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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance.

Jarkko SalojärviAditi RambaniZhe YuRomain GuyotSusan StricklerMaud LepelleyCui WangSitaram RajaramanPasi RastasChunfang ZhengDaniella Santos MuñozJoão MeidanisAlexandre Rossi PaschoalYves BawinTrevor J. KrabbenhoftZhen Qin WangSteven J. FleckRudy AusselLaurence BellangerAline CharpagneCoralie FournierMohamed KassamGregory LefebvreSylviane MétaironDéborah MoineMichel RigoreauJens StoltePerla HamonEmmanuel CouturonChristine Tranchant-DubreuilMinakshi MukherjeeTianying LanJan EngelhardtPeter StadlerSamara Mireza Correia De LemosSuzana Ivamoto SuzukiUcu SumiratChing Man WaiNicolas DauchotSimon Orozco-AriasAndrea GaravitoCatherine KiwukaPascal MusoliAnne NalukengeErwan GuichouxHavinga ReinoutMartin SmitLorenzo Carretero-PauletOliveiro Guerreiro FilhoMasako Toma BraghiniLilian PadilhaGustavo Hiroshi SeraTom RuttinkRobert HenryPierre MarracciniYves Van de PeerAlan AndradeDouglas DominguesGiovanni GiulianoLukas MuellerLuiz Filipe PereiraStephane PlaisanceValerie PoncetStephane RombautsDavid SankoffVictor A. AlbertDominique CrouzillatAlexandre de Kochko & Patrick Descombes

Nature Genetics volume 56, pages721–731 (2024)

Abstract

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

 

See https://www.nature.com/articles/s41588-024-01695-w

 

Fig. 1 | Patterns of synteny, fractionation and gene loss in C. arabica and its progenitor species C. canephora and C. eugenioides. a, Corresponding syntenic blocks between CA subgenomes subCC (orange) and subEE (blue), and with the CC (orange) and CE (blue) genomes. b, The base pairs in intergenic DNA in synteny block gaps caused by fractionation in a subCC–subEE comparison, compared with numbers of base pairs in homoeologous unfractionated regions, as a function of numbers of consecutive genes deleted. c, Gene retention rates in synteny blocks plotted along subCC chromosome 2; subCC is plotted in orange and subEE in blue. The green box indicates the pericentromeric region. CA, C. arabica; CC, C. canephora; CE, C. eugenioides.

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