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_sc0000071.1_422274SSRPav_sc0000071.1_422274SSRgenetic_marker
Pav_sc0000071.1_422385SSRPav_sc0000071.1_422385SSRgenetic_marker
Pav_sc0000129.1_55812SSRPav_sc0000129.1_55812SSRgenetic_marker
Pav_sc0004485.1_12317SSRPav_sc0004485.1_12317SSRgenetic_marker
Pav_sc0004485.1_12446SSRPav_sc0004485.1_12446SSRgenetic_marker
Pav_sc0001411.1_57132SSRPav_sc0001411.1_57132SSRgenetic_marker
Pav_sc0000013.1_80909SSRPav_sc0000013.1_80909SSRgenetic_marker
Pav_sc0000491.1_215039SSRPav_sc0000491.1_215039SSRgenetic_marker
Pav_sc0001106.1_393867SSRPav_sc0001106.1_393867SSRgenetic_marker
Pav_sc0000549.1_671349SSRPav_sc0000549.1_671349SSRgenetic_marker
Pav_sc0000409.1_63412SSRPav_sc0000409.1_63412SSRgenetic_marker
Pav_sc0000830.1_427490SSRPav_sc0000830.1_427490SSRgenetic_marker
Pav_sc0001080.1_613057SSRPav_sc0001080.1_613057SSRgenetic_marker
Pav_sc0002250.1_128882SSRPav_sc0002250.1_128882SSRgenetic_marker
Pav_sc0002250.1_128859SSRPav_sc0002250.1_128859SSRgenetic_marker
Pav_sc0000351.1_181935SSRPav_sc0000351.1_181935SSRgenetic_marker
Pav_sc0000910.1_360224SSRPav_sc0000910.1_360224SSRgenetic_marker
Pav_sc0002475.1_66307SSRPav_sc0002475.1_66307SSRgenetic_marker
Pav_sc0000138.1_167482SSRPav_sc0000138.1_167482SSRgenetic_marker
Pav_sc0000071.1_126721SSRPav_sc0000071.1_126721SSRgenetic_marker
Pav_sc0007972.1_3867SSRPav_sc0007972.1_3867SSRgenetic_marker
Pav_sc0000474.1_9949SSRPav_sc0000474.1_9949SSRgenetic_marker
Pav_sc0000624.1_216222SSRPav_sc0000624.1_216222SSRgenetic_marker
Pav_sc0002828.1_73524SSRPav_sc0002828.1_73524SSRgenetic_marker
Pav_sc0000554.1_131942SSRPav_sc0000554.1_131942SSRgenetic_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