1. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee)
- Author
-
Dominique Crouzillat, Jean-Jacques Rakotomalala, Coralie Fournier, Serigne Ndiawar Ly, Piet Stoffelen, Eva N. Raharimalala, Steven Janssens, Andrea Garavito, Christophe Guyeux, Romain Guyot, Patrick Descombes, Perla Hamon, Jean-Claude Charr, Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad de Caldas [Manizales, Colombia], Nestle Centre R & D [Tours], Nestlé Centre R & D [Lausanne, Suisse], Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de Recherche Appliquée au Développement Rural (FOFIFA), Botanic Garden Meise, Universidad Autónoma de Manizales (UAM), Meise Botanic Garden, Institut de Recherche pour le Developpement (IRD), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Meise Botanic Garden [Belgium] (Plantentuin)
- Subjects
0106 biological sciences ,0301 basic medicine ,Canephora ,Genome, Plastid ,Coffea ,Coffea canephora ,010603 evolutionary biology ,01 natural sciences ,Polymorphism, Single Nucleotide ,Coalescent theory ,[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics ,Evolution, Molecular ,03 medical and health sciences ,Evolutionary history ,Species Specificity ,Genus ,Genetics ,Cluster Analysis ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Clade ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Cell Nucleus ,Nuclear SNPs ,Phylogenetic tree ,biology ,Coffee species - Coffea canephora ,Full plastid genome sequencing ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,Taxon ,Evolutionary biology - Abstract
International audience; For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid fullgenome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.
- Published
- 2020
- Full Text
- View/download PDF