Cerasus x yedoensis Somei-Yoshino Genome v1.0 Assembly & Annotation

Genome Overview
Analysis NameCerasus x yedoensis Somei-Yoshino Genome v1.0 Assembly & Annotation
MethodFALCON assembler (v. 2.1.2)
SourceCerasus x yedoensis Somei-Yoshino Genome v1.0
Date performed2019-08-05

About the Assembly

The phased genome sequence of an interspecific hybrid, the flowering cherry ‘Somei-Yoshino’ (Cerasus × yedoensis) is reported. The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants, is established. A whole genome resequencing analysis of flowering cherries suggested that ‘Somei-Yoshino’ might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

Publication

Shirasawa K, Esumi T, Hirakawa H, Tanaka H, Itai A, Ghelfi A, Nagasaki H, Isobe S. Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis). DNA research : an international journal for rapid publication of reports on genes and genomes. 2019 Jul 23. pii: dsz016. doi: 10.1093/dnares/dsz016 (Journal | GDR)

External site

DBcherry

Properties
Additional information about this analysis:
Property NameValue
JBrowse URLhttps://www.rosaceae.org/jbrowse/index.html?data=data/fragaria/fvesca_v2.0.a1&loc=
Analysis Typewhole_genome
Assembly

The Cerasus x yedoensis Genome v1.0 assembly files are available in FASTA format and GFF3 format.

Downloads

Pseudomolecule (FASTA file) cyedoensis-v1.0.fasta.gz
Repeats (FASTA file) cyedoensis-v1.0.repeats.gff.gz

 

Gene Predictions

The Cerasus x yedoensis v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) cyedoensis-v1.0.proteins.fasta.gz
CDS (FASTA file) cyedoensis-v1.0.CDs.fasta.gz
Genes (GFF3 file) cyedoensis-v1.0.genes.gff3.gz

 

Downloads

All assembly and annotation files are available for download by selecting the desired data type in the right-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

Homology

Homology of the Cerasus x yedoensis genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Cerasus x yedoensis v1.0 proteins with NCBI nr homologs (EXCEL file) Cyedoensis-v1.0_vs_nr.xlsx.gz
Cerasus x yedoensis v1.0 proteins with NCBI nr (FASTA file) Cyedoensis-v1.0_vs_nr_hit.fasta.gz
Cerasus x yedoensis v1.0 proteins without NCBI nr (FASTA file) Cyedoensis-v1.0_vs_nr_noHit.fasta.gz
Cerasus x yedoensis v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Cyedoensis-v1.0_vs_arabidopsis.xlsx.gz
Cerasus x yedoensis v1.0 proteins with arabidopsis (Araport11) (FASTA file) Cyedoensis-v1.0_vs_arabidopsis_hit.fasta.gz
Cerasus x yedoensis v1.0 proteins without arabidopsis (Araport11) (FASTA file) Cyedoensis-v1.0_vs_arabidopsis_noHit.fasta.gz
Cerasus x yedoensis v1.0 proteins with SwissProt homologs (EXCEL file) Cyedoensis-v1.0_vs_swissprot.xlsx.gz
Cerasus x yedoensis v1.0 proteins with SwissProt (FASTA file) Cyedoensis-v1.0_vs_swissprot_hit.fasta.gz
Cerasus x yedoensis v1.0 proteins without SwissProt (FASTA file) Cyedoensis-v1.0_vs_swissprot_noHit.fasta.gz
Cerasus x yedoensis v1.0 proteins with TrEMBL homologs (EXCEL file) Cyedoensis-v1.0_vs_trembl.xlsx.gz
Cerasus x yedoensis v1.0 proteins with TrEMBL (FASTA file) Cyedoensis-v1.0_vs_trembl_hit.fasta.gz
Cerasus x yedoensis v1.0 proteins without TrEMBL (FASTA file) Cyedoensis-v1.0_vs_trembl_noHit.fasta.gz