Vaccinium vitis-idaea ssp. minus v1.0 genome

Genome Overview
Analysis NameVaccinium vitis-idaea ssp. minus v1.0 genome
MethodOxford Nanopore, Illumina NovaSeq (Canu, 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 518,703,823 bp
Number of scaffolds 76
N50 42,798,974 bp
Assembly BUSCO score (embryophyta_odb10) 97.2%
Annotation BUSCO score (embryophyta_odb10) 95.7%
Homology

Homology of the Vaccinium vitis-idaea ssp. minus 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 ssp. minus genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vvi_Minus_v1_vs_tair.xlsx.gz
V.vitis-idaea ssp. minus genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vvi_Minus_v1_vs_tair_hit.fasta.gz
V.vitis-idaea ssp. minus genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vvi_Minus_v1_vs_tair_noHit.fasta.gz
V.vitis-idaea ssp. minus genome v1.0 proteins with SwissProt homologs (EXCEL file) Vvi_Minus_v1_vs_swissprot.xlsx.gz
V.vitis-idaea ssp. minus genome v1.0 proteins with SwissProt (FASTA file) Vvi_Minus_v1_vs_swissprot_hit.fasta.gz
V.vitis-idaea ssp. minus genome v1.0 proteins without SwissProt (FASTA file) Vvi_Minus_v1_vs_swissprot_noHit.fasta.gz
V.vitis-idaea ssp. minus genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vvi_Minus_v1_vs_trembl.xlsx.gz
V.vitis-idaea ssp. minus genome v1.0 proteins with TrEMBL (FASTA file) Vvi_Minus_v1_vs_trembl_hit.fasta.gz
V.vitis-idaea ssp. minus genome v1.0 proteins without TrEMBL (FASTA file) Vvi_Minus_v1_vs_trembl_noHit.fasta.gz
Assembly
Assembly: 

The Vaccinium vitis-idaea ssp. minus genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Vvitis-idaea_ssp_minus_v1.0.fasta.gz
Gene Prediction
Gene Prediction: 

The Vaccinium vitis-idaea ssp. minus v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Vvitis-idaea_ssp_minus_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vvitis-idaea_ssp_minus_v1.0.cds.fasta.gz
Genes (GFF3 file) Vvitis-idaea_ssp_minus_v1.0.genes.gff3.gz
Functional Analysis
Functional Analysis: 

Functional annotation files for the Vaccinium vitis-idaea ssp. minus genome v1.0 are available for download below. The Vaccinium vitis-idaea ssp. minus 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 Vvi_Minus_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Vvi_Minus_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vvi_Minus_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vvi_Minus_v1_KEGG-pathways.xlsx.gz