Prunus yedoensis var. nudiflora Genome v1.0 Assembly & Annotation

Genome Overview
Analysis NamePrunus yedoensis var. nudiflora Genome v1.0 Assembly & Annotation
MethodFALCON
SourcePrunus_yedoensis_var_nudiflora_Genome_v1.0
Date performed2018-09-19

Publication:

Baek S, Choi K, Kim GB, Yu HJ, Cho A, Jang H, Kim C, Kim HJ, Chang KS, Kim JH, Mun JH. Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries. Genome biology. 2018 Sep 04; 19(1):127. | PubMed | GDR |

 

About the Assembly:

The genome assembly  of wild Prunus yedoensis covers >93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm

 

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.rosaceae.org/jbrowse/index.html?data=data/prunus/pyedoensis_v1.0&loc=
Assembly

The Prunus yedoensis v1.0 genome assembly file is available in FASTA format.

Downloads

Scaffolds (FASTA file)  Prunus yedoensis_v1.0_genome.fasta.gz

 

Gene Predictions

The Prunus yedoensis var. nudiflora v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript CDS sequences (FASTA file) P.yedoensis_v1.0.transcripts.fasta.gz
Protein sequences  (FASTA file) P.yedoensis_v1.0.proteins.fasta.gz
Genes (GFF3 file) P.yedoensis_v1.0.genes.gff3.gz
Repetitive elements(GFF3 file) P.yedoensis_v1.0.Repetitive elements.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 to download.  Alternatively, you can browse all available files on the FTP repository.

Homology

Homology of the Prunus yedoensis var. nudiflora v1.0 transcripts was determined by pairwise sequence comparison using the blastx 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 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus yedoensis v1.0 transcripts with NCBI nr homologs (EXCEL file) P.yedoensis_v1.0_vs_nr.xlsx.gz
Prunus yedoensis v1.0 transcripts with NCBI nr (FASTA file) P.yedoensis_v1.0_vs_nr_hit.fasta.gz
Prunus yedoensis v1.0 transcripts without NCBI nr (FASTA file) P.yedoensis_v1.0_vs_nr_noHit.fasta.gz
Prunus yedoensis v1.0 transcripts with arabidopsis (TAIR10) homologs (EXCEL file) P.yedoensis_v1.0_vs_tair.xlsx.gz
Prunus yedoensis v1.0 transcripts with arabidopsis (TAIR10) (FASTA file) P.yedoensis_v1.0_vs_tair_hit.fasta.gz
Prunus yedoensis v1.0 transcripts without arabidopsis (TAIR10) (FASTA file) P.yedoensis_v1.0_vs_tair_noHit.fasta.gz
Prunus yedoensis v1.0 transcripts with SwissProt homologs (EXCEL file) P.yedoensis_v1.0_vs_swissprot.xlsx.gz
Prunus yedoensis v1.0 transcripts with SwissProt (FASTA file) P.yedoensis_v1.0_vs_swissprot_hit.fasta.gz
Prunus yedoensis v1.0 transcripts without SwissProt (FASTA file) P.yedoensis_v1.0_vs_swissprot_noHit.fasta.gz
Prunus yedoensis v1.0 transcripts with TrEMBL homologs (EXCEL file) P.yedoensis_v1.0_vs_trembl.xlsx.gz
Prunus yedoensis v1.0 transcripts with TrEMBL (FASTA file) P.yedoensis_v1.0_vs_trembl_hit.fasta.gz
Prunus yedoensis v1.0 transcripts without TrEMBL (FASTA file) P.yedoensis_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Prunus yedoensis var. nudiflora v1.0 genome are available for download below. The Prunus yedoensis var. nudiflora proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan P.yedoensis_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan P.yedoensis_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways P.yedoensis_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs P.yedoensis_v1.0_KEGG-pathways.xlsx.gz