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Nature. 2018 Feb 15;554(7692):311-316. doi: 10.1038/nature25447. Epub 2018 Feb 7.

Genomics of the origin and evolution of Citrus.

Author information

US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain.
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
AGAP Research Unit, Institut National de la Recherche Agronomique (INRA), San Giuliano, France.
Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, Florida, USA.
AGAP Research Unit, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe, France.
Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA.
Functional Genomics Node, Spanish National Institute of Bioinformatics (ELIXIR-es) at CIPF, Valencia, Spain.
Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California, Berkeley, Berkeley, California, USA.
Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.


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.

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