Genomics of the origin and evolution of Citrus

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

doi:10.1038/nature25447

Genomics of the origin and evolution of Citrus

Journal Article · Thu Feb 01 00:00:00 EST 2018 · Nature (London)

DOI:https://doi.org/10.1038/nature25447· OSTI ID:1543733

Wu, Guohong Albert ^[1]; Terol, Javier ^[2]; Ibanez, Victoria ^[2]; López-García, Antonio ^[2]; Pérez-Román, Estela ^[2]; Borredá, Carles ^[2]; Domingo, Concha ^[2]; Tadeo, Francisco R. ^[2]; Carbonell-Caballero, Jose ^[3]; Alonso, Roberto ^[3]; Curk, Franck ^[4]; Du, Dongliang ^[5]; Ollitrault, Patrick ^[6]; Roose, Mikeal L. ^[7]; Dopazo, Joaquin ^[8]; Gmitter, Frederick G. ^[5]; Rokhsar, Daniel S. ^[9]; Talon, Manuel ^[2]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Inst. Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia (Spain). Centro de Genómica
Centro de Investigación Príncipe Felipe (CIPF), Valencia (Spain)
Inst. National de la Recherche Agronomique (INRA), San Giuliano (France)
Univ. of Florida, Lake Alfred, FL (United States). Inst. of Food and Agricultural Sciences (IFAS)
AGAP Research Unit, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Petit-Bourg, Guadeloupe (France)
Univ. of California, Riverside, CA (United States)
Centro de Investigación Príncipe Felipe (CIPF), Valencia (Spain); Spanish National Inst. of Bioinformatics (ELIXIR-es) at CIPF, Valencia (Spain)
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)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE

OSTI ID:: 1543733

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7692 Vol. 554; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Zhang, Jisen; Zhang, Xingtan; Tang, Haibao Nature Genetics, Vol. 50, Issue 11 https://doi.org/10.1038/s41588-018-0237-2	journal	October 2018
Genotyping by sequencing can reveal the complex mosaic genomes in gene pools resulting from reticulate evolution: a case study in diploid and polyploid citrus Ahmed, Dalel; Comte, Aurore; Curk, Franck Annals of Botany, Vol. 123, Issue 7 https://doi.org/10.1093/aob/mcz029	journal	March 2019
Differential Impacts of Citrus Thrips Across Sweet Orange and Mandarin Species Mueller, Tobias G.; Kahl, Hanna M.; Cass, Bodil N. Journal of Economic Entomology, Vol. 112, Issue 6 https://doi.org/10.1093/jee/toz178	journal	July 2019
Resistance of Fruits From a Mandarin Cultivar to Feeding by Fork-Tailed Bush Katydids Cass, Bodil N.; Grafton-Cardwell, Elizabeth E.; Rosenheim, Jay A. Journal of Economic Entomology, Vol. 112, Issue 6 https://doi.org/10.1093/jee/toz241	journal	October 2019
Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes Baurens, Franc-Christophe; Martin, Guillaume; Hervouet, Catherine Molecular Biology and Evolution, Vol. 36, Issue 1 https://doi.org/10.1093/molbev/msy199	journal	November 2018
Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut Zhang, Bo-Wen; Xu, Lin-Lin; Li, Nan Molecular Biology and Evolution, Vol. 36, Issue 11 https://doi.org/10.1093/molbev/msz112	journal	June 2019
Hesperidin supplementation has no effect on blood glucose control: A systematic review and meta‐analysis of randomized controlled clinical trials Shams‐Rad, Shamim; Mohammadi, Mohammad; Ramezani‐Jolfaie, Nahid British Journal of Clinical Pharmacology, Vol. 86, Issue 1 https://doi.org/10.1111/bcp.14120	journal	December 2019
The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events Liu, Shuo; Cornille, Amandine; Decroocq, Stéphane Molecular Ecology, Vol. 28, Issue 24 https://doi.org/10.1111/mec.15296	journal	November 2019
Occurrence of prophage and historical perspectives associated with the dissemination of huanglongbing in mainland China Fu, S.; Bai, Z.; Su, H. Plant Pathology, Vol. 69, Issue 1 https://doi.org/10.1111/ppa.13100	journal	October 2019
Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency Zhang, Xiao-Yong; Qiu, Jie-Ya; Hui, Qiu-Ling BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6644-7	journal	March 2020
Genome-wide analysis of the citrus B3 superfamily and their association with somatic embryogenesis Liu, Zheng; Ge, Xiao-Xia; Wu, Xiao-Meng BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6715-9	journal	April 2020
Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes Cottin, Aurélien; Penaud, Benjamin; Glaszmann, Jean-Christophe G3: Genes\|Genomes\|Genetics, Vol. 10, Issue 2 https://doi.org/10.1534/g3.119.400873	journal	December 2019
A Phylogenomic Supertree of Birds Kimball, Rt; Oliveros, Ch; Wang, N. MDPI AG https://doi.org/10.17863/cam.41670	journalarticle	January 2019
Volatile Compounds in Citrus Essential Oils: A Comprehensive Review González-Mas, M. Carmen; Rambla, José L.; López-Gresa, M. Pilar Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00012	journal	February 2019
Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops De Ollas, Carlos; Morillón, Raphaël; Fotopoulos, Vasileios Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00427	journal	April 2019
A Phylogenomic Supertree of Birds Kimball, Rebecca T.; Oliveros, Carl H.; Wang, Ning Diversity, Vol. 11, Issue 7 https://doi.org/10.3390/d11070109	journal	July 2019
Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices Morello, Laura; Braglia, Luca; Gavazzi, Floriana Genes, Vol. 10, Issue 3 https://doi.org/10.3390/genes10030229	journal	March 2019
Leaf Transcriptome Assembly of Protium copal (Burseraceae) and Annotation of Terpene Biosynthetic Genes Damasco, Gabriel; Shivakumar, Vikram S.; Misciewicz, Tracy M. Genes, Vol. 10, Issue 5 https://doi.org/10.3390/genes10050392	journal	May 2019

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