Journal Article

Partial sequencing reveals the transposable element composition of Coffea genomes and provides evidence for distinct evolutionary stories

Dupeyron, Mathilde, Crouzillat, Dominique, Rakotomalala, Jean-Jacques, Akaffou, Sélastique Doffou, de Kochko, Alexandre, Hamon, Serge, Rigoreau, Michel, Guyot, Romain, Couturon, Emmanuel, Raharimalala, Nathalie E., Hamon, Perla, Darré, Thibaud

2016

Overview

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.

• Publisher: Springer Berlin Heidelberg,Springer Nature B.V,Springer Verlag
• Subject: Animal Genetics and Genomics / Australasian region / Biochemistry / Biochemistry, Molecular Biology / Biogeography / Biomedical and Life Sciences / Central Africa / Coffea / Coffea - classification / Coffea - genetics / elemental composition / evolution / Evolution, Molecular / Genetic Variation / genome / Genome Size / Genome, Plant / Genomes / Genomics / geographical distribution / Human Genetics / India / Indian Ocean Islands / Life Sciences / Microbial Genetics and Genomics / Original Article / Phylogeography / Plant Genetics and Genomics / Retroelements / retrotransposons / Sequence Analysis, DNA - methods / sires / transposons / Vegetal Biology