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_sc0001013.1_13912SSRPav_sc0001013.1_13912SSRgenetic_marker
Pav_sc0004634.1_51948SSRPav_sc0004634.1_51948SSRgenetic_marker
Pav_sc0010641.1_592SSRPav_sc0010641.1_592SSRgenetic_marker
Pav_sc0001478.1_316792SSRPav_sc0001478.1_316792SSRgenetic_marker
Pav_sc0003129.1_13602SSRPav_sc0003129.1_13602SSRgenetic_marker
Pav_sc0004923.1_30077SSRPav_sc0004923.1_30077SSRgenetic_marker
Pav_sc0000980.1_52861SSRPav_sc0000980.1_52861SSRgenetic_marker
Pav_sc0007633.1_1357SSRPav_sc0007633.1_1357SSRgenetic_marker
Pav_sc0007633.1_1413SSRPav_sc0007633.1_1413SSRgenetic_marker
Pav_sc0001461.1_75268SSRPav_sc0001461.1_75268SSRgenetic_marker
Pav_sc0001109.1_82988SSRPav_sc0001109.1_82988SSRgenetic_marker
Pav_sc0002375.1_89542SSRPav_sc0002375.1_89542SSRgenetic_marker
Pav_sc0003189.1_5870SSRPav_sc0003189.1_5870SSRgenetic_marker
Pav_sc0000998.1_10892SSRPav_sc0000998.1_10892SSRgenetic_marker
Pav_sc0001015.1_71468SSRPav_sc0001015.1_71468SSRgenetic_marker
Pav_sc0008065.1_96SSRPav_sc0008065.1_96SSRgenetic_marker
Pav_sc0001215.1_194656SSRPav_sc0001215.1_194656SSRgenetic_marker
Pav_sc0001006.1_102306SSRPav_sc0001006.1_102306SSRgenetic_marker
Pav_sc0000659.1_329117SSRPav_sc0000659.1_329117SSRgenetic_marker
Pav_sc0000659.1_329140SSRPav_sc0000659.1_329140SSRgenetic_marker
Pav_sc0001003.1_7057SSRPav_sc0001003.1_7057SSRgenetic_marker
Pav_sc0002659.1_89213SSRPav_sc0002659.1_89213SSRgenetic_marker
Pav_sc0002659.1_89238SSRPav_sc0002659.1_89238SSRgenetic_marker
Pav_sc0001467.1_48765SSRPav_sc0001467.1_48765SSRgenetic_marker
Pav_sc0001270.1_77955SSRPav_sc0001270.1_77955SSRgenetic_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