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Nat Biotechnol. 2014 Jul;32(7):656-62. doi: 10.1038/nbt.2906. Epub 2014 Jun 8.

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.

Author information

  • 11] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2].
  • 2HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
  • 3Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France.
  • 4US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
  • 5Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
  • 6Istituto di Genomica Applicata, Udine, Italy.
  • 7Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
  • 8Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil.
  • 9Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
  • 101] Istituto di Genomica Applicata, Udine, Italy. [2] Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
  • 11Centro de Protección Vegetal y Biotecnología-Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain.
  • 121] Lifesequencing, Valencia, Spain. [2] Secugen, Madrid, Spain.
  • 13Lifesequencing, Valencia, Spain.
  • 141] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] INRA, US 1279 Etude du Polymorphisme des Génomes Végétaux (EPGV), Evry, France.
  • 15INRA Génétique et Écophysiologie de la Qualité des Agrumes (GEQA), San Giuliano, France.
  • 161] Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA. [2].
  • 17Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
  • 18454 Life Sciences, Roche, Branford, Connecticut, USA.
  • 191] 454 Life Sciences, Roche, Branford, Connecticut, USA. [2].
  • 201] Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. [2] School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.
  • 211] Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. [2] School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA. [3] Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
  • 22Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy.
  • 231] Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil. [2] Embrapa Cassava and Fruits, Cruz das Almas, Brazil.
  • 241] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] Département de Biologie, Université d'Evry, Evry, France.
  • 25Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA.
  • 261] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] Département de Biologie, Université d'Evry, Evry, France. [3] Centre National de Recherche Scientifique (CNRS), Evry, France.
  • 271] Istituto di Genomica Applicata, Udine, Italy. [2] Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy.
  • 28Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA.
  • 291] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2] Division of Genetics, Genomics and Development, University of California, Berkeley, Berkeley, California, USA.

Abstract

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.

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PMID:
24908277
[PubMed - indexed for MEDLINE]
PMCID:
PMC4113729
Free PMC Article
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