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)).

Features
This publication contains information about 370,918 features:
Feature NameUniquenameType
Pav_sc0000739.1_19892IPav_sc0000739.1_19892Igenetic_marker
Pav_sc0000739.1_19894IPav_sc0000739.1_19894Igenetic_marker
Pav_sc0000739.1_19908IPav_sc0000739.1_19908Igenetic_marker
Pav_sc0000739.1_20271DPav_sc0000739.1_20271Dgenetic_marker
Pav_sc0000739.1_24794IPav_sc0000739.1_24794Igenetic_marker
Pav_sc0000739.1_25631IPav_sc0000739.1_25631Igenetic_marker
Pav_sc0000739.1_27159DPav_sc0000739.1_27159Dgenetic_marker
Pav_sc0000746.1_12371DPav_sc0000746.1_12371Dgenetic_marker
Pav_sc0000746.1_12480DPav_sc0000746.1_12480Dgenetic_marker
Pav_sc0000746.1_16641IPav_sc0000746.1_16641Igenetic_marker
Pav_sc0000746.1_26672DPav_sc0000746.1_26672Dgenetic_marker
Pav_sc0000746.1_26839DPav_sc0000746.1_26839Dgenetic_marker
Pav_sc0000757.1_5775IPav_sc0000757.1_5775Igenetic_marker
Pav_sc0000757.1_6308DPav_sc0000757.1_6308Dgenetic_marker
Pav_sc0000757.1_7105IPav_sc0000757.1_7105Igenetic_marker
Pav_sc0000757.1_7750IPav_sc0000757.1_7750Igenetic_marker
Pav_sc0000757.1_12356DPav_sc0000757.1_12356Dgenetic_marker
Pav_sc0000757.1_12358DPav_sc0000757.1_12358Dgenetic_marker
Pav_sc0000757.1_12718DPav_sc0000757.1_12718Dgenetic_marker
Pav_sc0000757.1_16761DPav_sc0000757.1_16761Dgenetic_marker
Pav_sc0000757.1_16780DPav_sc0000757.1_16780Dgenetic_marker
Pav_sc0000757.1_17370IPav_sc0000757.1_17370Igenetic_marker
Pav_sc0000757.1_17371IPav_sc0000757.1_17371Igenetic_marker
Pav_sc0000757.1_17372IPav_sc0000757.1_17372Igenetic_marker
Pav_sc0000757.1_17379IPav_sc0000757.1_17379Igenetic_marker

Pages

Stocks
This publication contains information about 13 stocks:
Stock NameUniquenameType
C-303C-303accession
C-309C-309accession
HROHROaccession
BeniyutakaBeniyutakaaccession
BenikirariBenikirariaccession
NanyoNanyoaccession
BenisayakaBenisayakaaccession
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