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

G Albert Wu; Simon Prochnik; Jerry Jenkins; Jerome Salse; Uffe Hellsten; Florent Murat; Xavier Perrier; Manuel Ruiz; Simone Scalabrin; Javier Terol; Marco Aurélio Takita; Karine Labadie; Julie Poulain; Arnaud Couloux; Kamel Jabbari; Federica Cattonaro; Cristian Del Fabbro; Sara Pinosio; Andrea Zuccolo; Jarrod Chapman; Jane Grimwood; Francisco R Tadeo; Leandro H Estornell; Juan V Muñoz-Sanz; Victoria Ibanez; Amparo Herrero-Ortega; Pablo Aleza; Julián Pérez-Pérez; Daniel Ramón; Dominique Brunel; François Luro; Chunxian Chen; William G Farmerie; Brian Desany; Chinnappa Kodira; Mohammed Mohiuddin; Tim Harkins; Karin Fredrikson; Paul Burns; Alexandre Lomsadze; Mark Borodovsky; Giuseppe Reforgiato; Juliana Freitas-Astúa; Francis Quetier; Luis Navarro; Mikeal Roose; Patrick Wincker; Jeremy Schmutz; Michele Morgante; Marcos Antonio Machado; Manuel Talon; Olivier Jaillon; Patrick Ollitrault; Frederick Gmitter; Daniel Rokhsar

doi:10.1038/nbt.2906

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

Journal article

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

G Albert Wu, Simon Prochnik, Jerry Jenkins, Jerome Salse, Uffe Hellsten, Florent Murat, Xavier Perrier, Manuel Ruiz, Simone Scalabrin, Javier Terol, …

Nature biotechnology, Vol.32(7), pp.656-662

01/07/2014

DOI: https://doi.org/10.1038/nbt.2906

PMCID: PMC4113729

PMID: 24908277

Abstract

Base Sequence

Breeding

Citrus - classification

Citrus - genetics

Conserved Sequence - genetics

Crops, Agricultural - genetics

Evolution, Molecular

Genetic Variation - genetics

Genome, Plant - genetics

Molecular Sequence Data

Sequence Analysis, DNA

Species Specificity

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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Title: Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
Creators - without role: G Albert Wu - Joint Genome Institute
Simon Prochnik - Joint Genome Institute
Jerry Jenkins - HudsonAlpha Institute for Biotechnology
Jerome Salse - Genetics, Diversity and Ecophysiology of Cereals
Uffe Hellsten - Joint Genome Institute
Florent Murat - Genetics, Diversity and Ecophysiology of Cereals
Xavier Perrier - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Manuel Ruiz - Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
Simone Scalabrin - Istituto di Genomica Applicata
Javier Terol - Instituto Valenciano de Investigaciones Agrarias
Marco Aurélio Takita - Agronomical Institute of Campinas
Karine Labadie - Genoscope
Julie Poulain - Genoscope
Arnaud Couloux - Genoscope
Kamel Jabbari - Genoscope
Federica Cattonaro - Istituto di Genomica Applicata
Cristian Del Fabbro - Istituto di Genomica Applicata
Sara Pinosio - Istituto di Genomica Applicata
Andrea Zuccolo - Istituto di Genomica Applicata
Jarrod Chapman - Joint Genome Institute
Jane Grimwood - HudsonAlpha Institute for Biotechnology
Francisco R Tadeo - Instituto Valenciano de Investigaciones Agrarias
Leandro H Estornell - Instituto Valenciano de Investigaciones Agrarias
Juan V Muñoz-Sanz - Instituto Valenciano de Investigaciones Agrarias
Victoria Ibanez - Instituto Valenciano de Investigaciones Agrarias
Amparo Herrero-Ortega - Instituto Valenciano de Investigaciones Agrarias
Pablo Aleza - Instituto Valenciano de Investigaciones Agrarias
Julián Pérez-Pérez - 1] Lifesequencing, Valencia, Spain. Secugen, Madrid, Spain
Daniel Ramón - Lifesequencing, Valencia, Spain
Dominique Brunel - Fondation Jean Dausset-CEPH
François Luro - INRA Génétique et Écophysiologie de la Qualité des Agrumes (GEQA), San Giuliano, France
Chunxian Chen - Florida Department of Citrus
William G Farmerie - University of Florida
Brian Desany - Enzo Life Sciences
Chinnappa Kodira - Enzo Life Sciences
Mohammed Mohiuddin - Enzo Life Sciences
Tim Harkins - Enzo Life Sciences
Karin Fredrikson - Enzo Life Sciences
Paul Burns - The Wallace H. Coulter Department of Biomedical Engineering
Alexandre Lomsadze - The Wallace H. Coulter Department of Biomedical Engineering
Mark Borodovsky - The Wallace H. Coulter Department of Biomedical Engineering
Giuseppe Reforgiato - Istituto Sperimentale per la Frutticoltura
Juliana Freitas-Astúa - Agronomical Institute of Campinas
Francis Quetier - Genoscope
Luis Navarro - Instituto Valenciano de Investigaciones Agrarias
Mikeal Roose - University of California, Riverside
Patrick Wincker - University of Évry Val d'Essonne
Jeremy Schmutz - HudsonAlpha Institute for Biotechnology
Michele Morgante - University of Udine
Marcos Antonio Machado - Agronomical Institute of Campinas
Manuel Talon - Instituto Valenciano de Investigaciones Agrarias
Olivier Jaillon - University of Évry Val d'Essonne
Patrick Ollitrault - Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
Frederick Gmitter - Florida Department of Citrus
Daniel Rokhsar - Joint Genome Institute
Publication Details: Nature biotechnology, Vol.32(7), pp.656-662
Grant note: HG00783 / NHGRI NIH HHS R01 HG000783 / NHGRI NIH HHS
Identifiers: 9943738708331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article