Evolution of Coffea Genomes lab

picture ©Emmanuel couturon IRD

Wild coffea species db.  https://doi.org/10.23708/JZA8I2


Coffee is a beverage enjoyed by millions of people around the world. It is also an important product for millions of small coffee growers living in tropical countries. Two main species are cultivated: Arabica (Coffea arabica) and Robusta (Coffea canephora). Currently, coffee plantations are deeply affected by climate change and the appearance of new and more serious diseases. 

In addition to cultivated coffee trees, numerous wild coffee species are known to botanists, but are largely ignored by agronomists and plant breeders, despite the fact that these species may be crucial for the future development of coffee cultivation to cope with climate change. Based on morphological data, the phylogenetically closest genus, Psilanthus, has recently been included in Coffea. The genus Coffea (broadly defined) includes woody plants belonging to the family Rubiaceae. It comprises 124 species and 17 additional taxa, with a natural distribution spanning tropical Africa, Madagascar, Comoros, Mauritius and the Reunion Islands, extending into South and Southeast Asia and Australasia. However, the two genera differ mainly in flower morphology. The formerPsilanthus genus is present on the African continent, Asia (India, Sri Lanka, tropical and Southeast Asia) and Oceania (northern Australia), but absent from the islands of the western Indian Ocean (Madagascar, Mascarene and Comoros). The merger of these two genera introduced a possible source of naming confusion, as numerous works focus only on Coffea sensu stricto. Another source of species name confusion is the presence of numerous past or modern synonymies.

Fourteen years ago, it was revealed that numerous wild coffee species are vulnerable (23 species), endangered (30 species) or critically endangered (19 species). A recent reassessment confirmed that 60% of them are now threatened with extinction, suggesting a poor outlook for wild coffee species throughout the tropical world. Living collections of wild coffee species began in the 1960s in Africa and Madagascar. Currently, only 55% of them are in such collections: at the research station of the Centre National de Recherche en Agronomie, Divo, Ivory Coast (for African species), at the Centre de Ressources Biologiques (CRB) Bassin-Martin, Reunion Island (for African, Comorian and Mascarene species) and at the research station of the National Center for Applied Research in Rural Development (FOFIFA) in Kianjavato, Madagascar (for Malagasy species). Analysis of wild coffee species preserved in living collections revealed a large morphological variation, such as flower morphology, fruit size and color, plant height and leaf morphology, days to fruit ripening, and growth and adaptation habitats. In addition to morphology, large variations were observed in terms of seed biochemical compounds involved in coffee quality, such as caffeine, trigonelline, sucrose and mangiferin content, among others. However, so far this diversity has not been reported comprehensively in any publication or publicly available database.

From a genomic point of view, the first Coffea genome was published in 2014 and referred to Coffea canephora. Since this first release, several sequencing data have been published, such as sequencing genotyping data to provide the first resolved phylogeny of the genus Coffea, partial sequencing of 16 Coffea species, and chloroplast reconstructions and nuclear SNP mining. The genus is currently the subject of intensive genome sequencing (C. arabica, C. eugenioides, and C. canephora; 82 wild coffee species), allowing investigation of genes of agronomic interest, genome composition, and evolutionary studies.

Our researches

Our researches are mainly focused on the understanding of the molecular evolution of Coffea and Rubiaceae species using next generation sequencing technologies and the development of new bioinformatics tools under the following axes :

1- Genetic, biochemical and morphological diversities of Coffea species 

2- Evolutionary history of the Coffea wild and cultivated species genomes

3- Diversity and Evolution of transposable elements in plants' genomes

4- Developpement of bioinformatic and Artificial Intelligence tools for genomics analyses 

5- Evolution of Rubiaceae species

Some web databases, repositories (pictures and sequences) and broad audiences publications :

DataSud: A repository for Coffea pictures

DataSud: InpactorDB: A repository fasta files for Plant LTR Retrotransposons

DataSud: A repository for Chloroplast sequence