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Genomics of the origin and evolution of Citrus      

Guohong Albert Wu, Javier Terol, Victoria Ibanez, Antonio López-García, Estela Pérez-Román, Carles Borredá, Concha Domingo, Francisco R. Tadeo, Jose Carbonell-Caballero, Roberto Alonso, Franck Curk, Dongliang Du, Patrick Ollitrault, Mikeal L. Roose, Joaquin Dopazo, Frederick G. Gmitter, Daniel S. Rokhsar & Manuel Talon

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.

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Figure 1. Genetic structure, heterozygosity and phylogeny of Citrus species.  a, Principal coordinate analysis of 58 citrus accessions based on pairwise nuclear genome distances and metric multidimensional scaling. The first two axes separate the three main citrus groups (citrons, pummelos and mandarins) with interspecific hybrids (oranges, grapefruit, lemon and limes) situated at intermediate positions relative to their parental genotypes. b, Violin plots of the heterozygosity distribution in 58 citrus accessions, representing 10 taxonomic groups as well as 2 related genera, Poncirus (Poncirus trifoliata, also known as Citrus trifoliata) and Chinese box orange (Severinia). White dot, median; bar limits, upper and lower quartiles; whiskers, 1.5× interquartile range. The bimodal separation of intraspecies (light blue) and interspecies (light pink) genetic diversity is manifested among the admixed mandarins and across different genotypes including interspecific hybrids. Three-letter codes are listed in parenthesis with additional descriptions in Supplementary Table 2. c, Chronogram of citrus speciation. Two distinct and temporally well-separated phases of species radiation are apparent, with the southeast Asian citrus radiation followed by the Australian citrus diversification. Age calibration is based on the citrus fossil C. linczangensis16 from the Late Miocene (denoted by a filled red circle). The 95% confidence intervals are derived from 200 bootstraps. Bayesian posterior probability is 1.0 for all nodes. d, Proposed origin of citrus and ancient dispersal routes. Arrows suggest plausible migration directions of the ancestral citrus species from the centre of origin—the triangle formed by northeastern India, northern Myanmar and northwestern Yunnan. The proposal is compatible with citrus biogeography, phylogenetic relationships, the inferred timing of diversification and the paleogeography of the region, especially the geological history of Wallacea and Japan. The red star marks the fossil location of C. linczangensis. Citrus fruit images in c and d are not drawn to scale.

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Figure 2: Admixture proportion and citrus genealogy. a, Allelic proportion of five progenitor citrus species in 50 accessions. CI, C. medica; FO, Fortunella; MA, C. reticulata; MC, C. micrantha; PU, C. maxima; UNK, unknown. The pummelos and citrons represent pure citrus species, whereas in the heterogeneous set of mandarins, the degree of pummelo introgression subdivides the group into pure (type-1) and admixed (type-2 and -3) mandarins. Three-letter code as in Fig. 1, see Supplementary Table 2 for details. b, Genealogy of major citrus genotypes. The five progenitor species are shown at the top. Blue lines represent simple crosses between two parental genotypes, whereas red lines represent more complex processes involving multiple individuals, generations and/or backcrosses. Whereas type-1 mandarins are pure species, type-2 (early-admixture) mandarins contain a small amount of pummelo admixture that can be traced back to a common pummelo ancestor (with P1 or P2 haplotypes). Later, additional pummelo introgressions into type-2 mandarins gave rise to both type-3 (late-admixture) mandarins and sweet orange. Further breeding between sweet orange and mandarins or within late-admixture mandarins produced additional modern mandarins. Fruit images are not to scale and represent the most popular citrus types. See Supplementary Note 1.1 for nomenclature usage. 

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Figure 3: Citrus relatedness network and haplotype sharing with sweet orange.a, Genetic relatedness among 48 citrus accessions derived from four progenitor species including citrons, pummelos, pure mandarins and micrantha. Solid lines connect pairs with coefficient of relatedness r > 0.45, with parent–child pairs denoted by arrows pointing from parent to child. Dashed and dotted lines correspond to 0.35

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 https://www.nature.com/articles/nature25447#f2
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