03600naa a2200961 a 450000100080000000500110000800800410001910000160006024501570007626000090023352011310024265000320137365000130140570000160141870000110143470000140144570000180145970000170147770000130149470000180150770000150152570000140154070000180155470000170157270000200158970000140160970000230162370000160164670000170166270000150167970000180169470000180171270000170173070000150174770000170176270000180177970000140179770000170181170000150182870000140184370000170185770000270187470000180190170000120191970000190193170000160195070000230196670000180198970000160200770000150202370000160203870000210205470000170207570000150209270000150210770000180212270000170214070000160215770000130217370000250218670000240221170000200223570000160225570000160227170000160228770000140230370000190231770000190233670000190235570000180237470000170239270000160240970000220242570000180244770000150246570000170248070000160249770000180251370000190253170000180255070000180256877300520258621636462024-04-19       2024    bl uuuu     u00u1 u    #d1 aSALOJÄRVI.  aThe genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.h[electronic resource]  c2024  aCoffea 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.  aCoffea arabica var. arabica  aGenomics1 aRAMBANI, A.1 aYU, Z.1 aGUYOT, R.1 aSTRICKLER, S.1 aLEPELLEY, M.1 aWANG, C.1 aRAJARAMAN, S.1 aRASTAS, P.1 aZHENG, C.1 aMUÑOZ, D. S.1 aMEIDANIS, J.1 aPASCHOAL, A. R.1 aBAWIN, Y.1 aKRABBENHOFT, T. J.1 aWANG, Z. Q.1 aFLECK, S. J.1 aAUSSEL, R.1 aBELLANGER, L.1 aCHARPAGNE, A.1 aFOURNIER, C.1 aKASSAM, M.1 aLEFEBVRE, G.1 aMÉTAIRON, S.1 aMOINE, D.1 aRIGOREAU, M.1 aSTOLTE, J.1 aHAMON, P.1 aCOUTURON, E.1 aTRANCHANT-DUBREUIL, C.1 aMUKHERJEE, M.1 aLAN, T.1 aENGELHARDT, J.1 aSTADLER, P.1 aLEMOS, S. M. C. de1 aSUZUKI, S. I.1 aSUMIRAT, U.1 aWAI, C. M.1 aDAUCHOT, N.1 aOROZCO-ARIAS, S.1 aGARAVITO, A.1 aKIWUKA, C.1 aMUSOLI, P.1 aNALUKENGE, A.1 aGUICHOUX, E.1 aREINOUT, H.1 aSMIT, M.1 aCARRETERO-PAULET, L.1 aGUERREIRO FILHO, O.1 aBRAGHINI, M. T.1 aPADILHA, L.1 aSERA, G. H.1 aRUTTINK, T.1 aHENRY, R.1 aMARRACCINI, P.1 aPEER, Y. V. de1 aANDRADE, A. C.1 aDOMINGUES, D.1 aGIULIANO, G.1 aMUELLER, L.1 aPEREIRA, L. F. P.1 aPLAISANCE, S.1 aPONCET, V.1 aROMBAUTS, S.1 aSANKOFF, D.1 aALBERT, V. A.1 aCROUZILLAT, D.1 aKOCHKO, A. de1 aDESCOMBES, P.  tNature Geneticsgv. 56, n. 4, p. 721-731, 2024.