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Title: Genomics of the origin and evolution of Citrus

Abstract

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2];  [3];  [3];  [4];  [5];  [6];  [7];  [8];  [5];  [9];  [2]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Inst. Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia (Spain). Centro de Genómica
  3. Centro de Investigación Príncipe Felipe (CIPF), Valencia (Spain)
  4. Inst. National de la Recherche Agronomique (INRA), San Giuliano (France)
  5. Univ. of Florida, Lake Alfred, FL (United States). Inst. of Food and Agricultural Sciences (IFAS)
  6. AGAP Research Unit, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe (France)
  7. Univ. of California, Riverside, CA (United States)
  8. Centro de Investigación Príncipe Felipe (CIPF), Valencia (Spain); Spanish National Inst. of Bioinformatics (ELIXIR-es) at CIPF, Valencia (Spain)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States); Okinawa Inst. of Science and Technology Graduate Univ., Onna, Okinawa (Japan)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE
OSTI Identifier:
1543733
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 554; Journal Issue: 7692; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
Science & Technology - Other Topics

Citation Formats

Wu, Guohong Albert, Terol, Javier, Ibanez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco R., Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L., Dopazo, Joaquin, Gmitter, Frederick G., Rokhsar, Daniel S., and Talon, Manuel. Genomics of the origin and evolution of Citrus. United States: N. p., 2018. Web. doi:10.1038/nature25447.
Wu, Guohong Albert, Terol, Javier, Ibanez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco R., Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L., Dopazo, Joaquin, Gmitter, Frederick G., Rokhsar, Daniel S., & Talon, Manuel. Genomics of the origin and evolution of Citrus. United States. doi:10.1038/nature25447.
Wu, Guohong Albert, Terol, Javier, Ibanez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco R., Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L., Dopazo, Joaquin, Gmitter, Frederick G., Rokhsar, Daniel S., and Talon, Manuel. Thu . "Genomics of the origin and evolution of Citrus". United States. doi:10.1038/nature25447. https://www.osti.gov/servlets/purl/1543733.
@article{osti_1543733,
title = {Genomics of the origin and evolution of Citrus},
author = {Wu, Guohong Albert and Terol, Javier and Ibanez, Victoria and López-García, Antonio and Pérez-Román, Estela and Borredá, Carles and Domingo, Concha and Tadeo, Francisco R. and Carbonell-Caballero, Jose and Alonso, Roberto and Curk, Franck and Du, Dongliang and Ollitrault, Patrick and Roose, Mikeal L. and Dopazo, Joaquin and Gmitter, Frederick G. and Rokhsar, Daniel S. and Talon, Manuel},
abstractNote = {The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.},
doi = {10.1038/nature25447},
journal = {Nature (London)},
number = 7692,
volume = 554,
place = {United States},
year = {2018},
month = {2}
}

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