Genomics of the origin and evolution of Citrus

@article{Wu2018GenomicsOT,
  title={Genomics of the origin and evolution of Citrus},
  author={Guohong Albert Wu and Javier Terol and Victoria Ibanez and Antonio L{\'o}pez-Garc{\'i}a and Estela P{\'e}rez-Rom{\'a}n and Carles Borred{\'a} and Concha Domingo and Francisco R. Tadeo and Jos{\'e} Carbonell-Caballero and Roberto Alonso and Franck Curk and Dongliang Du and Patrick Ollitrault and Mikeal Roose and Joaqu{\'i}n Dopazo and Frederick G. Gmitter and Daniel S. Rokhsar and Manuel Tal{\'o}n},
  journal={Nature},
  year={2018},
  volume={554},
  pages={311-316}
}
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… 

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References

SHOWING 1-10 OF 50 REFERENCES
Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
TLDR
This study de novo sequenced and comprehensively studied the genomes of four representative citrus species and found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony.
The possible role of Yunnan, China, in the origin of contemporary citrus species (rutaceae)
The primitive center of origin of Citrus species has been a subject of speculation and discussion for some time. Japanese Citrus taxonomist Tanaka concluded that the center of origin was northeastern
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
TLDR
This work sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and shows that cultivated types derive from two progenitor species.
New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties
TLDR
It is shown that the evolution of domesticated apples occurred over a long time period and involved more than one wild species, supporting the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication.
Genetic structure and domestication history of the grape
TLDR
It is proposed that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses.
Citrus phylogeny and genetic origin of important species as investigated by molecular markers
TLDR
Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus and from each other.
Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
TLDR
The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzo, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties.
Citrus linczangensis sp. n., a Leaf Fossil of Rutaceae from the Late Miocene of Yunnan, China
TLDR
The unique morphological characters of this fossil provide definitive evidence of Citrus in the fossil record of Asia and expand the geological history of the genus back to the late Miocene.
The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms
TLDR
Phylogenetic analyses resolve relationships among several major clades of angiosperms and provide strong support for the monophyly of the eurosid II clade and the position of the Sapindales sister to the Brassicales/Malvales/Brassicales family.
Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers.
TLDR
The lime and lemon horticultural group appears to be highly polymorphic, with diploid, triploid and tetraploid varieties, and to result from many independent reticulation events which defined the sub-groups, as limes and lemons were vegetatively propagated and the intra-sub-group phenotypic diversity results from asexual variations.
...
1
2
3
4
5
...