Evolution of Coffea Genomes lab

picture ©Emmanuel couturon IRD

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


Coffee, a beloved beverage savored by countless individuals globally, not only stands as a daily staple but also plays a vital role in the livelihoods of millions of small-scale coffee producers residing in tropical regions. This industry primarily revolves around the cultivation of two major species: Arabica (Coffea arabica) and Robusta (Coffea canephora). However, the sustainability of coffee production faces significant threats from climate change and emerging, more virulent diseases.

Beyond the well-known cultivated varieties, a rich diversity of wild coffee species exists, largely overlooked by agricultural science and plant breeding. These wild relatives harbor potential keys to the future resilience of coffee cultivation, offering genetic resources to combat climate challenges. Notably, recent botanical studies have integrated the genus Psilanthus, once considered distinct due to its flower morphology, into the Coffea genus. This expanded definition of Coffea now encompasses over 140 species and taxa, distributed across tropical Africa, Madagascar, the Comoros and Mascarene Islands, Mauritius, the Reunion Islands, and extending to regions in South and Southeast Asia and Australasia. This merger, while enriching the genetic pool, has introduced complexities in nomenclature, particularly for research focusing on the traditional Coffea species.

Alarmingly, an assessment fourteen years ago highlighted the vulnerability of numerous wild coffee species, with recent updates indicating that 60% are now on the brink of extinction. This dire situation underscores the critical need for conservation efforts. Live collections of wild species, initiated in the 1960s in Africa and Madagascar, currently capture only 55% of these species. These collections showcase a vast array of morphological diversity and biochemical variance, which could be pivotal for enhancing coffee quality and resilience, yet this information remains underreported.

From a genomic perspective, the coffee genus has seen significant advancements since the first Coffea genome was sequenced in 2014. Subsequent research has delved into the genetic makeup of Coffea species, including comprehensive genome sequencing of both cultivated and 82 wild species. This genomic exploration is paving the way for understanding the agronomic traits, genetic diversity, and evolutionary history of coffee, offering hopeful avenues for sustaining coffee production in the face of environmental challenges.

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