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We present first solid insights on the origin, evolution and dispersal of citrus and elucidate the genealogy of the most important wild and cultivated varieties. These findings draw a new evolutionary framework for these fruit crops, a scenario that challenges current taxonomic and phylogenetic thoughts and points towards a reformulation of the genus Citrus. Based on genomic, phylogenetic and biogeographical analyses of the genus Citrus we propose that the center of origin of citrus was the Southeast foothills of the Himalayas, in a region including the eastern area of Assam, northern Myanmar and western Yunnan. Our analyses suggest that the ancestral citrus species underwent a sudden speciation during late Miocene and that the new species dispersed from there to surrounding regions, coinciding with a drastic transition from wetter monsoonal conditions to a drier climate. The Australian citrus and Tachibana mandarin split later from mainland citrus during the early Pliocene and Pleistocene, respectively.

The genius Citrus and related genera are widely distributed across the monsoon region from West Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands. Native habitats of these genera roughly extends throught this broad area, although the center of origin, timing, dispersal and domestication of citrus species across Southeast Asia remains unclear. The major hindrance to work out these unresolved ambiguities is intimately related to our poor understanding of the complex admixture genealogy of cultivated citrus as recently we revealed. Presumably, the historical association of humans with cultivated citrus that have been genetically fixed through grafting and apomixis, has led to foremost uncertainties on the genetic composition of citrus, a substantial gap precluding the elucidation of citrus ancestry. In this presentation, we combine genome sequence analysis and biogeographic evidence to characterize the genetic diversity and evolution of citrus. This information offers solid insights on the origin, dispersal and domestication of citrus, revealing a new evolutionary paradigm for the genus Citrus. (Texte intégral)

Citrus is the most globally significant tree fruit, but its history of domestication is not well understood. Cultivated citrus types are believed to be direct selections from, or hybrids of, several progenitor species; however, the identities of these species and their contributions to modern cultivars remain unclear and controversial. A collection of different genomes of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin, has been assembled. By comparative analyses we show that these cultivated types were derived from two progenitor species, C. maxima and C. reticulata. Although it was determined that the sequenced cultivated pummelos represent selections from C. maxima, the cultivated mandarins proved to be introgressions of C. maxima into a distinct second population identified as the ancestral wild mandarin species, C. reticulata. Sweet and sour oranges were found to be hybrids between these two species. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. Sour (or Seville) orange was found to be an F1 hybrid of pure C. maximaand C. reticulata parents, indicating that wild mandarins were at least a part of the early breeding germplasm. Sequence analysis also revealed that at least one Chinese "wild mandarin" actually represents a citrus species distinct from C. reticulata, suggesting the possibility that other unrecognized wild citrus species may be identified. Understanding the phylogeny of cultivated citrus by comparative genome analysis will clarify taxonomic relationships and potentially lead to previously inconceivable opportunities for genetic improvement. (Texte intégral)

Since its inception, the International Citrus Genome Consortium (ICGC) has pursued development of freely available genomics resources and tools for the benefit of the citrus research community; these efforts were conducted by citrus scientists in concert with researchers from some of the world's major genome sequencing centers and corporations. An early ICGC goal was to produce a full-length genome assembly. Two reference genome sequences were made publicly available in January 2011, from a 'Clemenules' clementine-derived haploid and diploid 'Ridge Pineapple' sweet orange, produced using Sanger and 454 sequencing technologies respectively. Subsequent work has proceeded to improve the assemblies and their annotation; a brief summary of their characteristics and status of the assemblies will be presented. As sequencing technology has evolved and costs have dramatically decreased, other citrus genomes have been sequenced (the diploid 'Clemenules', 'Ponkan', 'Willowleaf', 'W. Murcott' mandarins; 'Siamese Sweet' and 'Chandler' pummelo; and sour orange, among others). A comparative analysis of these genomes has made it possible to describe the genomic contributions from ancestral outbred populations to major cultivar types, and to propose likely underlying models. The results confirmed previous reports that clementine arose from a hybridization event between 'Willowleaf' mandarin and sweet orange. Further, introgressions of Citrus reticulata and Citrus maxima germplasm, long implicated in its ancestry, clearly defined the segmented mosaic genome of sweet orange, through the ancient admixture of these species. Finally, sour orange was found to be a direct hybrid of a pummelo and mandarin. Interestingly, although the two pummelos sequenced appear to have their derivations from a single wild species (C. maxima), the mandarins sequenced reveal ancestral admixture of C. maxima with C. reticulata. Implications and future directions for collaborative research will be discussed. (Texte intégral)

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. The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties. Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain. Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes. They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture. The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons. They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups.