transposable elements content of 11 Coffea species representatives of the natural biogeographic distribution. A total of 994 Mb from 454 reads were produced with a genome coverage ranging between 3.2 and 15.7 %. The analyses showed that highly repeated transposable elements, mainly LTR retrotransposons (LTR-RT), represent between 32 and 53 % of Coffea genomes depending on their biogeographic location and genome size. Species from West and Central Africa (Eucoffea) contained the highest LTR-RT content but with no strong variation relative to their genome size. At the opposite, for the insular species (Mascarocoffea), a strong variation of LTR-RT was observed suggesting differential dynamics of these elements in this group. Two LTR-RT lineages, SIRE and Del were clearly differentially accumulated between African and insular species, suggesting these lineages were associated to the genome divergence of Coffea species in Africa. Altogether, the information obtained in this study improves our knowledge and brings new data on the composition, the evolution and the divergence of wild Coffea genomes.
Plan de classement
Sciences du monde végétal [076]
Description Géographique
AFRIQUE ; ZONE TROPICALE ; ASIE DU SUD ; OCEAN INDIEN ILES ; MADAGASCAR ; INDE ; INDONESIE
Localisation
Fonds IRD [F B010068137]
Identifiant IRD
fdi:010068137
Contact