title: Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.
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.
authors.affiliation: 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2].
authors.forename: G Albert
authors.initials: GA
authors.lastname: Wu
authors.affiliation: 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2].
authors.forename: Simon
authors.initials: S
authors.lastname: Prochnik
authors.affiliation: HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France.
authors.forename: Jerome
authors.initials: J
authors.lastname: Salse
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
authors.forename: Xavier
authors.initials: X
authors.lastname: Perrier
authors.affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ruiz
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Scalabrin
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Terol
authors.affiliation: Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil.
authors.forename: Marco Aurélio
authors.initials: MA
authors.lastname: Takita
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
authors.forename: Kamel
authors.initials: K
authors.lastname: Jabbari
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.
authors.forename: Cristian
authors.initials: C
authors.lastname: Del Fabbro
authors.affiliation: Istituto di Genomica Applicata, Udine, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Pinosio
authors.affiliation: 1] Istituto di Genomica Applicata, Udine, Italy. [2] Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Jarrod
authors.initials: J
authors.lastname: Chapman
authors.affiliation: HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Francisco R
authors.initials: FR
authors.lastname: Tadeo
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Leandro H
authors.initials: LH
authors.lastname: Estornell
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Juan V
authors.initials: JV
authors.lastname: Muñoz-Sanz
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Victoria
authors.initials: V
authors.lastname: Ibanez
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Amparo
authors.initials: A
authors.lastname: Herrero-Ortega
authors.affiliation: Centro de Protección Vegetal y Biotecnología-Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Aleza
authors.affiliation: 1] Lifesequencing, Valencia, Spain. [2] Secugen, Madrid, Spain.
authors.forename: Julián
authors.initials: J
authors.lastname: Pérez-Pérez
authors.affiliation: Lifesequencing, Valencia, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Ramón
authors.affiliation: 1] 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.
authors.forename: Dominique
authors.initials: D
authors.lastname: Brunel
authors.affiliation: INRA Génétique et Écophysiologie de la Qualité des Agrumes (GEQA), San Giuliano, France.
authors.forename: François
authors.initials: F
authors.lastname: Luro
authors.affiliation: 1] Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA. [2].
authors.forename: Chunxian
authors.initials: C
authors.lastname: Chen
authors.affiliation: Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
authors.forename: William G
authors.initials: WG
authors.lastname: Farmerie
authors.affiliation: 454 Life Sciences, Roche, Branford, Connecticut, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Desany
authors.affiliation: 454 Life Sciences, Roche, Branford, Connecticut, USA.
authors.forename: Chinnappa
authors.initials: C
authors.lastname: Kodira
authors.affiliation: 454 Life Sciences, Roche, Branford, Connecticut, USA.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Mohiuddin
authors.affiliation: 1] 454 Life Sciences, Roche, Branford, Connecticut, USA. [2].
authors.forename: Tim
authors.initials: T
authors.lastname: Harkins
authors.affiliation: 454 Life Sciences, Roche, Branford, Connecticut, USA.
authors.forename: Karin
authors.initials: K
authors.lastname: Fredrikson
authors.affiliation: 1] 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.
authors.forename: Paul
authors.initials: P
authors.lastname: Burns
authors.affiliation: 1] 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.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Lomsadze
authors.affiliation: 1] 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.
authors.forename: Mark
authors.initials: M
authors.lastname: Borodovsky
authors.affiliation: Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Reforgiato
authors.affiliation: 1] Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil. [2] Embrapa Cassava and Fruits, Cruz das Almas, Brazil.
authors.forename: Juliana
authors.initials: J
authors.lastname: Freitas-Astúa
authors.affiliation: 1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] Département de Biologie, Université d'Evry, Evry, France.
authors.forename: Francis
authors.initials: F
authors.lastname: Quetier
authors.affiliation: Centro de Protección Vegetal y Biotecnología-Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Navarro
authors.affiliation: Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA.
authors.forename: Mikeal
authors.initials: M
authors.lastname: Roose
authors.affiliation: 1] 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.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: HudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: 1] Istituto di Genomica Applicata, Udine, Italy. [2] Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.affiliation: Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil.
authors.forename: Marcos Antonio
authors.initials: MA
authors.lastname: Machado
authors.affiliation: Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Talon
authors.affiliation: 1] 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.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.affiliation: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Ollitrault
authors.affiliation: Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA.
authors.forename: Frederick
authors.identifier: 0000000274990022
authors.initials: F
authors.lastname: Gmitter
authors.affiliation: 1] 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.
authors.forename: Daniel
authors.initials: D
authors.lastname: Rokhsar
mesh_terms: D001483:Base Sequence; D001947:Breeding; D002957:Citrus / Q000145:classification* / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D013045:Species Specificity