The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding

Publication Overview
TitleThe genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding
AuthorsShirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S
TypeJournal Article
Journal NameDNA research : an international journal for rapid publication of reports on genes and genomes
Year2017
CitationShirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA research : an international journal for rapid publication of reports on genes and genomes. 2017 May 25.

Abstract

We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).

Stocks
This publication contains information about 13 stocks:
Stock NameUniquenameType
C-303C-303cultivar
C-309C-309cultivar
HROHROcultivar
BeniyutakaBeniyutakacultivar
Benikirari mapBenikirari mapcultivar
NanyoNanyocultivar
BenisayakaBenisayakacultivar
C-303_x_BeniyutakaC-303_x_Beniyutakapopulation
C-303_x_BenikirariC-303_x_Benikiraripopulation
C-309_x_C-195-50C-309_x_C-195-50population
C-309_x_BenikirariC-309_x_Benikiraripopulation
HRO_x_NanyoHRO_x_Nanyopopulation
HRO_x_BenisayakaHRO_x_Benisayakapopulation
Cross References
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DatabaseAccession
PMID: PubMedPMID:28541388