Vaccinium vitis-idaea ssp. vitis-idaea cv. Red Candy v1.0 genome

Genome Overview
Analysis NameVaccinium vitis-idaea ssp. vitis-idaea cv. Red Candy v1.0 genome
MethodOxford Nanopore, Illumina NovaSeq (SmartDenovo v1.4.0)
SourcePRJNA998787
Date performed2023-09-28

Reference:  Hirabayashi K, Debnath SC, Owens GL. Unveiling the evolutionary history of lingonberry (Vaccinium vitis-idaea L.) through genome sequencing and assembly of European and North American subspecies. G3 (Bethesda, Md.). 2023 Dec 24.

Genome Assembly Summary:

Total size 547,986,428 bp
Number of scaffolds 90
N50 43,866,791 bp
Assembly BUSCO score (embryophyta_odb10) 96.9%
Annotation BUSCO score (embryophyta_odb10) 95.9%
Homology

Homology of the Vaccinium vitis-idaea cv. Red Candy 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-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

V. vitis-idaea cv. Red Candy genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vvitis-idaea_RedCandy_v1_vs_tair.xlsx.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vvitis-idaea_RedCandy_v1_vs_tair_hit.fasta.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vvitis-idaea_RedCandy_v1_vs_tair_noHit.fasta.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins with SwissProt homologs (EXCEL file) Vvitis-idaea_RedCandy_v1_vs_swissprot.xlsx.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins with SwissProt (FASTA file) Vvitis-idaea_RedCandy_v1_vs_swissprot_hit.fasta.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins without SwissProt (FASTA file) Vvitis-idaea_RedCandy_v1_vs_swissprot_noHit.fasta.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vvitis-idaea_RedCandy_v1_vs_trembl.xlsx.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins with TrEMBL (FASTA file) Vvitis-idaea_RedCandy_v1_vs_trembl_hit.fasta.gz
V. vitis-idaea cv. Red Candy genome v1.0 proteins without TrEMBL (FASTA file) Vvitis-idaea_RedCandy_v1_vs_trembl_noHit.fasta.gz
Assembly
Assembly: 

The Vaccinium vitis-idaea cv. Red Candy genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Vvitis-idaea_RedCandy_UBC_v1.0.fasta.gz
Gene Prediction
Gene Prediction: 

The Vaccinium vitis-idaea cv. Red Candy genome v1.0 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Vvitis-idaea_RedCandy_UBC_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vvitis-idaea_RedCandy_UBC_v1.0.cds.fasta.gz
Genes (GFF3 file) Vvitis-idaea_RedCandy_UBC_v1.0.genes.gff3.gz
Functional Analysis
Functional Analysis: 

Functional annotation files for the Vaccinium vitis-idaea cv. Red Candy genome v1.0 are available for download below. The Vaccinium vitis-idaea cv. Red Candy genome v1.0 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 Vvitis-idaea_RedCandy_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Vvitis-idaea_RedCandy_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vvitis-idaea_RedCandy_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vvitis-idaea_RedCandy_v1_KEGG-pathways.xlsx.gz