The genome and population genomics of allopolyploidCoffea arabicareveal the diversification history of modern coffee cultivars

• DOI: 10.1101/2023.09.06.556570
• Publication Date: 2023-09-07T03:40:32Z
• Authors: Jarkko Salojärvi; Aditi Rambani; Zhe Yu; Romain Guyot; Susan Strickler; Maud Lepelley; Cui Wang; Sitaram Rajaraman; Pasi Rastas; Chunfang Zheng; Daniella Santos M...; João Meidanis; Alexandre Rossi P...; Yves Bawin; Trevor Krabbenhoft; Zhen Qin Wang; Steven Fleck; Rudy Aussel; Laurence Bellanger; Aline Charpagne; Coralie Fournier; Mohamed Kassam; Gregory Lefebvre; Sylviane Métairon; Déborah Moine; Michel Rigoreau; Jens Stolte; Perla Hamon; Emmanuel Couturon; Christine Trancha...; Minakshi Mukherjee; Tianying Lan; Jan Engelhardt; Peter Stadler; Samara Mireza Cor...; Suzana Ivamoto Su...; Ucu Sumirat; Wai Ching Man; Nicolas Dauchot; Simon Orozco-Arias; Andrea Garavito; Catherine Kiwuka; Pascal Musoli; Anne Nalukenge; Erwan Guichoux; Havinga Reinout; Martin Smit; Lorenzo Carretero...; Oliveiro Guerreir...; Masako Toma Braghini; Lilian Padilha; Gustavo Hiroshi Sera; Tom Ruttink; Robert Henry; Pierre Marraccini; Yves Van de Peer; Alan Andrade; Douglas Domingues; Giovanni Giuliano; Lukas Mueller; Luiz Filipe Pereira; Stephane Plaisance; Valerie Poncet; Stephane Rombauts; David Sankoff; Victor A. Albert; Dominique Crouzillat; Alexandre de Kochko; Patrick Descombes
• Keywords: Coffea canephora

Abstract Coffea arabica , an allotetraploid hybrid of C. eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding polyploidy event 350,000-610,000 years ago, followed by pre-domestication bottlenecks, resulting in narrow genetic variation. A split wild cultivar progenitors occurred ∼30.5 kya, period migration two populations. Analysis varieties, including lines historically introgressed highlights their breeding histories loci that may contribute to pathogen resistance, laying groundwork future genomics-based