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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication</title><author><name sortKey="Wu, G Albert" sort="Wu, G Albert" uniqKey="Wu G" first="G. Albert" last="Wu">G. Albert Wu</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Prochnik, Simon" sort="Prochnik, Simon" uniqKey="Prochnik S" first="Simon" last="Prochnik">Simon Prochnik</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Jenkins, Jerry" sort="Jenkins, Jerry" uniqKey="Jenkins J" first="Jerry" last="Jenkins">Jerry Jenkins</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Salse, Jerome" sort="Salse, Jerome" uniqKey="Salse J" first="Jerome" last="Salse">Jerome Salse</name><affiliation><nlm:aff id="A3">INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Hellsten, Uffe" sort="Hellsten, Uffe" uniqKey="Hellsten U" first="Uffe" last="Hellsten">Uffe Hellsten</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Murat, Florent" sort="Murat, Florent" uniqKey="Murat F" first="Florent" last="Murat">Florent Murat</name><affiliation><nlm:aff id="A3">INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Perrier, Xavier" sort="Perrier, Xavier" uniqKey="Perrier X" first="Xavier" last="Perrier">Xavier Perrier</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Ruiz, Manuel" sort="Ruiz, Manuel" uniqKey="Ruiz M" first="Manuel" last="Ruiz">Manuel Ruiz</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Scalabrin, Simone" sort="Scalabrin, Simone" uniqKey="Scalabrin S" first="Simone" last="Scalabrin">Simone Scalabrin</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Takita, Marco Aurelio" sort="Takita, Marco Aurelio" uniqKey="Takita M" first="Marco Aurélio" last="Takita">Marco Aurélio Takita</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation></author><author><name sortKey="Labadie, Karine" sort="Labadie, Karine" uniqKey="Labadie K" first="Karine" last="Labadie">Karine Labadie</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Poulain, Julie" sort="Poulain, Julie" uniqKey="Poulain J" first="Julie" last="Poulain">Julie Poulain</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Couloux, Arnaud" sort="Couloux, Arnaud" uniqKey="Couloux A" first="Arnaud" last="Couloux">Arnaud Couloux</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Jabbari, Kamel" sort="Jabbari, Kamel" uniqKey="Jabbari K" first="Kamel" last="Jabbari">Kamel Jabbari</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Del Fabbro, Cristian" sort="Del Fabbro, Cristian" uniqKey="Del Fabbro C" first="Cristian" last="Del Fabbro">Cristian Del Fabbro</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="A26">Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Chapman, Jarrod" sort="Chapman, Jarrod" uniqKey="Chapman J" first="Jarrod" last="Chapman">Jarrod Chapman</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Tadeo, Francisco R" sort="Tadeo, Francisco R" uniqKey="Tadeo F" first="Francisco R." last="Tadeo">Francisco R. Tadeo</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Estornell, Leandro H" sort="Estornell, Leandro H" uniqKey="Estornell L" first="Leandro H." last="Estornell">Leandro H. Estornell</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Mu Oz Sanz, Juan V" sort="Mu Oz Sanz, Juan V" uniqKey="Mu Oz Sanz J" first="Juan V." last="Mu Oz-Sanz">Juan V. Mu Oz-Sanz</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Ibanez, Victoria" sort="Ibanez, Victoria" uniqKey="Ibanez V" first="Victoria" last="Ibanez">Victoria Ibanez</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Herrero Ortega, Amparo" sort="Herrero Ortega, Amparo" uniqKey="Herrero Ortega A" first="Amparo" last="Herrero-Ortega">Amparo Herrero-Ortega</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Aleza, Pablo" sort="Aleza, Pablo" uniqKey="Aleza P" first="Pablo" last="Aleza">Pablo Aleza</name><affiliation><nlm:aff id="A9">Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Perez Perez, Julian" sort="Perez Perez, Julian" uniqKey="Perez Perez J" first="Julián" last="Pérez-Pérez">Julián Pérez-Pérez</name><affiliation><nlm:aff id="A10">Lifesequencing SL, Valencia, Spain</nlm:aff></affiliation><affiliation><nlm:aff id="A27">Secugen SL, Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Ram N, Daniel" sort="Ram N, Daniel" uniqKey="Ram N D" first="Daniel" last="Ram N">Daniel Ram N</name><affiliation><nlm:aff id="A10">Lifesequencing SL, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Brunel, Dominique" sort="Brunel, Dominique" uniqKey="Brunel D" first="Dominique" last="Brunel">Dominique Brunel</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A11">INRA, US EPGV_1279, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Luro, Francois" sort="Luro, Francois" uniqKey="Luro F" first="François" last="Luro">François Luro</name><affiliation><nlm:aff id="A12">INRA GEQA, San Giuliano, France</nlm:aff></affiliation></author><author><name sortKey="Chen, Chunxian" sort="Chen, Chunxian" uniqKey="Chen C" first="Chunxian" last="Chen">Chunxian Chen</name><affiliation><nlm:aff id="A13">Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Farmerie, William G" sort="Farmerie, William G" uniqKey="Farmerie W" first="William G." last="Farmerie">William G. Farmerie</name><affiliation><nlm:aff id="A14">Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Desany, Brian" sort="Desany, Brian" uniqKey="Desany B" first="Brian" last="Desany">Brian Desany</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Kodira, Chinnappa" sort="Kodira, Chinnappa" uniqKey="Kodira C" first="Chinnappa" last="Kodira">Chinnappa Kodira</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Mohiuddin, Mohammed" sort="Mohiuddin, Mohammed" uniqKey="Mohiuddin M" first="Mohammed" last="Mohiuddin">Mohammed Mohiuddin</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Harkins, Tim" sort="Harkins, Tim" uniqKey="Harkins T" first="Tim" last="Harkins">Tim Harkins</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Fredrikson, Karin" sort="Fredrikson, Karin" uniqKey="Fredrikson K" first="Karin" last="Fredrikson">Karin Fredrikson</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Burns, Paul" sort="Burns, Paul" uniqKey="Burns P" first="Paul" last="Burns">Paul Burns</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation></author><author><name sortKey="Lomsadze, Alexandre" sort="Lomsadze, Alexandre" uniqKey="Lomsadze A" first="Alexandre" last="Lomsadze">Alexandre Lomsadze</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation></author><author><name sortKey="Borodovsky, Mark" sort="Borodovsky, Mark" uniqKey="Borodovsky M" first="Mark" last="Borodovsky">Mark Borodovsky</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A18">Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia</nlm:aff></affiliation></author><author><name sortKey="Reforgiato, Giuseppe" sort="Reforgiato, Giuseppe" uniqKey="Reforgiato G" first="Giuseppe" last="Reforgiato">Giuseppe Reforgiato</name><affiliation><nlm:aff id="A19">Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy</nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, Juliana" sort="Freitas Astua, Juliana" uniqKey="Freitas Astua J" first="Juliana" last="Freitas-Astúa">Juliana Freitas-Astúa</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation><affiliation><nlm:aff id="A20">Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil</nlm:aff></affiliation></author><author><name sortKey="Quetier, Francis" sort="Quetier, Francis" uniqKey="Quetier F" first="Francis" last="Quetier">Francis Quetier</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Navarro, Luis" sort="Navarro, Luis" uniqKey="Navarro L" first="Luis" last="Navarro">Luis Navarro</name><affiliation><nlm:aff id="A9">Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Roose, Mikeal" sort="Roose, Mikeal" uniqKey="Roose M" first="Mikeal" last="Roose">Mikeal Roose</name><affiliation><nlm:aff id="A22">Department of Botany and Plant Sciences, University of California, Riverside, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A23">Centre National de Recherche Scientifique (CNRS), Evry, France</nlm:aff></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="A24">Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Machado, Marcos Antonio" sort="Machado, Marcos Antonio" uniqKey="Machado M" first="Marcos Antonio" last="Machado">Marcos Antonio Machado</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation></author><author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Jaillon, Olivier" sort="Jaillon, Olivier" uniqKey="Jaillon O" first="Olivier" last="Jaillon">Olivier Jaillon</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A23">Centre National de Recherche Scientifique (CNRS), Evry, France</nlm:aff></affiliation></author><author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Gmitter, Frederick" sort="Gmitter, Frederick" uniqKey="Gmitter F" first="Frederick" last="Gmitter">Frederick Gmitter</name><affiliation><nlm:aff id="A13">Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Rokhsar, Daniel" sort="Rokhsar, Daniel" uniqKey="Rokhsar D" first="Daniel" last="Rokhsar">Daniel Rokhsar</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A25">Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24908277</idno><idno type="pmc">4113729</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113729</idno><idno type="RBID">PMC:4113729</idno><idno type="doi">10.1038/nbt.2906</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001322</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication</title><author><name sortKey="Wu, G Albert" sort="Wu, G Albert" uniqKey="Wu G" first="G. Albert" last="Wu">G. Albert Wu</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Prochnik, Simon" sort="Prochnik, Simon" uniqKey="Prochnik S" first="Simon" last="Prochnik">Simon Prochnik</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Jenkins, Jerry" sort="Jenkins, Jerry" uniqKey="Jenkins J" first="Jerry" last="Jenkins">Jerry Jenkins</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Salse, Jerome" sort="Salse, Jerome" uniqKey="Salse J" first="Jerome" last="Salse">Jerome Salse</name><affiliation><nlm:aff id="A3">INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Hellsten, Uffe" sort="Hellsten, Uffe" uniqKey="Hellsten U" first="Uffe" last="Hellsten">Uffe Hellsten</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Murat, Florent" sort="Murat, Florent" uniqKey="Murat F" first="Florent" last="Murat">Florent Murat</name><affiliation><nlm:aff id="A3">INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France</nlm:aff></affiliation></author><author><name sortKey="Perrier, Xavier" sort="Perrier, Xavier" uniqKey="Perrier X" first="Xavier" last="Perrier">Xavier Perrier</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Ruiz, Manuel" sort="Ruiz, Manuel" uniqKey="Ruiz M" first="Manuel" last="Ruiz">Manuel Ruiz</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Scalabrin, Simone" sort="Scalabrin, Simone" uniqKey="Scalabrin S" first="Simone" last="Scalabrin">Simone Scalabrin</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Takita, Marco Aurelio" sort="Takita, Marco Aurelio" uniqKey="Takita M" first="Marco Aurélio" last="Takita">Marco Aurélio Takita</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation></author><author><name sortKey="Labadie, Karine" sort="Labadie, Karine" uniqKey="Labadie K" first="Karine" last="Labadie">Karine Labadie</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Poulain, Julie" sort="Poulain, Julie" uniqKey="Poulain J" first="Julie" last="Poulain">Julie Poulain</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Couloux, Arnaud" sort="Couloux, Arnaud" uniqKey="Couloux A" first="Arnaud" last="Couloux">Arnaud Couloux</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Jabbari, Kamel" sort="Jabbari, Kamel" uniqKey="Jabbari K" first="Kamel" last="Jabbari">Kamel Jabbari</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Cattonaro, Federica" sort="Cattonaro, Federica" uniqKey="Cattonaro F" first="Federica" last="Cattonaro">Federica Cattonaro</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Del Fabbro, Cristian" sort="Del Fabbro, Cristian" uniqKey="Del Fabbro C" first="Cristian" last="Del Fabbro">Cristian Del Fabbro</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Pinosio, Sara" sort="Pinosio, Sara" uniqKey="Pinosio S" first="Sara" last="Pinosio">Sara Pinosio</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Zuccolo, Andrea" sort="Zuccolo, Andrea" uniqKey="Zuccolo A" first="Andrea" last="Zuccolo">Andrea Zuccolo</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="A26">Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy</nlm:aff></affiliation></author><author><name sortKey="Chapman, Jarrod" sort="Chapman, Jarrod" uniqKey="Chapman J" first="Jarrod" last="Chapman">Jarrod Chapman</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Grimwood, Jane" sort="Grimwood, Jane" uniqKey="Grimwood J" first="Jane" last="Grimwood">Jane Grimwood</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Tadeo, Francisco R" sort="Tadeo, Francisco R" uniqKey="Tadeo F" first="Francisco R." last="Tadeo">Francisco R. Tadeo</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Estornell, Leandro H" sort="Estornell, Leandro H" uniqKey="Estornell L" first="Leandro H." last="Estornell">Leandro H. Estornell</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Mu Oz Sanz, Juan V" sort="Mu Oz Sanz, Juan V" uniqKey="Mu Oz Sanz J" first="Juan V." last="Mu Oz-Sanz">Juan V. Mu Oz-Sanz</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Ibanez, Victoria" sort="Ibanez, Victoria" uniqKey="Ibanez V" first="Victoria" last="Ibanez">Victoria Ibanez</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Herrero Ortega, Amparo" sort="Herrero Ortega, Amparo" uniqKey="Herrero Ortega A" first="Amparo" last="Herrero-Ortega">Amparo Herrero-Ortega</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Aleza, Pablo" sort="Aleza, Pablo" uniqKey="Aleza P" first="Pablo" last="Aleza">Pablo Aleza</name><affiliation><nlm:aff id="A9">Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Perez Perez, Julian" sort="Perez Perez, Julian" uniqKey="Perez Perez J" first="Julián" last="Pérez-Pérez">Julián Pérez-Pérez</name><affiliation><nlm:aff id="A10">Lifesequencing SL, Valencia, Spain</nlm:aff></affiliation><affiliation><nlm:aff id="A27">Secugen SL, Madrid, Spain</nlm:aff></affiliation></author><author><name sortKey="Ram N, Daniel" sort="Ram N, Daniel" uniqKey="Ram N D" first="Daniel" last="Ram N">Daniel Ram N</name><affiliation><nlm:aff id="A10">Lifesequencing SL, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Brunel, Dominique" sort="Brunel, Dominique" uniqKey="Brunel D" first="Dominique" last="Brunel">Dominique Brunel</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A11">INRA, US EPGV_1279, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Luro, Francois" sort="Luro, Francois" uniqKey="Luro F" first="François" last="Luro">François Luro</name><affiliation><nlm:aff id="A12">INRA GEQA, San Giuliano, France</nlm:aff></affiliation></author><author><name sortKey="Chen, Chunxian" sort="Chen, Chunxian" uniqKey="Chen C" first="Chunxian" last="Chen">Chunxian Chen</name><affiliation><nlm:aff id="A13">Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Farmerie, William G" sort="Farmerie, William G" uniqKey="Farmerie W" first="William G." last="Farmerie">William G. Farmerie</name><affiliation><nlm:aff id="A14">Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Desany, Brian" sort="Desany, Brian" uniqKey="Desany B" first="Brian" last="Desany">Brian Desany</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Kodira, Chinnappa" sort="Kodira, Chinnappa" uniqKey="Kodira C" first="Chinnappa" last="Kodira">Chinnappa Kodira</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Mohiuddin, Mohammed" sort="Mohiuddin, Mohammed" uniqKey="Mohiuddin M" first="Mohammed" last="Mohiuddin">Mohammed Mohiuddin</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Harkins, Tim" sort="Harkins, Tim" uniqKey="Harkins T" first="Tim" last="Harkins">Tim Harkins</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Fredrikson, Karin" sort="Fredrikson, Karin" uniqKey="Fredrikson K" first="Karin" last="Fredrikson">Karin Fredrikson</name><affiliation><nlm:aff id="A15">454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</nlm:aff></affiliation></author><author><name sortKey="Burns, Paul" sort="Burns, Paul" uniqKey="Burns P" first="Paul" last="Burns">Paul Burns</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation></author><author><name sortKey="Lomsadze, Alexandre" sort="Lomsadze, Alexandre" uniqKey="Lomsadze A" first="Alexandre" last="Lomsadze">Alexandre Lomsadze</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation></author><author><name sortKey="Borodovsky, Mark" sort="Borodovsky, Mark" uniqKey="Borodovsky M" first="Mark" last="Borodovsky">Mark Borodovsky</name><affiliation><nlm:aff id="A16">Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A17">School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A18">Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia</nlm:aff></affiliation></author><author><name sortKey="Reforgiato, Giuseppe" sort="Reforgiato, Giuseppe" uniqKey="Reforgiato G" first="Giuseppe" last="Reforgiato">Giuseppe Reforgiato</name><affiliation><nlm:aff id="A19">Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy</nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, Juliana" sort="Freitas Astua, Juliana" uniqKey="Freitas Astua J" first="Juliana" last="Freitas-Astúa">Juliana Freitas-Astúa</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation><affiliation><nlm:aff id="A20">Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil</nlm:aff></affiliation></author><author><name sortKey="Quetier, Francis" sort="Quetier, Francis" uniqKey="Quetier F" first="Francis" last="Quetier">Francis Quetier</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation></author><author><name sortKey="Navarro, Luis" sort="Navarro, Luis" uniqKey="Navarro L" first="Luis" last="Navarro">Luis Navarro</name><affiliation><nlm:aff id="A9">Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Roose, Mikeal" sort="Roose, Mikeal" uniqKey="Roose M" first="Mikeal" last="Roose">Mikeal Roose</name><affiliation><nlm:aff id="A22">Department of Botany and Plant Sciences, University of California, Riverside, CA, USA</nlm:aff></affiliation></author><author><name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A23">Centre National de Recherche Scientifique (CNRS), Evry, France</nlm:aff></affiliation></author><author><name sortKey="Schmutz, Jeremy" sort="Schmutz, Jeremy" uniqKey="Schmutz J" first="Jeremy" last="Schmutz">Jeremy Schmutz</name><affiliation><nlm:aff id="A2">HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</nlm:aff></affiliation></author><author><name sortKey="Morgante, Michele" sort="Morgante, Michele" uniqKey="Morgante M" first="Michele" last="Morgante">Michele Morgante</name><affiliation><nlm:aff id="A5">Istituto di Genomica Applicata, Udine, Italy</nlm:aff></affiliation><affiliation><nlm:aff id="A24">Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy</nlm:aff></affiliation></author><author><name sortKey="Machado, Marcos Antonio" sort="Machado, Marcos Antonio" uniqKey="Machado M" first="Marcos Antonio" last="Machado">Marcos Antonio Machado</name><affiliation><nlm:aff id="A6">Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</nlm:aff></affiliation></author><author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name><affiliation><nlm:aff id="A8">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</nlm:aff></affiliation></author><author><name sortKey="Jaillon, Olivier" sort="Jaillon, Olivier" uniqKey="Jaillon O" first="Olivier" last="Jaillon">Olivier Jaillon</name><affiliation><nlm:aff id="A7">Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A21">Département de Biologie, Université d’Evry, Evry, France</nlm:aff></affiliation><affiliation><nlm:aff id="A23">Centre National de Recherche Scientifique (CNRS), Evry, France</nlm:aff></affiliation></author><author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name><affiliation><nlm:aff id="A4">CIRAD, UMR AGAP, Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Gmitter, Frederick" sort="Gmitter, Frederick" uniqKey="Gmitter F" first="Frederick" last="Gmitter">Frederick Gmitter</name><affiliation><nlm:aff id="A13">Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA</nlm:aff></affiliation></author><author><name sortKey="Rokhsar, Daniel" sort="Rokhsar, Daniel" uniqKey="Rokhsar D" first="Daniel" last="Rokhsar">Daniel Rokhsar</name><affiliation><nlm:aff id="A1">US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A25">Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Nature biotechnology</title><idno type="ISSN">1087-0156</idno><idno type="eISSN">1546-1696</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P4">The domestication of citrus, is poorly understood. Cultivated types are selections from, or hybrids of, wild progenitor species, whose identities and contributions remain controversial. By comparative analysis of a collection of citrus genomes, including a high quality haploid reference, we show that cultivated types were derived from two progenitor species. Though cultivated pummelos represent selections from a single progenitor species, <italic>C. maxima</italic>, cultivated mandarins are introgressions of <italic>C. maxima</italic> into the ancestral mandarin species, <italic>C. reticulata</italic>. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure <italic>C. maxima</italic> and <italic>C. reticulata</italic> parents, implying that wild mandarins were part of the early breeding germplasm. A wild “mandarin” from China exhibited substantial divergence from <italic>C. reticulata</italic>, suggesting the possibility of other unrecognized wild citrus species. 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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9604648</journal-id><journal-id journal-id-type="pubmed-jr-id">20305</journal-id><journal-id journal-id-type="nlm-ta">Nat Biotechnol</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Biotechnol.</journal-id><journal-title-group><journal-title>Nature biotechnology</journal-title></journal-title-group><issn pub-type="ppub">1087-0156</issn><issn pub-type="epub">1546-1696</issn></journal-meta><article-meta><article-id pub-id-type="pmid">24908277</article-id><article-id pub-id-type="pmc">4113729</article-id><article-id pub-id-type="doi">10.1038/nbt.2906</article-id><article-id pub-id-type="manuscript">NIHMS586218</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wu</surname><given-names>G. Albert</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="author-notes" rid="FN3">†</xref></contrib><contrib contrib-type="author"><name><surname>Prochnik</surname><given-names>Simon</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="author-notes" rid="FN3">†</xref></contrib><contrib contrib-type="author"><name><surname>Jenkins</surname><given-names>Jerry</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Salse</surname><given-names>Jerome</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Hellsten</surname><given-names>Uffe</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Murat</surname><given-names>Florent</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Perrier</surname><given-names>Xavier</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Ruiz</surname><given-names>Manuel</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Scalabrin</surname><given-names>Simone</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Terol</surname><given-names>Javier</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Takita</surname><given-names>Marco Aurélio</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Labadie</surname><given-names>Karine</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Poulain</surname><given-names>Julie</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Couloux</surname><given-names>Arnaud</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Jabbari</surname><given-names>Kamel</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Cattonaro</surname><given-names>Federica</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Del Fabbro</surname><given-names>Cristian</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Pinosio</surname><given-names>Sara</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib 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contrib-type="author"><name><surname>Ollitrault</surname><given-names>Patrick</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Gmitter</surname><given-names>Frederick</given-names></name><xref ref-type="aff" rid="A13">13</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Rokhsar</surname><given-names>Daniel</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A25">25</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="A1"><label>1</label>US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA</aff><aff id="A2"><label>2</label>HudsonAlpha Biotechnology Institute, Huntsville, AL, USA</aff><aff id="A3"><label>3</label>INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France</aff><aff id="A4"><label>4</label>CIRAD, UMR AGAP, Montpellier, France</aff><aff id="A5"><label>5</label>Istituto di Genomica Applicata, Udine, Italy</aff><aff id="A6"><label>6</label>Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil</aff><aff id="A7"><label>7</label>Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France</aff><aff id="A8"><label>8</label>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain</aff><aff id="A9"><label>9</label>Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain</aff><aff id="A10"><label>10</label>Lifesequencing SL, Valencia, Spain</aff><aff id="A11"><label>11</label>INRA, US EPGV_1279, Evry, France</aff><aff id="A12"><label>12</label>INRA GEQA, San Giuliano, France</aff><aff id="A13"><label>13</label>Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA</aff><aff id="A14"><label>14</label>Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA</aff><aff id="A15"><label>15</label>454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA</aff><aff id="A16"><label>16</label>Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA</aff><aff id="A17"><label>17</label>School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA</aff><aff id="A18"><label>18</label>Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia</aff><aff id="A19"><label>19</label>Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy</aff><aff id="A20"><label>20</label>Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil</aff><aff id="A21"><label>21</label>Département de Biologie, Université d’Evry, Evry, France</aff><aff id="A22"><label>22</label>Department of Botany and Plant Sciences, University of California, Riverside, CA, USA</aff><aff id="A23"><label>23</label>Centre National de Recherche Scientifique (CNRS), Evry, France</aff><aff id="A24"><label>24</label>Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy</aff><aff id="A25"><label>25</label>Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA</aff><aff id="A26"><label>26</label>Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy</aff><aff id="A27"><label>27</label>Secugen SL, Madrid, Spain</aff><author-notes><corresp id="cor1"><label>*</label>Correspondence to: D.S.R. (<email>dsrokhsar@gmail.com</email>); F.G.G. (<email>fgmitter@ufl.edu</email>)</corresp><fn id="FN1" fn-type="present-address"><label>‡</label><p id="P1">Current address: Life Technologies Corp., Grand Island, NY 14072, USA.</p></fn><fn id="FN2" fn-type="present-address"><label>¶</label><p id="P2">Current address: USDA, ARS, Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, USA</p></fn><fn id="FN3" fn-type="equal"><label>†</label><p id="P3">These authors contributed equally.</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>21</day><month>5</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>08</day><month>6</month><year>2014</year></pub-date><pub-date pub-type="ppub"><month>7</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>01</day><month>1</month><year>2015</year></pub-date><volume>32</volume><issue>7</issue><fpage>656</fpage><lpage>662</lpage><pmc-comment>elocation-id from pubmed: 10.1038/nbt.2906</pmc-comment>
<permissions><license xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms"><license-p>Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:<ext-link ext-link-type="uri" xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms">http://www.nature.com/authors/editorial_policies/license.html#terms</ext-link></license-p></license></permissions><abstract><p id="P4">The domestication of citrus, is poorly understood. Cultivated types are selections from, or hybrids of, wild progenitor species, whose identities and contributions remain controversial. By comparative analysis of a collection of citrus genomes, including a high quality haploid reference, we show that cultivated types were derived from two progenitor species. Though cultivated pummelos represent selections from a single progenitor species, <italic>C. maxima</italic>, cultivated mandarins are introgressions of <italic>C. maxima</italic> into the ancestral mandarin species, <italic>C. reticulata</italic>. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure <italic>C. maxima</italic> and <italic>C. reticulata</italic> parents, implying that wild mandarins were part of the early breeding germplasm. A wild “mandarin” from China exhibited substantial divergence from <italic>C. reticulata</italic>, suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and enables sequence-directed genetic improvement.</p></abstract></article-meta></front><body><p id="P5">Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of US$9 billion (<ext-link ext-link-type="uri" xlink:href="http://www.fas.usda.gov/psdonline/circulars/citrus.pdf">http://www.fas.usda.gov/psdonline/circulars/citrus.pdf</ext-link>). The very narrow genetic diversity of cultivated citrus makes it highly vulnerable to disease outbreaks, including citrus greening disease (also known as Huanglongbing or HLB), which is rapidly spreading throughout the world’s major citrus producing regions<sup><xref rid="R1" ref-type="bibr">1</xref></sup>. Understanding the population genomics and domestication of citrus will enable strategies for improvements including resistance to greening and other diseases.</p><p id="P6">The domestication and distribution of edible citrus types began several thousand years ago in Southeast Asia and spread globally following ancient land and sea routes. The lineages that gave rise to most modern cultivated varieties, however, are lost in undocumented antiquity, and their identities remain controversial<sup><xref rid="R2" ref-type="bibr">2</xref>, <xref rid="R3" ref-type="bibr">3</xref></sup>. Several features of <italic>Citrus</italic> biology and cultivation make deciphering these origins difficult. Cultivated varieties are typically propagated clonally by grafting and through asexual seed production (apomixis <italic>via</italic> nucellar polyembryony) to maintain desirable combinations of traits (<xref ref-type="fig" rid="F1">Fig. 1</xref>). Thus many important cultivar groups have characteristic basic genotypes that presumably arose through inter specific hybridization and/or successive introgressive hybridizations of wild ancestral species. These domestication events predated the global expansion of citrus cultivation by hundreds or perhaps thousands of years, with no record of the domestication process. Diversity within such groups arises through accumulated somatic mutations, generally without sexual recombination, either as limb sports on trees or variants among apomictic seedling progeny.</p><p id="P7">Two wild species are believed to have contributed to domesticated pummelos, mandarins and oranges (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 1</xref>). Based on morphology and genetic markers, “pummelos” have generally been identified with the wild species <italic>C. maxima</italic> (Burm.) Merrill that is indigenous to Southeast Asia. Although “mandarins” are similarly widely identified with the species <italic>C. reticulata</italic> Blanco<sup><xref rid="R4" ref-type="bibr">4</xref>–<xref rid="R6" ref-type="bibr">6</xref></sup>, wild populations of <italic>C. reticulata</italic> have not been definitively described. Various authors have taken different approaches to classifying mandarins, and several naming conventions have been developed<sup><xref rid="R7" ref-type="bibr">7</xref>, <xref rid="R8" ref-type="bibr">8</xref></sup>. Here we emphasize that the term “mandarin” is a commercial or popular designation referring to citrus with small, easy-peeling, sweet fruit, and not necessarily a taxonomic one. We use the qualifier “traditional” to refer to mandarins without previously suspected admixture from other ancestral species, to distinguish them from mandarin types that are known or believed to be recent hybrids. For clarity we use "×" in the systematic name of such known hybrids (see <italic>e.g</italic>., Ref.<sup><xref rid="R9" ref-type="bibr">9</xref></sup>). Recognizing that genome sequencing and diversity analysis has provided insights into the domestication history of several other fruit crops<sup><xref rid="R10" ref-type="bibr">10</xref>, <xref rid="R11" ref-type="bibr">11</xref></sup>, cereals<sup><xref rid="R12" ref-type="bibr">12</xref>, <xref rid="R13" ref-type="bibr">13</xref></sup> and other crops (reviewed in Ref.<sup><xref rid="R14" ref-type="bibr">14</xref></sup>), we sequenced and analyzed the genomes of a diverse collection of cultivated pummelos, mandarins and oranges to test the pummelo-mandarin species hypothesis and to uncover the origins of several important citrus cultivars.</p><sec sec-type="results" id="S1"><title>Results</title><sec id="S2"><title>A high quality reference Clementine genome</title><p id="P8">To provide a genomic platform for analyzing <italic>Citrus</italic>, we generated a high quality reference genome from ~7× Sanger dideoxy whole genome shotgun coverage of a haploid derivative of Clementine “mandarin” (<italic>C</italic>. × <italic>clementina</italic> cv. Clemenules)<sup><xref rid="R15" ref-type="bibr">15</xref></sup> (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 2</xref>). The use of haploid material (derived from a single ovule after induced gynogenesis<sup><xref rid="R15" ref-type="bibr">15</xref>, <xref rid="R16" ref-type="bibr">16</xref></sup>) removes complications that arise when assembling outbred diploid genomes. The resulting 301.4 Mbp reference sequence is nearly complete, with superior assembly contiguity (contig L50 = 119 kbp) and scaffolding (scaffold L50 before pseudochromosome construction = 6.8 Mbp) compared to a recently published sweet orange draft sequence<sup><xref rid="R17" ref-type="bibr">17</xref></sup> (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 2</xref>). The long scaffolds allowed us to construct pseudochromosomes by assigning 96% of the assembly to a location on the nine citrus chromosomes using the latest citrus genetic map<sup><xref rid="R18" ref-type="bibr">18</xref></sup>, compared with only 79% in the sweet orange draft<sup><xref rid="R17" ref-type="bibr">17</xref></sup>(<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 2</xref>). From sequence data we also inferred the phase of the two diploid Clementine haplotypes, identifying ten crossovers from the meiosis that produced the haploid Clementine (<xref ref-type="supplementary-material" rid="SD1">Supplementary Fig. 1</xref>), and annotated nominal centromeres as large regions of low recombination (<xref ref-type="supplementary-material" rid="SD1">Supplementary Figs. 2–11</xref>). Independently we also sequenced and assembled a draft genome of the (diploid) sweet orange variety ‘Ridge Pineapple’ by combining deep 454 sequence with light Sanger sampling (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 3</xref>) and inferred chromosome phasing using the recently reported rough draft genome of a sweet-orange-derived dihaploid<sup><xref rid="R17" ref-type="bibr">17</xref></sup>.</p><p id="P9">The citrus genome retains substantial segmental synteny (that is, local co-linearity) with other eudicots, although it has experienced extensive large-scale rearrangement on the chromosome scale (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 4</xref>). Based on analysis of synteny we propose a specific model for the origin of the citrus genome from the paleo-hexaploid eudicot ancestor<sup><xref rid="R19" ref-type="bibr">19</xref></sup> through a series of chromosome fissions and fusions (<xref ref-type="supplementary-material" rid="SD1">Supplementary Figs. 12,13</xref>). Despite the compactness of the citrus genome, 45% is repetitive, with long-terminal repeat retrotransposons and numerous uncharacterized elements, each making up nearly half of the repetitive content; the remainder comprises DNA transposons and LINEs (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 5</xref>). We identified ~25,000 protein-coding gene loci in both Clementine and sweet orange by computational methods combined with extensive long-read 454 and Sanger expressed sequence tags (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 5</xref>).</p></sec><sec id="S3"><title>Investigation of citrus ancestry</title><p id="P10">To investigate the origin of cultivated varieties, we sequenced the genomes of four mandarins (including Clementine), two pummelos and one sour orange, as well as the sweet orange genome reported above (<xref ref-type="table" rid="T1">Table 1</xref>, <xref ref-type="supplementary-material" rid="SD1">Supplementary Table 1, Supplementary Notes 1,6</xref>). (Cultivars derived from <italic>C. medica</italic> (the third purported wild species), <italic>i.e</italic>., citrons, limes and lemons, were not part of this study.) Two distinct types of chloroplast genomes (cpDNA) were readily identified, with mandarins all having one type (which we define as “M” for mandarin or <italic>C. reticulata</italic>) and pummelos and oranges sharing another type (defined as “P” for pummelo or <italic>C. maxima</italic>), with limited variation within each cpDNA type (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 6</xref>), consistent with prior studies of mitochondrial markers<sup><xref rid="R20" ref-type="bibr">20</xref></sup>. Citrus nuclear genomes tell a more complex story (<xref ref-type="supplementary-material" rid="SD1">Supplementary Notes 7, 8</xref>). We find that while the sequenced pummelos are evidently genotypes from the sexual <italic>C. maxima</italic> species with minimal introgression of other species, all the mandarin-type citrus we sequenced show substantial admixture with pummelo and therefore cannot simply be selections from an ancestral <italic>C. reticulata</italic> population (<xref ref-type="fig" rid="F2">Fig. 2</xref>,<xref ref-type="fig" rid="F3">3</xref>). The sweet and sour oranges are also hybrids of varying complexity, with pummelo-type chloroplast genomes in both cases.</p></sec><sec id="S4"><title>Ancestry of pummelos</title><p id="P11">The two diploid pummelos that we sequenced contain three distinct haplotypes, since Low acid (Siamese Sweet) pummelo is the known female parent of Chandler pummelo<sup><xref rid="R21" ref-type="bibr">21</xref></sup>, so that the two pummelos share one haplotype at each locus (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 9</xref>). Within the two sequenced pummelos and between their non-shared alleles (derived from the other parent of Chandler, <italic>i.e</italic>., Siamese Pink pummelo) modest levels of heterozygosity were observed, with a genome-wide nucleotide heterozygosity of 5.7 heterozygous (het) sites/kb (<xref ref-type="fig" rid="F2">Fig. 2a</xref>). The presence of a second low-heterozygosity peak (~1 het site/kb) in the distribution can be explained by a strong ancient bottleneck in the <italic>C. maxima</italic> population ~100–300 kya (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>). Our reanalysis of three Chinese pummelos previously reported<sup><xref rid="R17" ref-type="bibr">17</xref></sup> (including the Wusuan pummelo that we identify as from the same somatic lineage as Siamese Sweet pummelo), shows that both Thai and Chinese pummelos are derived from the same wild population (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 11</xref>). Only a single short 1.5 Mb segment on chromosome 2 of Chandler shows unusually high heterozygosity that could reflect interspecific introgression. These observations are consistent with pummelo domestication by selection from a wild sexual <italic>C. maxima</italic> population.</p></sec><sec id="S5"><title>Ancestry of mandarins</title><p id="P12">To sample a range of mandarin types, we sequenced two “traditional” mandarins without prior suspected admixture (Ponkan, an old and widely grown Asian variety that was presumed to be typical of <italic>C. reticulata</italic>, and Willowleaf, a common Mediterranean variety) as well as two mandarins believed to be hybrids of “traditional” mandarins with other citrus (Clementine, the diploid parent of the haploid reference accession, and W. Murcott (believed to be synonymous with the cultivar also known as Nadorcott and Afourer), widely grown in California and the Mediterranean (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 1</xref>)). In contrast to pummelos, the “mandarin” accessions we sequenced typically include segments of high nucleotide heterozygosity (~17 het sites/kb, consistent with inter-specific variation) that span tens of cM or Mbp (<xref ref-type="fig" rid="F2">Fig. 2b</xref>). These highly heterozygous blocks are interspersed with long segments of substantially lower levels of heterozygosity (~5 het sites/kilobase) that are consistent with intra-specific variation and clearly distinct from the higher-heterozygosity blocks (<xref ref-type="fig" rid="F2">Fig. 2c</xref>)). In the lower heterozygosity segments, both alleles are often distinct from those observed in the pummelos and presumably derive from <italic>C. reticulata</italic>, which is widely cited as the true species from which cultivated mandarins arose<sup><xref rid="R7" ref-type="bibr">7</xref></sup>. In contrast, the higher heterozygosity blocks typically carry one allele that matches the pummelos, and one non-pummelo allele, also presumably <italic>C. reticulata</italic>. The presumptive <italic>C. reticulata</italic> alleles are typically common to multiple mandarin accessions, further supporting their identification.</p><p id="P13">Thus, our surprising conclusion is that “traditional” mandarin types like Ponkan and Willowleaf, are in fact interspecific introgressions of <italic>C. maxima</italic> (pummelo) into <italic>C. reticulata</italic> (wild mandarin). Furthermore, although these traditional mandarins were previously thought to be unrelated, we detect extensive haplotype sharing between them (<xref ref-type="supplementary-material" rid="SD1">Supplemental Note 10</xref>). Because microsatellite-based population structure analyses of a wide range of citrus genotypes shows mandarins as a defined cluster of genotypes<sup><xref rid="R22" ref-type="bibr">22</xref></sup>, such admixture is likely widespread among mandarin types. Indeed, reanalysis of a recently sequenced Chinese mandarin<sup><xref rid="R17" ref-type="bibr">17</xref></sup> in the light of our discovery of interspecific introgression in multiple mandarin types, shows that the traditional Chinese Huanglingmiao mandarin (incorrectly treated previously<sup><xref rid="R16" ref-type="bibr">16</xref></sup> as a pure <italic>C. reticulata</italic>) also exhibits unsuspected admixture between <italic>C. reticulata</italic> and <italic>C. maxima</italic> (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 11</xref>).</p><p id="P14">Although none of our cultivated mandarin genotypes represent pure <italic>C. reticulata</italic>, we can nevertheless extract wild mandarin alleles from our data by comparing the (admixed) cultivated mandarins with each other and the two pure pummelos. By such genome-wide comparisons we identified 1,537,264 putative fixed single nucleotide differences between <italic>C. reticulata</italic> and <italic>C. maxima</italic> (<xref ref-type="supplementary-material" rid="SD1">Supplementary File 1, Supplementary Note 7</xref>). These diagnostic variants can in turn be used to partition the mandarin, pummelo and orange genomes into segments according to their species ancestry (<xref ref-type="fig" rid="F3">Fig. 3</xref>). The characterization of <italic>C. reticulata</italic> genomic segments from modern mandarins is analogous to the extraction of African haplotypes from Mexican Americans<sup><xref rid="R23" ref-type="bibr">23</xref></sup>[SEP1]and native American haplotypes from extant ethnic human populations that are admixtures with American, African and European roots<sup><xref rid="R24" ref-type="bibr">24</xref></sup>.</p><p id="P15">We can estimate the parameters of a simple population genetic model for the divergence of <italic>C. reticulata</italic> and <italic>C. maxima</italic> from an ancestral south Asian citrus founder population, using a coalescent framework and our collection of fixed interspecific differences and intraspecific variation (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 9</xref>). This analysis is consistent with effective population sizes of several hundred thousand trees for <italic>C. maxima</italic> and somewhat fewer for <italic>C. reticulata</italic>, with larger effective population size for pummelos in keeping with their higher heterozygosity. Note that the likely occurrence of apomixis in wild mandarin populations, a trait that seems to be absent in <italic>C. maxima</italic>, may contribute to reducing the effective <italic>C. reticulata</italic> population size relative to the census size. If we assume a per site mutation rate of µ ~1 –2 × 10<sup>−9</sup>/yr (comparable to that observed in poplar trees<sup><xref rid="R25" ref-type="bibr">25</xref></sup>) then we can estimate that <italic>C. reticulata</italic> and <italic>C. maxima</italic> diverged ~1.6–3.2 Mya, consistent with the divergence between <italic>Citrus</italic> and the related genus <italic>Poncirus</italic>, which is estimated at 4–9.6 Mya<sup><xref rid="R26" ref-type="bibr">26</xref></sup>. As noted, the excess of low heterozygosity segments in pummelo is consistent with a substantial population bottleneck several hundred thousand years ago and prior to the separation of Thai and Chinese pummelo lineages (<xref ref-type="supplementary-material" rid="SD1">Supplementary Notes 9, 11</xref>).</p><p id="P16">Some specific citrus genotypes are generally recognized as “hybrid” varieties. For example, Clementine mandarin (also known as Algerian tangerine) is believed to be a chance seedling from a Mediterranean mandarin (<italic>e.g</italic>., Willowleaf) selected just over a century ago in Algeria<sup><xref rid="R27" ref-type="bibr">27</xref></sup>. Although various male parents have been proposed, serological and molecular studies demonstrated that the Clementine was likely a mandarin × sweet orange hybrid<sup><xref rid="R6" ref-type="bibr">6</xref>, <xref rid="R18" ref-type="bibr">18</xref>, <xref rid="R28" ref-type="bibr">28</xref></sup>. We confirm this hypothesis at the sequence level by definitively identifying a Willowleaf and sweet orange allele at each Clementine locus; demarcating the recombination breakpoints in the meiosis that produced the haploid Clementine sequence; and determining the Willowleaf and sweet orange haplotypes that contributed to diploid Clementine (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10, Supplementary Fig. 14,15</xref>). Similarly, the W. Murcott mandarin is believed to be a chance zygotic seedling of Murcott tangor, itself a presumed F1 hybrid of sweet orange and an unknown mandarin. Our sequence analysis is consistent with the suspected grandparent/grandchild relationship between sweet orange and W. Murcott (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>). Although the other parent and grandparent of W. Murcott are not known (but see<sup><xref rid="R29" ref-type="bibr">29</xref></sup>), a search for these ancestors will be enabled by the other observed alleles.</p></sec><sec id="S6"><title>Ancestry of oranges</title><p id="P17">Sweet orange (<italic>C</italic>. × <italic>sinensis</italic> L. Osbeck) is the citrus type most widely cultivated for fruit and juice and is widely believed to be an interspecific hybrid, but its origin is unknown<sup><xref rid="R4" ref-type="bibr">4</xref>, <xref rid="R6" ref-type="bibr">6</xref></sup>. Different sweet orange cultivars share the same genomic organization with little sequence variation, having arisen by mutation from the original sweet orange domesticate (see, e.g. Ref.<sup><xref rid="R30" ref-type="bibr">30</xref></sup>). Using our genome-wide catalog of fixed <italic>C. reticulata</italic> vs. <italic>C. maxima</italic> alleles, we can represent the sweet orange genome as segments of these two parental species or hybrid segments thereof (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>; <xref ref-type="fig" rid="F2">Fig. 2d</xref>), with clear boundaries between different segments types (<xref ref-type="fig" rid="F3">Fig. 3a</xref>). A recently proposed “(P×M)×M” backcross scheme for the derivation of sweet orange from mandarin and pummelo<sup><xref rid="R17" ref-type="bibr">17</xref></sup>, however, is easily ruled out by the presence of clear “P/P” (<italic>i.e</italic>., <italic>C. maxima</italic>/<italic>C. maxima</italic>) segments in sweet orange, which requires both parents to have some pummelo ancestry. (The P/P segment on chromosome 2 has been confirmed by directed resequencing of three genes in this region<sup><xref rid="R31" ref-type="bibr">31</xref></sup>.)</p><p id="P18">Unexpectedly, in our analysis we found that sweet orange shares alleles with Ponkan mandarin across nearly three-quarters of the genome, and many of the same segments are also shared with Willowleaf and Huanglingmiao (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10; Supplementary Fig. 16</xref>). This leads to the surprising conclusion that these three traditional mandarins, previously considered independent selections, in fact show substantial kinship with each other and an ancestor of sweet orange, suggesting much more limited genetic diversity among the traditional mandarins than previously recognized (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>). The nature of the other parent of sweet orange is more difficult to infer, but the distribution of heterozygous segments in sweet orange (<xref ref-type="supplementary-material" rid="SD1">Supplementary Fig. 17</xref>) and its pummelo-type chloroplast genome are more readily accounted for if the female parent was itself a pummelo with substantial introgression of wild mandarin (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 9</xref>).</p><p id="P19">Finally, Seville or sour orange (also known as <italic>C</italic>. × <italic>aurantium</italic>), which has historically been an important rootstock for citrus and, more familiarly, is used in marmalade and other products, is another traditional cultivar type that is widely regarded as a pummelo-mandarin hybrid. Our genomic analysis shows that sour orange is indeed the direct result of a simple interspecific F1 cross between a pummelo (<italic>C. maxima</italic>) seed parent and a wild mandarin (<italic>C. reticulata</italic>) pollen parent (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>). Surprisingly in light of our discovery of widespread pummelo admixture among traditional mandarins, no such admixture is found in the <italic>C. reticulata</italic> parent of sour orange, but the specific parental genotypes remain unknown. Sour orange may have arisen as a natural hybrid of two wild <italic>Citrus</italic> species, and persisted by virtue of its reproduction through apomixis, followed by deliberate human cultivation and distribution. We found no detectable recent relationship between sweet and sour orange.</p></sec><sec id="S7"><title>Chinese Mangshan represents a distinct species, <italic>C. mangshanensis</italic></title><p id="P20">Among cultivars traditionally classified as “mandarins”, however, we found another surprise. Our analysis of the genome of a presumed “wild mandarin” from Mangshan, China<sup><xref rid="R17" ref-type="bibr">17</xref></sup> (CMS) shows (i) a chloroplast genome that is distinct from both <italic>C. reticulata</italic> and <italic>C. maxima</italic> (<xref ref-type="fig" rid="F4">Fig. 4a</xref>); (ii) limited heterozygosity (<xref ref-type="fig" rid="F4">Fig. 4b</xref>), again uniformly distributed across the genome, and no segments of pummelo or mandarin ancestry, indicating no admixture; (iii) ~2% homozygous differences from both <italic>C. reticulata</italic> and <italic>C. maxima</italic> uniformly across the genome, a rate comparable to the divergence between <italic>C. maxima</italic> and <italic>C. reticulata</italic> (<xref ref-type="fig" rid="F4">Fig. 4b</xref>). At the level of nucleotide diversity, CMS is as diverged from C. <italic>maxima</italic> and <italic>C. reticulata</italic> as they are from each other (<xref ref-type="fig" rid="F4">Fig. 4b</xref>) and is clearly separated from pummelos, oranges and mandarins by principal coordinate analysis (<xref ref-type="fig" rid="F4">Fig. 4c</xref>, <xref ref-type="supplementary-material" rid="SD1">Supplementary Note 11</xref>). By all these measures, we find that Mangshan “mandarin”is unrelated to the other cultivated mandarins discussed above (including Huanglingmiao mandarin). We therefore propose that despite its morphology Mangshan “mandarin” represents a distinct species from <italic>C. reticulata</italic>, supporting the nomenclature <italic>C. mangshanensis</italic><sup><xref rid="R32" ref-type="bibr">32</xref></sup>.</p></sec></sec><sec sec-type="discussion" id="S8"><title>Discussion</title><p id="P21">Our genomic analyses clarify some of the murky early history of citrus domestication. The nuclear and chloroplast genomes of cultivated pummelos are consistent with the identification of pummelos as a single <italic>Citrus</italic> species, <italic>C. maxima</italic>. In contrast, the nuclear genomes of sequenced “mandarin” type cultivars all contain substantial admixture of <italic>C. maxima</italic>, despite the similarity of mandarin chloroplast sequences. Our results thus show that the various conventional <italic>Citrus</italic> taxonomies that associate mandarin citrus types with the ancestral <italic>Citrus</italic> species <italic>C. reticulata</italic> are too simplistic. It is particularly surprising that even the traditional mandarin types with no prior suspicion of relatedness or admixture such as Ponkan, Willowleaf and Huanglingmiao mandarin show substantial haplotype sharing and all include introgressed pummelo segments. A supposed “wild mandarin” from Mangshan, China, turns out to represent a distinct taxon only distantly related to <italic>C. reticulata</italic>, based on analysis of its nuclear and chloroplast genomes. (In a previous analysis of sweet orange ancestry<sup><xref rid="R17" ref-type="bibr">17</xref></sup>, Mangshan “mandarin” Clementine and Huanglingmiao were used to represent <italic>C. reticulata</italic>. Our discovery of substantial pummelo admixture in Clementine and Huanglingmiao, and the distinctness of Mangshan “mandarin” from <italic>C. reticulata</italic>, further invalidates their conclusions.)</p><p id="P22">Remarkably, even in the absence of a pure type specimen for <italic>C. reticulata</italic>, we can characterize the genome of this wild mandarin progenitor species from genome-wide comparative analysis of admixed descendants<sup><xref rid="R23" ref-type="bibr">23</xref></sup>. Our collection of 1,537,264 SNPs (<xref ref-type="supplementary-material" rid="SD1">Supplementary File 1</xref>) that differentiate <italic>C. reticulata</italic> from <italic>C. maxima</italic> can be used to guide the search for pure <italic>C. reticulata</italic> mandarin types (or recognize other cryptic species) among the hundreds of known cultivars and other germplasm accessions. Small-fruited mandarins that are less desirable for fresh consumption based on appearance, flavor, texture and aroma may be considered likely candidates. With the discovery that <italic>C. mangshanensis</italic> is a distinct group, the possibility of additional undescribed wild <italic>Citrus</italic> species must also be considered.</p><p id="P23">The prevalence of interspecific admixture in cultivated citrus suggests that either early in domestication or in a natural hybrid zone prior to domestication, <italic>C. reticulata</italic> and <italic>C. maxima</italic> interbreeding occurred. Given the typical size of the hybrid blocks, only a few generations of introgression occurred prior to the selection of attractive cultivars, which were then propagated asexually by apomictic or vegetative means, perhaps in southern China<sup><xref rid="R33" ref-type="bibr">33</xref></sup>. Our analysis of sweet orange and sour orange shows that these ancient and widely cultivated genotypes are pummelo-mandarin admixtures that are unrelated to each other, despite some degree of phenotypic similarity<sup><xref rid="R34" ref-type="bibr">34</xref></sup>. The discovery that sour orange is a simple F1 hybrid of <italic>C. maxima</italic> and <italic>C. reticulata</italic> implies that pure <italic>C. reticulata</italic> individuals were part of the breeding germplasm at the origin of sour orange. Remarkably, we found that extant Ponkan, Willowleaf and Huanglingmiao mandarins are related to each other and to the male parent of sweet orange. Although the female parent of sweet orange remains unknown, it cannot have been a pure pummelo (though it had pummelo cytoplasm, based on cpDNA and mtDNA<sup><xref rid="R20" ref-type="bibr">20</xref></sup>). Its identity is constrained by the high proportion of hybrid P/M segments in sweet orange, which can be naturally explained if the female parent of sweet orange were (P×M)×P.</p><p id="P24">Like many other agricultural enterprises, the global citrus industry relies substantially on large-scale monoculture which makes it particularly challenging to meet consumer demand for greater product diversity while trying to incorporate tolerance and/or resistance to biotic and potentially catastrophic abiotic stresses<sup><xref rid="R35" ref-type="bibr">35</xref></sup>. Advances in citrus genomics<sup><xref rid="R36" ref-type="bibr">36</xref>, <xref rid="R37" ref-type="bibr">37</xref></sup> should soon allow the identification of the somatic mutations that, with their ancient genetic backgrounds, underlie the diversity of citrus color, flavor and aroma in modern cultivars. Our analysis of the relationships between cultivated citrus and the ancestral species from which they were derived emphasizes the limited ancestral germplasm that contributed to the commercially important cultivar types like sweet orange, and highlights the opportunities for the creation of new combinations of the ancestral citrus types with novel fruit quality traits or even the re-creation of sweet orange with improved disease resistance <italic>via</italic> sexual hybridization, beyond the current approaches based on somatic mutations and genetic engineering.</p></sec><sec sec-type="methods" id="S9"><title>Online Methods</title><sec id="S10"><title>Haploid <italic>C</italic>. × <italic>clementina</italic> ‘Clemenules’ sequencing and assembly</title><p id="P25">A total of 4.6M Sanger reads (including 469k fosmid end and 73k BAC end reads), were obtained from an induced haploid plant <italic>C</italic>. × <italic>clementina</italic> ‘Clemenules’, assembled with Arachne and integrated with a genetic map producing chromosome-scale pseudo-molecules (nearly 97% of ESTs aligned to the genome) (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 2</xref>).</p></sec><sec id="S11"><title><italic>C</italic>. × <italic>sinensis</italic> genome sequencing and assembly</title><p id="P26">A total of 16.5 Gb sequence (36M 454 reads and 750k Sanger PE reads) was generated from <italic>C</italic>. × <italic>sinensis</italic> ‘Ridge Pineapple’ and assembled with Newbler (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 3</xref>).</p></sec><sec id="S12"><title>Annotation of repeats and genes in citrus genome assemblies</title><p id="P27">Repeat analysis was performed separately in the Clementine and sweet orange genomes. The method used RepeatModeler to find novel repeats in the genome sequence, which were masked with RepeatMasker. Following this, PASA was used to align and assemble ESTs (1.6M for clementine; 6.5M for sweet orange) and integrate Fgenesh+, exonerate and GenomeScan gene predictions to generate gene models (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 4</xref>).</p></sec><sec id="S13"><title>Evolutionary comparisons with other plant genomes</title><p id="P28">Evolutionary comparisons to plant genomes used ortholog assignment to generate chromosome to chromosome relationships within and between genomes and predict ancestral genome structures (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 5</xref>).</p></sec><sec id="S14"><title>Analysis of resequencing datasets</title><p id="P29">Illumina shotgun sequence reads from eight accessions (17×−110× depth; <xref ref-type="table" rid="T1">Table 1</xref>) were mapped to the haploid Clementine reference using bwa, and single nucleotide variants were identified using samtools and in-house scripts (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 6</xref>). Heterozygosity in diploid accessions was estimated in windows of 100–500 kb by dividing the number of confidently inferred heterozygous single nucleotide variant (“het”) sites by the number of eligible sites in the window at which confident variant calls could be made, based on depth and alignment quality (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 6</xref>).</p></sec><sec id="S15"><title>Identification of two ancestral species (<italic>C. maximavs</italic>. <italic>C. reticulata</italic> alleles) and admixture analysis</title><p id="P30">Diagnostic alleles for the two ancestral <italic>Citrus</italic> species, <italic>C. maxima</italic> and <italic>C. reticulata</italic>, were derived from a comparative analysis of two pummelos and two traditional mandarin types, and were used to study the admixture patterns in the sequenced cultivars (<xref ref-type="supplementary-material" rid="SD1">Supplementary Notes 7 and 8</xref>).</p></sec><sec id="S16"><title>Population genetic analysis and simulations</title><p id="P31">Population genetic analysis of the two citrus species and demographic inference were based on coalescent simulations conducted using MaCS (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>).</p></sec><sec id="S17"><title>Analysis of relatedness in citrus</title><p id="P32">Parentage and relatedness analysis for Clementine and other citrus genomes made use of homozygous SNPs in each diploid genome relative to the haploid Clementine reference as well as to the inferred second haplotype of Clementine (<xref ref-type="supplementary-material" rid="SD1">Supplementary Notes 9 and 11</xref>). In the same way, the haploid sweet orange assembly was used for identifying shared haplotypes with sweet orange (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 9</xref>). A modified identical-by-state (IBS) method was used for haplotype sharing analysis among mandarins and other citrus pairs (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 9</xref>).</p></sec></sec><sec sec-type="supplementary-material" id="SM"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="SD1"><label>1</label><media xlink:href="NIHMS586218-supplement-1.pdf" orientation="portrait" xlink:type="simple" id="d37e1523" position="anchor"></media></supplementary-material></sec></body><back><ack id="S18"><title>Acknowledgments</title><p id="P33">National Science and Technology Institute of Genomics for Citrus Breeding (FAPESP 2008/57909-2 and CNPq573848/08-4) and Brazilian Agricultural Research Corporation (Embrapa) (MAT, JF-A, MAMach) and Embrapa-Monsanto Agreement (JF-A); Agence nationale de la recherche (ANR) grant CITRUSSEQ PCS-08-GENO (OJ, XP, MR, PO, FL, KJ) and program ANR Blanc-PAGE, ref: ANR-2011-BSV6-00801 (JS, FM);US National Institute of Health grant HG00783 (MB, PB, AL); Grant PrometeoII/2013/008 from the Generalitat Valenciana, Spain and grant (AGL2011-26490) from the Ministry of Economy and Innovation-Fondo Europeo de Desarrollo Regional (FEDER), Spain (PA, LN); Conselleria de Agricultura, Pesca, Alimentación y Água from the Generalitat Valenciana (JPP, DR); Ministerio de Economia e Innovación grants PSE-060000-2009-8 and IPT-010000-2010-43 and Citruseq-Citrusgenn consortium companies (Anecoop S. Coop., Eurosemillas S.A., Fundación Ruralcaja Valencia, GCM Variedades Vegetales A.I.E, Investigación Citrícola Castellón, S.A and Source Citrus Genesis – SNFL) (JT, FRT, LHE, JVM-S, VI, AH-O, MT); Florida Citrus Production Research Advisory Council (FCPRAC), the Florida Department of Agriculture and Consumer Services (Grant # 013646), the Florida Department of Citrus (FDOC), and the Citrus Research and Development Foundation, Inc. (Grant #71), on behalf of the Florida citrus growers (FG, CC, WGF); Project Citrustart from Ministero delle Politiche Agricole Alimentari e Forestali; Project IT-Citrus Genomics PON_01623 from MIUR, Programma Operativo Nazionale “Ricerca e Competitività” 2007–2013 (MMorg, SS, FC, CDF, SPin, AZ). Pineapple Ridge sweet orange sequencing by 454 Life Sciences, a Roche company. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.</p></ack><fn-group><fn id="FN4" fn-type="con"><p id="P34"><bold>Author Contributions</bold></p><p id="P35">GW Developed and applied methods to analyze citrus genetic diversity, population history, and ancestry; SP genome annotation and initial analysis of genetic diversity; JJ sequence assembly and map integration of haploid Clementine reference; JS, FM Analysis of synteny and genome evolution.; UH Analysis of population history and ancestry; KL, JPP, AC, KJ Dideoxy shotgun sequencing and analysis of haploid Clementine reference; SS, SPin, AZ, CDF, XP, MRu Analysis of sequencing and resequencing data, and repetitive sequence annotation and analysis.; FC Sanger and Illumina sequencing; AL, PB, MB sweet orange gene model predictions; CC, WGF 454 sequencing of sweet orange and Illumina sequencing of Siamese Sweet pummelo; CC contributions to sweet orange transcriptome, annotation, and the strategic rationale for comparative analyses; PA, JPP, LN haploid Clementine DNA; JPP, DR haploid Clementine transcriptome; JT, FRT, LHE, JVM-S, VI, AH-O, MT generation of BAC clones of the haploid Clementine and provided genome sequences of sweet orange, Ponkan, diploid Clementine and Willowleaf mandarins; BD, CK, MMohi, TH, KF Sweet orange 454 transcriptome, and genome sequencing and assembly; MAMach and MAT Ponkan shotgun sequence; MRo W. Murcott shotgun sequence; MMorg Chandler pummelo, Seville sour orange shotgun sequence; GR, JF-A, FQ, LN, MRo Project coordination; DSR, FG, GW, SP wrote the paper with substantial input from MT, PO, MM, OJ, Mro; FG, DSR, OJ, PO, MAMach, MMorg, MT, JSch, PW Project coordination and scientific leadership.</p></fn><fn id="FN5"><p id="P36"><bold>Competing Financial Interests Statement</bold></p><p id="P37">The authors declare no competing financial interests.</p></fn><fn id="FN6"><p id="P38"><bold>Accessions</bold></p><p id="P39">The reference haploid Clementine assembly and annotation is deposited inNCBI’s genome database (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/genome">http://www.ncbi.nlm.nih.gov/genome</ext-link>) under the accession AMZM00000000. Sanger WGS for Clementine is deposited in the NCBI trace archive (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/Traces/trace.cgi">http://www.ncbi.nlm.nih.gov/Traces/trace.cgi</ext-link>) under SPECIES_CODE=’CITRUS CLEMENTINA’. The sweet orange assembly and annotation is deposited in NCBI’s genome database under Accession XXXXX000000. WGS sequence for the sweet orange is deposited in NCBI’s Sequence Read Archive (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/Traces/sra/">http://www.ncbi.nlm.nih.gov/Traces/sra/</ext-link>) under BioProject PRJNA225968 (454 data) and in the NCBI trace archive under SPECIES_CODE=’CITRUS SINESIS’ AND CENTER_NAME=’JGI’. Citrus resequencing data are in the Sequence Read Archive at NCBI under the following accessions:SRX372786 (sour orange), SRX372703 (sweet orange), SRX372702 (Low acid pummelo), SRX372688 (Chandler pummelo), SRX372685 (Willowleaf mandarin), SRX372687 (W. 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Oranges (8, 10) are generally intermediate in tree and fruit size, flesh (10) and rind color is commonly orange, and apomictic reproduction is always present. (The sour orange shown (12) is immature.)</p></caption><graphic xlink:href="nihms586218f1"></graphic></fig><fig id="F2" orientation="portrait" position="float"><label>Figure 2</label><caption><p id="P41">Nucleotide diversity distribution in citrus.(<bold>a</bold>) Nucleotide heterozygosity distribution computed in overlapping 100kb windows (with 5 kb step size) across the Low acid (LAP) and Chandler (CHP) pummelo genomes and between the non-shared haplotypes of this parent-child pair (LAP/CHP) is shown. The peak at ~6 heterozygous sites/kb in all three pairwise comparisons represents the characteristic nucleotide diversity of the species <italic>C. maxima</italic>; the peak near ~1 heterozygous site/kb reflects a bottleneck in the ancestral <italic>C. maxima</italic> population after divergence from <italic>C. reticulata</italic> (<xref ref-type="supplementary-material" rid="SD1">Supplementary Note 10</xref>). <bold>(b)</bold> Nucleotide heterozygosity for the traditional Willowleaf mandarin (WLM) plotted along chromosome 6, computed in overlapping windows of 200 kb (with 100 kb step size). This chromosome shows an example of the clear discontinuity in single nucleotide variant heterozygosity levels between ~5/kb in the M/M segment (orange bar) and ~17/kb in the M/P segment (blue bar). <bold>(c)</bold> Nucleotide heterozygosity distribution computed in overlapping 500kb windows (with 5 kb step size) in Ponkan (PKM, solid line) and Willowleaf (WLM, dashed line) mandarins. Genomic segments are designated M/M, M/P or P/P based on a set of 1,537,264 SNPs that differentiate <italic>C. reticulata</italic> (M) from C. <italic>maxima</italic> (P). Both mandarins contain admixed segments from <italic>C. maxima</italic> introgression (M/P) as well as M/M segments, and these are plotted and normalized separately for easy comparison.. <bold>(d)</bold> Nucleotide heterozygosity distribution computed in overlapping windows of 500kb (5 kb offsets) for sweet orange (SWO) and sour orange (SSO). The three different genotypes of the SWO genome (M/M, P/P and M/P), and the SSO genotype M/P are normalized and plotted separately</p></caption><graphic xlink:href="nihms586218f2"></graphic></fig><fig id="F3" orientation="portrait" position="float"><label>Figure 3</label><caption><p id="P42">Admixture patterns and nucleotide diversity in cultivated citrus. For each of the three groups of sequenced citrus, variation in nucleotide diversity (averaged over 500kb windows with step size 250kb) is shown across the genome for one representative cultivar above genotype maps (horizontal bars: green = <italic>C. maxima/C. maxima</italic>; blue = <italic>C. maxima/C. reticulata</italic>; orange= <italic>C. reticulata/C. reticulata</italic>; grey=unknown; the 9 chromosomes are numbered at the top). <bold>(a)</bold> Sweet orange (SWO) nucleotide diversity with genotype maps for SWO and sour orange (SSO). Note the <italic>C. maxima/C. maxima</italic> genotype (green segments present on chromosomes 2 and 8) in SWO. <bold>(b)</bold> Willowleaf mandarin (WLM) nucleotide diversity and genotype maps for three traditional mandarins (Ponkan mandarin (PKM), WLM, Huanglingmiao (HLM)) and three recent mandarin types (Clementine (CLM), W. Murcott mandarin (WMM), haploid Clementine reference (HCR)). For the haploid Clementine reference sequence (HCR), red and green segments indicate <italic>C.reticulata</italic> and <italic>C. maxima</italic> haplotypes, respectively. All five mandarin types show pummelo introgressions (blue or green segments). <bold>(c)</bold> Low acid pummelo (LAP) nucleotide diversity and genotype maps for two pummelos (LAP, Chandler pummelo (CHP)).</p></caption><graphic xlink:href="nihms586218f3"></graphic></fig><fig id="F4" orientation="portrait" position="float"><label>Figure 4</label><caption><title>Mangshan mandarin is a species distinct from <italic>C. maxima</italic> and <italic>C. reticulata</italic></title><p id="P43">(<bold>a</bold>) Midpoint-rooted neighbor-joining phylogenetic tree of citrus chloroplast genomes. (<bold>b</bold>) The frequency distributions of the pairwise sequence divergences (across 100 kb windows) between Mangshan mandarin (CMS) and <italic>C. maxima</italic> (green), CMS and <italic>C. reticulata</italic> (orange), <italic>C. reticulata</italic> and <italic>C. maxima</italic> (light blue), as well as the distinctly lower CMS intrinsic nucleotide diversity (dashed blue). (c) The first two coordinates of principal coordinate analysis of the citrus nuclear genomes, based on pairwise distances and the metric multidimensional scaling. The <italic>C. maxima</italic> - <italic>C. reticulata</italic> axis (Principle coordinate 1, 47.5% variance) separates pummelos (green) from mandarins (orange), with oranges (blue) lying in between; Principle coordinate 2 (19.6% of variance) separates CMS (purple) from the others.</p></caption><graphic xlink:href="nihms586218f4"></graphic></fig><table-wrap id="T1" position="float" orientation="landscape"><label>Table 1</label><caption><title>Sequenced cultivars and proportions derived from the ancestral species <italic>C. reticulata</italic> and <italic>C. maxima</italic></title><p id="P44">Three letter abbreviations as used throughout this work and common systematic designation are shown. Sequence depth reported as count of aligned reads to reference, after removal of duplicate reads. Chloroplast genome type inferred from shotgun reads aligning to the sweet orange chloroplast genome<sup><xref rid="R38" ref-type="bibr">38</xref></sup>, with M indicating mandarin type and P indicating pummelo type. Diploid nuclear genotype proportions refer to fraction of genome in megabases using the HCR physical map (proportions of unknown genotype are not shown but can be inferred by subtracting the three genotype proportions from 100%). The last two columns show proportions of <italic>C. maxima</italic> and <italic>C. reticulata</italic> haplotypes, and are derived from the three genotype proportions. max. = <italic>C. maxima</italic>; ret. = <italic>C.reticulata</italic>.</p></caption><table frame="box" rules="all"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1">Cultivar</th><th align="left" valign="top" rowspan="1" colspan="1">Abbr.</th><th align="left" valign="top" rowspan="1" colspan="1">Common<break></break>designation</th><th align="left" valign="top" rowspan="1" colspan="1">Sequence<break></break>generated</th><th align="center" valign="top" rowspan="1" colspan="1">Cp<break></break>type</th><th align="center" valign="top" rowspan="1" colspan="1">ret./<break></break>ret.</th><th align="center" valign="top" rowspan="1" colspan="1">ret./<break></break>max.</th><th align="center" valign="top" rowspan="1" colspan="1">max./<break></break>max.</th><th align="center" valign="top" rowspan="1" colspan="1">ret.</th><th align="center" valign="top" rowspan="1" colspan="1">max.</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Haploid Clementine</td><td align="left" rowspan="1" colspan="1">HCR</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. × <italic>clementina</italic></td><td align="left" rowspan="1" colspan="1">7× Sanger</td><td align="center" rowspan="1" colspan="1">M</td><td align="center" rowspan="1" colspan="1">n/a</td><td align="center" rowspan="1" colspan="1">n/a</td><td align="center" rowspan="1" colspan="1">n/a</td><td align="center" rowspan="1" colspan="1">89%</td><td align="center" rowspan="1" colspan="1">11%</td></tr><tr><td align="left" rowspan="1" colspan="1">Clementine mandarin</td><td align="left" rowspan="1" colspan="1">CLM</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. × <italic>clementina</italic></td><td align="left" rowspan="1" colspan="1">110× Illumina</td><td align="center" rowspan="1" colspan="1">M</td><td align="center" rowspan="1" colspan="1">58%</td><td align="center" rowspan="1" colspan="1">42%</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">79%</td><td align="center" rowspan="1" colspan="1">21%</td></tr><tr><td align="left" rowspan="1" colspan="1">Ponkan mandarin</td><td align="left" rowspan="1" colspan="1">PKM</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. <italic>reticulata</italic><xref ref-type="table-fn" rid="TFN1">*</xref></td><td align="left" rowspan="1" colspan="1">55× Illumina</td><td align="center" rowspan="1" colspan="1">M</td><td align="center" rowspan="1" colspan="1">85%</td><td align="center" rowspan="1" colspan="1">14%</td><td align="center" rowspan="1" colspan="1">0.7%</td><td align="center" rowspan="1" colspan="1">92%</td><td align="center" rowspan="1" colspan="1">8%</td></tr><tr><td align="left" rowspan="1" colspan="1">Willowleaf mandarin</td><td align="left" rowspan="1" colspan="1">WLM</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. × <italic>deliciosa</italic></td><td align="left" rowspan="1" colspan="1">110× Illumina</td><td align="center" rowspan="1" colspan="1">M</td><td align="center" rowspan="1" colspan="1">91%</td><td align="center" rowspan="1" colspan="1">8.8%</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">95%</td><td align="center" rowspan="1" colspan="1">4.4%</td></tr><tr><td align="left" rowspan="1" colspan="1">W. Murcott mandarin</td><td align="left" rowspan="1" colspan="1">WMM</td><td align="left" rowspan="1" colspan="1"><italic>C. reticulata</italic></td><td align="left" rowspan="1" colspan="1">25× Illumina</td><td align="center" rowspan="1" colspan="1">M</td><td align="center" rowspan="1" colspan="1">69%</td><td align="center" rowspan="1" colspan="1">30%</td><td align="center" rowspan="1" colspan="1">0.4%</td><td align="center" rowspan="1" colspan="1">85%</td><td align="center" rowspan="1" colspan="1">15%</td></tr><tr><td align="left" rowspan="1" colspan="1">Chandler pummelo</td><td align="left" rowspan="1" colspan="1">CHP</td><td align="left" rowspan="1" colspan="1"><italic>C. maxima</italic></td><td align="left" rowspan="1" colspan="1">22× Illumina</td><td align="center" rowspan="1" colspan="1">P</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">0.4%</td><td align="center" rowspan="1" colspan="1">99.6%</td><td align="center" rowspan="1" colspan="1">0.2%</td><td align="center" rowspan="1" colspan="1">99.8%</td></tr><tr><td align="left" rowspan="1" colspan="1">Low acid pummelo</td><td align="left" rowspan="1" colspan="1">LAP</td><td align="left" rowspan="1" colspan="1"><italic>C. maxima</italic></td><td align="left" rowspan="1" colspan="1">17× Illumina</td><td align="center" rowspan="1" colspan="1">P</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">100%</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">100%</td></tr><tr><td align="left" rowspan="1" colspan="1">Sweet orange</td><td align="left" rowspan="1" colspan="1">SWO</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. × <italic>sinensis</italic></td><td align="left" rowspan="1" colspan="1">80× Illumina</td><td align="center" rowspan="1" colspan="1">P</td><td align="center" rowspan="1" colspan="1">14%</td><td align="center" rowspan="1" colspan="1">82%</td><td align="center" rowspan="1" colspan="1">3%</td><td align="center" rowspan="1" colspan="1">55%</td><td align="center" rowspan="1" colspan="1">44%</td></tr><tr><td align="left" rowspan="1" colspan="1">Seville sour orange</td><td align="left" rowspan="1" colspan="1">SSO</td><td align="left" rowspan="1" colspan="1"><italic>C</italic>. × <italic>aurantium</italic></td><td align="left" rowspan="1" colspan="1">36× Illumina</td><td align="center" rowspan="1" colspan="1">P</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">98%</td><td align="center" rowspan="1" colspan="1">0%</td><td align="center" rowspan="1" colspan="1">49%</td><td align="center" rowspan="1" colspan="1">49%</td></tr></tbody></table><table-wrap-foot><fn id="TFN1"><label>*</label><p id="P45">Ponkan mandarin is widely assumed to represent <italic>C. reticulata</italic>, but as shown here it has substantial admixture from <italic>C. maxima</italic>.</p></fn></table-wrap-foot></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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