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 world- wide. It is also an important commodity for millions of small coffee farmers living in tropical countries. Two species are mainly cultivated Arabica (Coffea arabica) and Robusta (Coffea canephora). Now, coffee fields are deeply impacted by climate change and the emergence of new and more severe diseases.

Beside cultivated coffee trees, numerous wild coffee species are known to botanists, but largely ignored by agronomists and breeders although these species may be crucial for future coffee crop development to face climate changes. Based on morphological data, the phylogenetically closest genus called Psilanthus has been recently placed into Coffea. The genus Coffea (broad sense) includes woody plants belonging to the Rubiaceae family. It comprises 124 species and 17 additional taxa, with a natural distribution covering tropical Africa, Madagascar, Comoros, Mauritius and the Reunion Islands extending to Southern and Southeast Asia and Australasia. However, the two genera mainly differ by the flower morphology. The former genusPsilanthus 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 West Indian Ocean (Madagascar, Mascarenes and Comoros). The merging of these two genera introduced a possible source of name confusion as numerous works are focused only on Coffea sensu stricto. Another source of species name confusion is the presence of numerous past or modern synonymies.

Fourteen years ago, It has been revealed that numerous wild coffee species are vulnerable (23 species), endangered (30 species) or seriously threatened (19 species). A recent reassessment confirmed that 60% of them are now threatened with extinction, suggesting a bad prospect for wild coffee species all over the tropical world. Wild coffee species living collections were initiated in the years 1960 in Africa and Madagascar. Today only 55% of them are in such collections: at the research station of the Centre National de Recherche en Agronomie, Divo, Côte d’Ivoire (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 Centre for Applied Research for Rural Development (FOFIFA) in Kianjavato, Madagascar (for Madagascan species). The analysis of wild coffee species conserved in living collection revealed large morphological variation such as flower morphology, size and color of fruits, plant height and leaf morphologies, days to fruit maturation and growth habitats and adaptation. In addition to morphology, large variations were observed in terms of seed biochemical compounds involved in the quality of coffee such as caffeine, trigonelline, sucrose and mangiferin contents into others. However, this diversity is not comprehensively reported so far in any publication or any publicly available database.

At genomic point of view, the first Coffea genome has been published in 2014 and concerned Coffea canephora. Since this first release, several sequencing data have been published such as the genotyping-by-sequencing data to provide the first resolved phylogeny of the Coffea genus, the partial sequencing of 16 Coffea species and the chloroplast reconstructions and nuclear SNP mining. Now the Genus is subjected to intensive genome sequencing (C. arabica, C. eugenioides and C. canephora; 82 wild coffee species), allowing research of genes of agronomical 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