The genome of the domesticated apple (Malus × domestica Borkh.)

@article{Velasco2010TheGO,
  title={The genome of the domesticated apple (Malus × domestica Borkh.)},
  author={Riccardo Velasco and Andrey A. Zharkikh and Jason P. Affourtit and Amit Dhingra and Alessandro Cestaro and A. Kalyanaraman and Paolo Fontana and Satish Bhatnagar and Michela Troggio and Dmitry Pruss and Silvio Salvi and Massimo Pindo and Paolo Baldi and Sara Castelletti and Marina Cavaiuolo and Giuseppina Coppola and Fabrizio Costa and Valentina Cova and Antonio Dal Ri and Vadim V. Goremykin and Matteo Komjanc and Sara Longhi and Pierluigi Magnago and Giulia Malacarne and Mickael A. Malnoy and Diego Micheletti and Marco Moretto and Michele Perazzolli and Azeddine Si-Ammour and Silvia Vezzulli and Elena Zini and Glenn Eldredge and Lisa M. Fitzgerald and Natalia Gutin and Jerry S. S. Lanchbury and Teresita Macalma and Jeff T Mitchell and Julia E. Reid and Bryan Wardell and Chinnappa D. Kodira and Zhoutao Chen and Brian A. Desany and Faheem Niazi and Melanie J. Palmer and Tyson Koepke and Derick Jiwan and Scott Schaeffer and Vandhana Krishnan and Changjun Wu and Vu Tuan Chu and Stephen T King and Jessica L Vick and Quanzhou Tao and Amy Mraz and Aimee Stormo and Keith E. Stormo and Robert Bogden and Davide Ederle and Alessandra Stella and Alberto Vecchietti and Martin M. Kater and Simona Masiero and Pauline Lasserre and Yves Lespinasse and Andrew C. Allan and Vincent G. M. Bus and David Chagn{\'e} and Ross Crowhurst and Andrew Peter Gleave and Enrico Lavezzo and Jeffrey A. Fawcett and Sebastian Proost and Pierre Rouz{\'e} and Lieven Sterck and Stefano Toppo and Barbara Lazzari and Roger P Hellens and C. E. Durel and Alexander Gutin and Roger E Bumgarner and Susan E Gardiner and Mark H. Skolnick and Michael Wayland Egholm and Yves Van de Peer and Francesco Salamini and Roberto Viola},
  journal={Nature Genetics},
  year={2010},
  volume={42},
  pages={833-839}
}
We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the… 
Molecular Cloning and Analysis of Two Flowering Related Genes from Apple (Malus × domestica)
TLDR
Cloned and analysed the sequences and features of two genes, MdMADS1 and MdM ADS3, from apple ‘Golden Delicious’ and showed that the structure of both genes has noticeably differed from other SEP-like genes in evolution.
The Siberian wild apple, Malus baccata (L.) Borkh., is an additional contributor to the genomes of cultivated European and Chinese apples
TLDR
The role of gene flow during apple domestication is demonstrated, as seen in other woody perennials, and it is shown that domestication of the apple tree involved several wild apple species.
Genome-wide identification and analysis of the apple (Malus × domestica Borkh.) TIFY gene family
TLDR
This genome-wide identification and characterization of evolutionary relationships and expression profiles of apple TIFY genes will not only be useful for further analysis of this gene family and its role in stress response but may also aid in future agricultural improvement of apple stress tolerance.
Origins of the Apple: The Role of Megafaunal Mutualism in the Domestication of Malus and Rosaceous Trees
TLDR
The process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment) of the late Miocene.
A genome-wide analysis of the expansin genes in Malus × Domestica
TLDR
This study identified 41 members of the expansin gene family in the genome of apple and revealed that expansin genes in apple could be divided into four subfamilies according to their gene structures and protein motifs.
Analyzing the Papaya Genome
TLDR
The papaya draft genome, integrated genetic and physical maps, the EST database, and other genomic resources built for the genome sequencing project will expedite papaya improvement and the exploration of its nutritional and medicinal applications in developing countries.
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication
TLDR
The haplotype-resolved genomes of the cultivated apple and its two major wild progenitors are reported and it is revealed that introgression of new genes/alleles is a hallmark of apple domestication through hybridization.
Malus x domestica
TLDR
The origin of the domestic apple is still unresolved, and indications of the use of wild Malus genotypes in the (local) cultivation process of M. domestica and cytoplasmic introgression of chloroplast haplotypes into M. sylvestris are found.
Apple ( Malus spp.) Breeding: Present and Future
TLDR
The aim in apple breeding was the combination of different kinds of resistance and good fruit quality to produce dessert cultivars and cultivars for processing, and the recent molecular genetic tool CRISPR/Cas9 to edit and correct the genome.
The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution
TLDR
This study obtained a chromosome-scale genome assembly for ‘Youshi’ (Diospyros oleifera), the diploid species of persimmon, by integrating Illumina sequencing, single-molecule real-time sequencing, and high-throughput chromosome conformation capture techniques, and it is the first assembled genome for any member of the Ebenaceae.
...
...

References

SHOWING 1-10 OF 86 REFERENCES
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
TLDR
A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
TLDR
Analyzing the draft genome of the black cottonwood tree, Populus trichocarpa, revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome.
Taxonomy of the genus Malus Mill. (Rosaceae) with emphasis on the cultivated apple, Malus domestica Borkh.
TLDR
Maximum parsimony analysis generated nuclear and chloroplast cladograms that provide reasonable resolution of sub-generic groups, as recognised in classifications.
Chloroplast diversity in the genus Malus: new insights into the relationship between the European wild apple (Malus sylvestris (L.) Mill.) and the domesticated apple (Malus domestica Borkh.)
To unravel the relationship between the European wild apple, Malus sylvestris (L.) Mill., and its domesticated relative M. domestica Borkh., we studied chloroplast DNA variation in 634 wild and 422
The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes.
TLDR
The results falsify the wide-hybridization hypothesis and are consistent with a polyploid origin involving only members of a lineage that contained the ancestors of Gillenia.
Origins and evolution of subfam. Maloideae (Rosaceae)
TLDR
It is favoured the idea that several clades of Maloideae originated independently in a highly reticulate system existing shortly after the original allotetraploid cross, which makes sense of the general correspondence of phenetic genera to cladistic genera, remarkably low consistency index, great instability of the cladogram with respect to changing only a few OTU's, and the manifestly great ability of most maloideanGenera to hybridize.
Genetic identity and relationships of Iranian apple (Malus × domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis
TLDR
It is proposed that Iran could be one of the major players in apples’ domestication and transfer from Central Asia to the western countries and that the Iranian apples may occupy an intermediate position between the domesticated varieties and wild species.
A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety
TLDR
A high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens.
Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae
TLDR
Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome, suggesting that the dependence of synteny erosion on gene location along the centromere–telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.
Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome
TLDR
The increased coverage of theapple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs, which are generally more polymorphic than sequences containing trinucleotide repeats.
...
...