The domestication of citrus, is poorly understood. Cultivated types are selections from, or hybrids of, wild progenitor species, whose identities and contributions remain controversial. By comparative analysis of a collection of citrus genomes, including a high quality haploid reference, we show that cultivated types were derived from two progenitor species. Though cultivated pummelos represent selections from a single progenitor species, C. maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species, C. 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, implying that wild mandarins were part of the early breeding germplasm. A wild “mandarin” from China exhibited substantial divergence from C. reticulata, suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and enables sequence-directed genetic improvement.

Genomics of the origin and evolution of CitrusGuohong albert Wu 1 , Javier Terol 2 , Victoria ibanez 2 , antonio López-García 2 , estela Pérez-román 2 , carles borredá 2 , concha Domingo 2 , francisco r. Tadeo 2 , Jose carbonell-caballero 3 , roberto alonso 3 , franck curk 4 , Dongliang Du 5 , Patrick Ollitrault 6 , Mikeal L. roose 7 , Joaquin Dopazo 3,8 , frederick G. Gmitter Jr 5 , Daniel S. rokhsar 1,9,10 & Manuel Talon 2The genus Citrus and related genera (Fortunella, Poncirus, Eremocitrus and Microcitrus) belong to the angiosperm subfamily Aurantioideae of the Rutaceae family, which is widely distributed across the monsoon region from west Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and the Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands 1 . Native habitats of citrus and related genera roughly extend throughout this broad area (Extended Data Fig. 1a and Supplementary Table 1), although the geogra phical origin, timing and dispersal of citrus species across southeast Asia remain unclear. A major obstacle to resolving these uncertainties is our poor understanding of the genealogy of complex admixture in cultivated citrus, as has recently been shown 2 . Some citrus are clonally propagated apomictically 3 through nucellar embryony, that is, the development of non-sexual embryos originating in the maternal nucellar tissue of the ovule, and this natural process may have been co-opted during domestication; grafting is a relatively recent phenomenon 4 . Both modes of clonal propagation have led to the domestication of fixed (desirable) genotypes, including interspecific hybrids, such as oranges, limes, lemons, grapefruits and other types.Under this scenario, it is not surprising that the current chaotic citrus taxonomy-based on long-standing, conflicting proposals 5,6 -requires a solid reformulation consistent with a full understanding of the hybrid and/or admixture nature of cultivated citrus species. Here we analyse genome sequences of diverse citrus to characterize the diversity and evolution of citrus at the species level and identify citrus admixtures and interspecific hybrids. We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication. Diversity and evolution of the genus CitrusTo investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations. These sequences represent a diverse sampling of citrus species, their admixtures and hybrids (Supplementary Tables 2, 3 and Supplementary Notes 1, 2). Our collection includes accessions from eight previously unsequ...

To specify the genotypic variation of Mediterranean Citrus juices, the contents of carotenoids, flavonoids, and vitamin C were determined by high-performance liquid chromatography. A selection of orange varieties and Mandarin species from the Mediterranean area (Citrus sinensis, Citrus deliciosa Ten, and Citrus clementina Hort. ex Tan) was evaluated using carotenoid profiles and flavanones contents. Among the eight varieties of orange (Salustiana, Hamlin, Shamouti, Pera, Valencia, Maltaise, Sanguinelli, and Cara-cara) and two Mandarin species, only three cultivars (Pera, Sanguinelli, and Shamouti) and the two Mandarin species displayed a high content of vitamin A (374, 381, and 272 ER L(-1) for the three orange cultivars and 1156 and 960 retinol equivalent (RE) L(-1) for the Mandarins) due to a high content of beta-cryptoxanthin. These same Citrus were also rich in hesperidin (502, 537, 552, 767, and 754 mg L(-1), respectively). Principal component analysis allowed the Mediterranean orange varieties and Mandarin species to be differentiated on the basis of nutritional criteria. Strong correlations were observed between beta-cryptoxanthin and hesperidin (r = 0.92) and between beta-cryptoxanthin and beta-carotene (r = 0.98). In contrast, vitamin C content was not correlated with carotenoids and flavanone glycosides. The Mandarin and orange group was quite distinct. The orange varieties could be divided in two groups. In addition, a diversity tree allowed a genetic approach to differentiating Citrus cultivars on the basis of Euclidian distances. This representation showed that the hybrid Clementine was nearer to its parent Mandarin than to its parent orange, suggesting that beta-cryptoxanthin was a dominant genetic factor. With regard to vitamin A, Mandarin and its hybrid Clementine appeared to be the best Citrus species.