BRIDGES_COFFEA

Franco-Brazilian Project "Bridges_Coffea": Bridging the Gap Between Knowledge of Biological Resources in the Coffea Genus and Crop Improvement in the Face of Global Changes 

Launched on January 1, 2024, this project called "Bridges_Coffea" brings together 12 partners from 4 different countries under the leadership of Romain Guyot (IRD, UMR DIADE, France) and Douglas Domingues (USP, Brazil). 

This 4-year project is funded by the French National Research Agency (ANR) under the AAPG 2023 call and by FAPESP (Brazil). 

The "Bridges_Coffea" project aims to leverage new sequencing technologies and bioinformatics tools to deepen our understanding of the Coffea genus. 

The specific objectives are: 

A Reference Genome Assembly: Generate genome and reference transcriptome assemblies for 33 representative wild species of the Coffea genus. 

Knowledge of Genome Evolution: Provide a comprehensive view of the evolution of the Coffea genome structure, focusing on the analysis of significant structural variations (SV) and the contraction-expansion of transposable elements (TE). This analysis will illuminate genomic changes that have occurred within the genus. 

Knowledge of the Evolution of Biosynthetic Pathways: Examine the detailed evolutionary history of significant biosynthetic pathways, including those responsible for the production of caffeine and diterpenes. Understanding these pathways will illuminate how specific adaptive traits have evolved in the Coffea genus. 

A Super-Pangenome Assembly: Construct a genus-level super-pangenome that integrates core and dispensable genomes. This assembly will explore the relationship between the dispensable genome and environmental adaptation factors, offering insights into the genetic basis of adaptability in Coffea species. 

The Development of a Genomic Data Visualization System: Develop an integrated visualization system to facilitate the exploration of annotations, gene families, orthologous and paralogous relationships, collinearity of loci of interest, and the display of super-pangenomes.