Coffea Diversity

picture ©Emmanuel couturon IRD

Wild coffea species db.

Phenotypic Diversity of African Coffea Fruits

Pictures © Emmanuel Couturon, IRD

Right: Internodes, fruits and seeds of C. richardii (A); Fruit of C. tsirananae (B); leaf of C. heimii (C) (Rimlinger et al., 2020)

The tropical rainforests of Africa and Madagascar show huge biodiversity characterized by great species richness and endemicity. In such context, for the genera that experienced radiative speciation, phenotypic divergence can be important while the associated genetic differentiation could remain low. It results in low congruency between genetic and phenotypic diversity. Actually, 58 and 47 Coffea species (excluding ex-Psilanthus genus and Baracoffea groups) respectively from Madagascar and Africa were described (although three and seven species from Madagascar and Africa respectively are not yet formally recognized). These Coffea species show a high phenotypic diversity in term of phenological traits, fruit size and color, fruit maturation time, tree height, biochemical composition of leaves and fruits, and indeed genetic diversity.

Recently, a completely resolved molecular phylogenetic tree was obtained using 28,800 concatenated Single-Nucleotide Polymorphisms (SNPs) markers obtained from Genotyping-By-Sequencing (GBS) methodology (Hamon et al., 2017).

The necessity to use GBS for assessment of between-species genetic divergence could be explained by two non-exclusive mechanisms:

1) the absence of strong genetic barrier and therefore the maintenance of gene flow between species even at a low rate and

2) recent speciation coupled with rapid morphological divergence.

In this section, we present some recent studies describing the huge diversity of Coffea species at the phenotypic and genetic levels. Our current project include now the analysis of species not included into living collections.

List of publications

Phenotypic diversity assessment within a major ex situ collection of wild endemic coffees in Madagascar. Aurore Rimlinger, Nathalie Raharimalala, Véronique Letort, Jean-Jacques Rakotomalala, Dominique Crouzillat, Romain Guyot, Perla Hamon, Sylvie Sabatier. Annals of Botany, Volume 126, Issue 5, 9 October 2020, Pages 849–863,

WCSdb: a database of wild Coffea species. Database, Volume 2020, 2020, baaa069,

A photo bank of Coffea species: Guyot, Romain; Hamon, Perla; Couturon, Emmanuel; Raharimalala, Nathalie; Rakotomalala, Jean-Jacques, 2020, "Photo bank for: WCSdb: A database of Wild Coffea Species",, DataSuds, V1, UNF:6:D4jmlyKfcJyf9HHyxzxguQ== [fileUNF]

Garavito A, Montagnon C, Guyot R, Bertrand B. Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol. 2016 Nov 4;16(1):242. doi: 10.1186/s12870-016-0933-y.

Roncal J, Guyot R, Hamon P, Crouzillat D, Rigoreau M, Konan ON, Rakotomalala JJ, Nowak MD, Davis AP, de Kochko A. Active transposable elements recover species boundaries and geographic structure in Madagascan coffee species. Mol Genet Genomics. 2016 Feb;291(1):155-68. doi: 10.1007/s00438-015-1098-3.

Couturon Emmanuel, Raharimalala N.E., Rakotomalala J.J., Hamon Serge, De Kochko Alexandre, Guyot Romain, Hamon Perla. (2016). Caféiers sauvages : un trésor en péril au coeur des forêts tropicales ! = Wild coffee-trees : a threatened treasure in the heart of tropical forests !. Montpellier : Association Biodiversité, Ecovalorisation et Caféiers, 117 p. ISBN 978-2-7466-9109-4

Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C, Poncet V, De Kochko A, Rakotomalala JJ, Hamon P. Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Ann Bot. 2013 Feb;111(2):229-48. doi: 10.1093/aob/mcs283.