Abstract
Advances in sequencing techniques and genome assembly pipelines have allowed the development of large-scale projects focused on generating high-quality reference genomes that will contribute to a better understanding of species diversity and evolution. The establishment of reference genomic resources is also key to biodiversity conservation issues. Data from these and other initiatives have allowed pangenome-wide studies, enabling researchers to move from individual-level to species-level analysis of genomic diversity, as well as in identifying key genes implicated in the adaptation to contrasting environments. Results from such research have redefined the importance of wild species in the search for adaptive traits to climate adaptation, since some genes that could be a target for selection are simply not present in cultivated species. In addition, new innovative research is looking at the use of comparative analysis and pangenomes towards understanding species' evolution and adaptation. Coffee is mainly produced by two species of the genus Coffea: C. arabica and C. canephora. They are sensitive to climatic variations and a loss of 50% of cultivable areas is expectedby 2050 with considerable socio-economic impacts for the 100 million people worldwide depending on this production. However, alternatives exist via wild coffee tree species that are better adapted to contrasting climates and could replace cultivated species or be used in breeding programs via interspecific hybridization. Nevertheless, the diversity of wild Coffea species remains poorly known at the genetic and genomic levels and the factors related to their adaptation to contrasting climates are poorly studied. Our current knowledge is insufficient to obtain a complete understanding of the evolution of genome structure, structural variations and genes of interest in coffee trees due to the lack of genomic resources. The goal of our project is to begin tackling this situation by taking advantage of the development of new sequencing technologies, and state-of-the-art bioinformatics tools for genome assembly, comparative genomics, and pangenome integration. The diversity of wild species conserved in ex-situ collections, phenotypic resources and environmental information are available. Our main goals are to obtain via an interdisciplinary approach: (i) highly contiguous, accurate, and annotated reference genome assemblies and transcriptomes of 33 wild Coffea species, representing the diversity of the genus based on the phylogenetic relationships we established; (ii) A complete view of structural genome evolution in the genus Coffea with the integration of genomic elements such as large structural variations and transposable element over an evolutionary time step of 15 My; (iii) A detailed evolutionary history of biosynthetic pathways and clusters, like the caffeine biosynthetic pathway; (iv) An assembly of a genus-level super-pangenome integrating the core and dispensable genomes and the relationships between the dispensable genome and factors involved in environmental adaptation; and finally (v) integrating the research outputs into a visualization system allowing to browse annotations, gene families, orthologous and paralogous relationships, collinearity of loci of interest and display pangenomes. The results of our project will have major implications on the knowledge of the evolution of the structural features of a tropical tree genus, the evolutionary pattern of biosynthesis pathways and on the association between the function of the genes of the "shell" and "cloud" genomes and their implication in the adaptation to environmental constraints. Our long-term ambition is to provide open resources and collaborative platforms to promote the use of wild species in future crop improvement schemes and to promote their protection and conservation species in their natural environment and in ex situ collections. (AU)
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