Première phylogénie des caféiers totalement résolue



Grâce aux espèces de caféiers malgaches maintenues à la station de Kianjavato, des chercheurs du FOFIFA et de l'IRD, membres de l’association BEC, ont pu proposer, en collaboration avec des chercheurs de différentes institutions scientifiques internationales, la première phylogénie complètement résolue.


Les chercheurs travaillant sur les caféiers avaient, depuis très longtemps comme objectif de proposer une hypothèse phylogénétique complète et résolue. Mais, jusqu’à présent, les études avaient été freinées d’une part parce que les marqueurs moléculaires disponibles ne le permettaient pas et d'autre part par les faibles divergences génétiques entre les espèces notamment pour les espèces originaires de Madagascar.


Dans cet article, pour la première fois, grâce au génotypage par séquençage, une phylogénie totalement résolue est présentée de même qu'une hypothèse sur l’évolution du contenu en caféine des grains.



Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species GBS coffee phylogeny and the evolution of caffeine content.

Molecular Phylogenetics and Evolution 109 (2017) 351–361


Perla Hamona,, Corrinne E. Grover b, Aaron P. Davis c, Jean-Jacques Rakotomalala d, Nathalie E., Raharimalala d, Victor A. Albert e, Hosahalli L. Sreenath f, Piet Stoffelen g, Sharon E. Mitchell h, Emmanuel Couturon a, Serge Hamona, Alexandre de Kochko a, Dominique Crouzillat i, Michel Rigoreau i, Ucu Sumirat j,Sélastique Akaffou k, Romain Guyot

aUMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France, b Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA, c Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom, d FOFIFA, BP 1444, Ambatobe, Antananarivo 101, Madagascar, e Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA, f Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India, g Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium, h Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA, i Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France, j Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia, k University Jean Lorougnon Guédé, Daloa, Cote d’Ivoire, lUMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France

a b s t r a c t

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.