The ANR-FAPESP project: Bridges-Coffea

The advent of advanced sequencing technologies and sophisticated genome assembly methodologies has catalyzed the launch of ambitious projects aimed at producing high-quality reference genomes. These endeavors are pivotal for deepening our understanding of species diversity and evolutionary processes. Moreover, they are crucial for addressing biodiversity conservation challenges. The wealth of data emerging from these projects facilitates pangenome-wide studies, allowing scientists to escalate their analyses from individual to species-level genomic diversity. This shift is crucial for pinpointing genes crucial for adaptation to diverse environments, underscoring the critical role of wild species in identifying adaptive traits crucial for climate resilience. Interestingly, some genes essential for selection may be absent in cultivated species, highlighting the untapped potential of wild varieties.

Innovative research is increasingly leveraging comparative analysis and pangenomic approaches to shed light on species evolution and adaptation mechanisms. Coffee production, reliant mainly on Coffea arabica and C. canephora, faces significant threats from climatic variations. Predictions suggest a loss of 50% of cultivable areas by 2050, posing substantial socio-economic risks to the approximately 100 million people globally dependent on coffee production. However, wild coffee species, adapted to a range of climates, offer a beacon of hope. These species could either supplement or replace the current cultivars or be integrated into breeding programs through interspecific hybridization. Yet, the genetic and genomic diversity of wild Coffea species, along with their adaptation strategies to varying climates, remains underexplored.

Our project aims to bridge this knowledge gap by harnessing cutting-edge sequencing technologies and bioinformatics tools for genome assembly, comparative genomics, and pangenome analysis. Utilizing the diversity of wild species housed in ex-situ collections, alongside phenotypic and environmental data, we set forth several ambitious objectives. These include producing highly contiguous and annotated reference genome assemblies and transcriptomes for 33 wild Coffea species, reflecting the genus's diversity based on established phylogenetic relationships. We also aim to elucidate the structural genome evolution within Coffea by mapping large structural variations and transposable elements over a 15 million-year evolutionary timeline. Additionally, we seek to unravel the evolutionary trajectory of key biosynthetic pathways, such as caffeine biosynthesis, and to construct a comprehensive super-pangenome that integrates core and dispensable genomes, elucidating their roles in environmental adaptation.

Our project aspires to offer invaluable insights into the evolution of tropical tree genus structure, biosynthesis pathway evolution, and the gene function within the "shell" and "cloud" genomes in relation to environmental adaptation. Ultimately, we aim to develop open-access resources and collaborative platforms to foster the use of wild species in crop improvement initiatives, promoting their conservation both in their natural habitats and in ex-situ collections.