Integrative bioinformatics analysis: from the super-pangenome to biosynthetic pathways in species of Coffea spp.

• Grant number: 25/05520-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: September 01, 2025
• End date: August 31, 2027
• Field of knowledge: Agronomical Sciences - Agronomy
• Principal Investigator: Douglas Silva Domingues
• Grantee: Daisy Sotero Chacon
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 23/03353-3 - Bridging gaps between biological resources in Coffea genus and future crop improvement facing global changes: BRIDGES-COFFEA, AP.R

Abstract

The genus Coffea, belonging to the Rubiaceae family, comprises approximately 141 species, withcoffee being one of the most consumed beverages worldwide. Brazil is the largest producer andexporter, playing a fundamental role in global production. Currently, coffee production is concentrated in two main species: Coffea arabica and Coffea canephora, which, despite dominating the global market, face high vulnerability to climate change, with projections indicating significant losses. On the other hand, wild Coffea species offer promising genetic potential for breeding, as they may exhibit tra its such as greater resistance to pests and diseases, as well as higher tolerance to adverse environmental conditions. The construction of a super-pangenome for these species is a relevant strategy to explore this potential. Alongside this approach, the study of structural variations (SVs) can provide valuable insights into the adaptation and environmental plasticity of these species. This knowledge can be further complemented by the analysis of the biosynthetic pathways of bioactive compounds, which are essential both for plant defense and the sensory characteristics of coffee. Thus, this project aims to investigate the genomic diversity and the evolution of biosynthetic pathways in commercial and wild Coffea species through comparative genomics and integrative analyses. The results obtained may serve as a foundation for studies on genome evolution and genetic resource management for coffee breeding, as well as provide a genomic resource for the scientific community interested in this globally important crop.