The popularity of coffee has made it one of the world’s most important commodities ( and the source of livelihood for around 100 million coffee farmers. Despite a huge body of scientific research, much of the fundamental evolutionary data relevant to coffee has been elucidated in the last decade or so. In particular, knowledge of wild coffee species has recently accelerated, including new insights into the two major crop species, Arabica (Coffea arabica) and Robusta coffee (C. canephora), which are largely unchanged from their wild forest relatives. This is still the case for Arabica coffee, despite having been in cultivation for many hundreds, if not thousands, of years. Robusta coffee has had a recent and spectacular ascendancy, having only been in general cultivation for just over 100 years.

Studies with sequence data and large sampling revealed geographic groupings, monophyly for the Mascarene species, and monophyly for a dry-adapted lineage from the western coast of Madagascar. Despite the gradual advances in phylogenetic resolution over time, previous studies failed to provide clear and robust hypotheses of relationships between and among groupings and, more generally, between species. Typically, past studies lacked strong statistical support, especially for early-diverging lineages and for species-level resolution in some geographic areas, most notably Madagascar, which is home to nearly half species of the genus. On the basis of a larger sampling of Psilanthus, and on review of morphological data, Davis et al. (2011) concluded on the systematic placement of the genus Psilanthus into Coffea, although branch support for some relationships was negligible. With the inclusion of Psilanthus, Coffea comprises 124 species (141 with taxa), with a natural distribution covering tropical Africa, Madagascar, Comoros, Mauritius and the Reunion Islands extending to southern and southeast Asia, and Australasia.

Resolving full phylogenetic relationships among recently diverged lineages is one of the greatest challenges in evolutionary biology. Genotyping-by-sequencing (GBS) and restriction site associated DNA sequencing (RADseq) are two technologies that generate sequences for a myriad of orthologous regions scattered throughout entire genomes. They offer a possible solution for phylogenetic studies of recently diverged lineages. Bioinformatic advances have been developed for these technologies, which can be used to resolve phylogenetic relationships at lower taxonomic levels without the requirement of reference genomes.

Here we present our studies on phylogenetic using whole-genome approaches and complete plastid reconstruction.

Discrepancies between maternal and nuclear phylogenies of the two main cultivated coffee species (i.e. Arabica and Robusta) were clearly identified (Guyeux et al., 2019). While Coffea arabica belongs to the Coffea clade, C. canephora, was seemingly more closely related to the Psilanthus clade. In previous works, incongruent plastid and nuclear relationships were also highlighted, but clear conclusions could not be reached mainly due to the low support values obtained for the two molecular trees (nuclear and maternal). All together, these results have an important impact on the current assumption of the evolutionary history of C. canephora as well as between the other wild coffee species.

Using whole plastid genome data for a set of 52 taxa (including Coffea s.s. and Psilanthus) combined with multiple nuclear SNPs we aimed here to address the following research objectives: (1) reconstructing a maternal tree based on complete plastid genomes, (2) characterizing each maternal phylogenetic clade through detection of highly mutated genes and gene mutation rates, (3) independently of the known phylogenetic organization, identifying the internal structure of the studied set of species according to the method of Matar et al. (2019), 4) constructing a nuclear tree based on 28,800 nuclear SNPs. Observation of discrepancies between nuclear and maternal genomes will allow us to gain a better view on the complex evolutionary history of Coffee including Coffea canephora (Robusta coffee).

All together our studies suggest that the evolutionay history is more complex than expected previously. Our current project include now the full spequencing of the genus to understend more precisely the complex relastionships between species and their patterm of genome evolution.