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Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

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

Author
item WU, ALBERT - Department Of Energy Joint Genome
item PROCHNIK, SIMON - Department Of Energy Joint Genome
item JENKINS, JERRY - Hudsonalpha Institute For Biotechnology
item SALSE, JEROME - Institut National De La Recherche Agronomique (INRA)
item HELLSTEN, UFFE - Department Of Energy Joint Genome
item MURAT, FLORENT - Institut National De La Recherche Agronomique (INRA)
item PERRIER, XAVIER - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item RUIZ, MANUEL - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item SCALABRIN, SIMONE - Istituto Di Genomica Applicata (IGA)
item TEROL, JAVIER - Non ARS Employee
item TAKITA, MARCO - Sylvio Moreira Citrus Research
item ROKSAR, DANIEL - Department Of Energy Joint Genome
item LABADIE, KARINE - Non ARS Employee
item PAULAIN, JULIE - Non ARS Employee
item CAULOUX, ARNAUD - Non ARS Employee
item JABBARI, KAMEL - Non ARS Employee
item CATTONARO, FEDERICA - Istituto Di Genomica Applicata (IGA)
item FABBRO, CRISTIAN - Istituto Di Genomica Applicata (IGA)
item PINOSIO, SARA - Istituto Di Genomica Applicata (IGA)
item ZUCCOLO, ANDREA - Istituto Di Genomica Applicata (IGA)
item CHAPMAN, JARROD - Department Of Energy Joint Genome
item GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology
item TADEO, FRANCISCO - Valencian Institute For Agricultural Research
item ESTORNELL, LEANDRO - Valencian Institute For Agricultural Research
item MUNOZ-SANZ, JUAN - Valencian Institute For Agricultural Research
item IBANEZ, VICTORIA - Valencian Institute For Agricultural Research
item HERRERO-ORTEGA, AMPARO - Valencian Institute For Agricultural Research
item ALEZA, PABLO - Valencian Institute For Agricultural Research
item PEREZ-PEREZ, JULIAN - Non ARS Employee
item RAMON, DANIEL - Non ARS Employee
item BRUNEL, DOMINIQUE - Non ARS Employee
item LURO, FRANCOIS - Institut National De La Recherche Agronomique (INRA)
item Chen, Chunxian
item FARMERIE, WILLIAM - University Of Florida
item DESANY, BRIAN - Roche Diagnostics
item KODIRA, CHINNAPPA - Roche Diagnostics
item MOHIUDDIN, MOHAMMED - Roche Diagnostics
item HARKINS, TIM - Roche Diagnostics
item FREDRIKSON, KARIN - Roche Diagnostics
item BURNS, PAUL - Georgia Institute Of Technology
item LOMSADZE, ALEXANDRE - Georgia Institute Of Technology
item BORODOVSKY, MARK - Georgia Institute Of Technology
item REFORGIATO, GIUSEPPE - Non ARS Employee
item FREITA-ASTUA, JULIANA - Sylvio Moreira Citrus Research
item QUETIER, FRANCIS - Non ARS Employee
item NAVARRO, LUIS - Valencian Institute For Agricultural Research
item ROOSE, MIKEAL - University Of California
item WINCKER, PATRICK - Non ARS Employee
item SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology
item MORGANTE, MICHELE - Istituto Di Genomica Applicata (IGA)
item MACHADO, MARCOS - Sylvio Moreira Citrus Research
item TALON, MANUEL - Non ARS Employee
item JAILLON, OLIVIER - Non ARS Employee
item OLLITRAULT, PATRICK - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item GMITTER, FREDERICK - University Of Florida

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/4/2014
Publication Date: 6/8/2014
Citation: Wu, A.G., Prochnik, S., Jenkins, J., Salse, J., Hellsten, U., Murat, F., Perrier, X., Ruiz, M., Scalabrin, S., Terol, J., Takita, M.A., Roksar, D., Labadie, K., Paulain, J., Cauloux, A., Jabbari, K., Cattonaro, F., Fabbro, C.D., Pinosio, S., Zuccolo, A., Chapman, J., Grimwood, J., Tadeo, F.R., Estornell, L.H., Munoz-Sanz, J.V., Ibanez, V., Herrero-Ortega, A., Aleza, P., Perez-Perez, J., Ramon, D., Brunel, D., Luro, F., Chen, C., Farmerie, W.G., Desany, B., Kodira, C., Mohiuddin, M., Harkins, T., Fredrikson, K., Burns, P., Lomsadze, A., Borodovsky, M., Reforgiato, G., Freita-Astua, J., Quetier, F., Navarro, L., Roose, M., Wincker, P., Schmutz, J., Morgante, M., Machado, M.A., Talon, M., Jaillon, O., Ollitrault, P., Gmitter, F. 2014. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology. 32(7):656-662.

Interpretive Summary: Diverse types of commercial citrus cultivars were domesticated several thousand years ago in Southeast Asia and spread globally. According to limited morphologic traits and molecular marker data, most citrus types are presumably originated from interspecific hybridization and multi-generational introgression with different wild ancestral species. However, it remains controversial how main modern varieties evolved from what ancestral species. This study is to sequence and compare the genomes of main citrus types, including mandarins, pummelos, sweet oranges and sour oranges. The results help understand taxonomic relationship from genomic phylogenetic perspectives and facilitate sequence-directed genetic improvement in the crop.

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