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

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
VolumeN/A
IssueN/A
Year2017
Page(s)N/A
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)).

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Pages

Properties
Additional details for this publication include:
Property NameValue
Journal CountryEngland
Publication TypeJournal Article
Language Abbreng
LanguageEnglish
Copyright© The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
Elocation10.1093/dnares/dsx020
DOI10.1093/dnares/dsx020
Journal AbbreviationDNA Res.
Publication Date2017 May 25
eISSN1756-1663
ISSN1756-1663
Publication ModelPrint-Electronic
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DatabaseAccession
PMID: PubMedPMID:28541388