ArticleNature biotechnology2014
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.
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Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 313 papers.
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313citing papers in PubMed
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313 citing papers in PubMed, 717 citations in OpenAlex.
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- Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance.The plant genome · 2026Article
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- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- Whole-genome resequencing of 495Horticulture research · 2026Article
- Haplotype-resolved genome of Citrus × sinensis 'Pera IAC', the most widely cultivated sweet orange in Brazil.Scientific data · 2026Article
- AlleleMiner: a long-read pipeline for gene-wise de novo allele phasing and variant detection in diploid citrus cultivars.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Evidence of Hybrid Origin for DomesticatedPlants (Basel, Switzerland) · 2026Article
- De Novo Chromosome-Level Assembly of the Endangered Pilocarpus Microphyllus Highlights Genomic Resources for Conservation and Sustainable Pilocarpine Extraction.Genome biology and evolution · 2026Article
- Facilitating genomic breeding in citrus via reference panel-based whole-genome imputation of low-coverage sequencing-derived genotype data.Breeding science · 2026Article
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.Molecular ecology resources · 2026Article
- Genotyping-by-Sequencing Reveals Marker-Based Genome Stability in Tetraploid Clementines for Triploid Breeding.Plants (Basel, Switzerland) · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Comparative analysis of PRR receptors and R genes reveals structural and functional divergence between wild, ancestral, and commercial citrus species.BMC genomics · 2026Article
- Integrative chloroplast omics in citrus: computational insights into genomic structural adaptation and phylogenetic relationships from 35 species.Frontiers in plant science · 2026Article
- Integrative morphological, palynological, and phylogenomic evidence supports the recognition ofFrontiers in plant science · 2026Article
- High-density genetic mapping reveals QTLs associated with Huanglongbing tolerance in citrus.Frontiers in plant science · 2026Article
- Tracing the Holocene hybrid origin of cultivated walnut in southwestern China.Forestry research · 2026Article
253 more citing papers are in PubMed but not listed here.
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Authors and funding
55 authors at 18 institutions in 6 countries.
G Albert Wu1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2].
Simon Prochnik1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2].
Jerry JenkinsHudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
Jerome SalseInstitut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France.
Uffe HellstenUS Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Florent MuratInstitut National de la Recherche Agronomique (INRA), Université Blaise Pascal (UBP) UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales (GDEC), Clermont Ferrand, France.
Xavier PerrierCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
Manuel RuizCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
Simone ScalabrinIstituto di Genomica Applicata, Udine, Italy.
Javier TerolCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Marco Aurélio TakitaCentro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil.
Karine LabadieCommissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
Julie PoulainCommissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
Arnaud CoulouxCommissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
Kamel JabbariCommissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France.
Federica CattonaroIstituto di Genomica Applicata, Udine, Italy.
Cristian Del FabbroIstituto di Genomica Applicata, Udine, Italy.
Sara PinosioIstituto di Genomica Applicata, Udine, Italy.
Andrea Zuccolo1] Istituto di Genomica Applicata, Udine, Italy. [2] Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
Jarrod ChapmanUS Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Jane GrimwoodHudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
Francisco R TadeoCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Leandro H EstornellCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Juan V Muñoz-SanzCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Victoria IbanezCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Amparo Herrero-OrtegaCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Pablo AlezaCentro de Protección Vegetal y Biotecnología-Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain.
Julián Pérez-Pérez1] Lifesequencing, Valencia, Spain. [2] Secugen, Madrid, Spain.
Daniel RamónLifesequencing, Valencia, Spain.
Dominique Brunel1] 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.
François LuroINRA Génétique et Écophysiologie de la Qualité des Agrumes (GEQA), San Giuliano, France.
Chunxian Chen1] Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA. [2].
William G FarmerieInterdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA.
Brian Desany454 Life Sciences, Roche, Branford, Connecticut, USA.
Chinnappa Kodira454 Life Sciences, Roche, Branford, Connecticut, USA.
Mohammed Mohiuddin454 Life Sciences, Roche, Branford, Connecticut, USA.
Tim Harkins1] 454 Life Sciences, Roche, Branford, Connecticut, USA. [2].
Karin Fredrikson454 Life Sciences, Roche, Branford, Connecticut, USA.
Paul Burns1] 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.
Alexandre Lomsadze1] 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.
Mark Borodovsky1] 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.
Giuseppe ReforgiatoConsiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy.
Juliana Freitas-Astúa1] Centro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil. [2] Embrapa Cassava and Fruits, Cruz das Almas, Brazil.
Francis Quetier1] Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France. [2] Département de Biologie, Université d'Evry, Evry, France.
Luis NavarroCentro de Protección Vegetal y Biotecnología-Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain.
Mikeal RooseDepartment of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA.
Patrick Wincker1] 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.
Jeremy SchmutzHudsonAlpha Biotechnology Institute, Huntsville, Alabama, USA.
Michele Morgante1] Istituto di Genomica Applicata, Udine, Italy. [2] Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy.
Marcos Antonio MachadoCentro de Citricultura Sylvio Moreira, Instituto Agronômico (IAC), Cordeirópolis, Brazil.
Manuel TalonCentro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain.
Olivier Jaillon1] 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.
Patrick OllitraultCentre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Montpellier, France.
Frederick GmitterCitrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA.ORCID 0000000274990022
Daniel Rokhsar1] 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.
Instituto Valenciano de Investigaciones Agrarias · ESCommissariat à l'Énergie Atomique et aux Énergies Alternatives · FRJoint Genome Institute · USRoche (United States) · USIstituto di Genomica Applicata · ITAgronomical Institute of Campinas · BRBiotechnology Institute · USCentre de Coopération Internationale en Recherche Agronomique pour le Développement · FRGeorgia Institute of Technology · USCentre National de la Recherche Scientifique · FRFlorida Department of Citrus · USGénétique, Diversité, Écophysiologie des Céréales · FRIstituto Sperimentale per la Frutticoltura · ITLife Length (Spain) · ESScuola Superiore Sant'Anna · ITUniversity of California, Riverside · USUniversity of Florida · USUniversity of Udine · IT
Funding
PREDICTION OF GENE LOCATIONS USING STOCHASTIC MODELSR01HG000783 · NHGRI · GEORGIA INSTITUTE OF TECHNOLOGY · PI BORODOVSKY, MARK · 1993 to 2014
$4.7MNHGRI NIH HHS HG00783NHGRI NIH HHS R01 HG000783
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.
Indexed as
BreedingBase SequenceCitrusConserved SequenceCrops, AgriculturalEvolution, MolecularGenetic VariationGenome, PlantMolecular Sequence DataSequence Analysis, DNASpecies Specificity
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