Vaccinium duclouxii SGLD20220023 v1.0 genome

Genome Overview
Analysis NameVaccinium duclouxii SGLD20220023 v1.0 genome
MethodPacBio, Nanopore, Hi-C (Assembled with NextDenovo)
SourcePRJCA016292
Date performed2023-12-13

Reference: Zeng T, He Z, He J, Lv W, Huang S, Li J, Zhu L, Wan S, Zhou W, Yang Z, Zhang Y, Luo C, He J, Wang C, Wang L. The telomere-to-telomere gap-free reference genome of wild blueberry (Vaccinium duclouxii) provides its high soluble sugar and anthocyanin accumulation. Horticulture research. 2023 Nov; 10(11):uhad209.  This data is the complete genome assembly with accession number GWHDUEK00000000.

Genome Assembly Summary:

Total size 573,668,591 bp
Number of scaffolds 12
N50 48,509,392 bp
Assembly BUSCO score (embryophyta_odb10) 97.6%
Annotation BUSCO score (embryophyta_odb10) 98.1%
Homology

Homology of the Vaccinium duclouxii SGLD20220023 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. duclouxii SGLD20220023 genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vd_SGLD20220023_v1.0_vs_tair.xlsx.gz
V. duclouxii SGLD20220023 genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vd_SGLD20220023_v1.0_vs_tair_hit.fasta.gz
V. duclouxii SGLD20220023 genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vd_SGLD20220023_v1.0_vs_tair_noHit.fasta.gz
V. duclouxii SGLD20220023 genome v1.0 proteins with SwissProt homologs (EXCEL file) Vd_SGLD20220023_v1.0_vs_swissprot.xlsx.gz
V. duclouxii SGLD20220023 genome v1.0 proteins with SwissProt (FASTA file) Vd_SGLD20220023_v1.0_vs_swissprot_hit.fasta.gz
V. duclouxii SGLD20220023 genome v1.0 proteins without SwissProt (FASTA file) Vd_SGLD20220023_v1.0_vs_swissprot_noHit.fasta.gz
V. duclouxii SGLD20220023 genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vd_SGLD20220023_v1.0_vs_trembl.xlsx.gz
V. duclouxii SGLD20220023 genome v1.0 proteins with TrEMBL (FASTA file) Vd_SGLD20220023_v1.0_vs_trembl_hit.fasta.gz
V. duclouxii SGLD20220023 genome v1.0 proteins without TrEMBL (FASTA file) Vd_SGLD20220023_v1.0_vs_trembl_noHit.fasta.gz
Assembly
Assembly: 

The Vaccinium duclouxii SGLD20220023 genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Vvitis-idaea-SGLD20220023_v1.0.fasta.gz
Gene Prediction
Gene Prediction: 

The Vaccinium duclouxii SGLD20220023 genome v1.0 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Vvitis-idaea-SGLD20220023_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vvitis-idaea-SGLD20220023_v1.0.cds.fasta.gz
Genes (GFF3 file) Vvitis-idaea-SGLD20220023_v1.0.genes.gff3.gz
Functional Analysis
Functional Analysis: 

Functional annotation files for the Vaccinium duclouxii SGLD20220023 genome v1.0 are available for download below. The Vaccinium duclouxii SGLD20220023 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 Vd_SGLD20220023_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Vd_SGLD20220023_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vd_SGLD20220023_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vd_SGLD20220023_v1.0_KEGG-pathways.xlsx.gz