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_sc0000909.1_352801RPav_sc0000909.1_352801Rgenetic_marker
Pav_sc0000909.1_410648MPav_sc0000909.1_410648Mgenetic_marker
Pav_sc0000909.1_434460MPav_sc0000909.1_434460Mgenetic_marker
Pav_sc0000910.1_164704KPav_sc0000910.1_164704Kgenetic_marker
Pav_sc0000910.1_242368MPav_sc0000910.1_242368Mgenetic_marker
Pav_sc0000910.1_242384KPav_sc0000910.1_242384Kgenetic_marker
Pav_sc0000910.1_242388KPav_sc0000910.1_242388Kgenetic_marker
Pav_sc0000910.1_242533YPav_sc0000910.1_242533Ygenetic_marker
Pav_sc0000910.1_347358YPav_sc0000910.1_347358Ygenetic_marker
Pav_sc0000910.1_423703SPav_sc0000910.1_423703Sgenetic_marker
Pav_sc0000910.1_437502YPav_sc0000910.1_437502Ygenetic_marker
Pav_sc0000910.1_450149MPav_sc0000910.1_450149Mgenetic_marker
Pav_sc0000910.1_83677YPav_sc0000910.1_83677Ygenetic_marker
Pav_sc0000910.1_83990YPav_sc0000910.1_83990Ygenetic_marker
Pav_sc0000912.1_111029YPav_sc0000912.1_111029Ygenetic_marker
Pav_sc0000912.1_65549MPav_sc0000912.1_65549Mgenetic_marker
Pav_sc0000912.1_65696RPav_sc0000912.1_65696Rgenetic_marker
Pav_sc0000915.1_32122RPav_sc0000915.1_32122Rgenetic_marker
Pav_sc0000926.1_96871YPav_sc0000926.1_96871Ygenetic_marker
Pav_sc0000926.1_96889YPav_sc0000926.1_96889Ygenetic_marker
Pav_sc0000934.1_20020YPav_sc0000934.1_20020Ygenetic_marker
Pav_sc0000934.1_20082YPav_sc0000934.1_20082Ygenetic_marker
Pav_sc0000934.1_20091KPav_sc0000934.1_20091Kgenetic_marker
Pav_sc0000934.1_20096MPav_sc0000934.1_20096Mgenetic_marker
Pav_sc0000941.1_24193RPav_sc0000941.1_24193Rgenetic_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