Vigna stipulacea acc. JP252948 genome v2.a1

Genome Overview
Analysis NameVigna stipulacea acc. JP252948 genome v2.a1
MethodPacBio (Assembly with Canu v2.0)
SourceVIGGS
Date performed2024-06-27

The genome was sequenced and assembled as outlined in Takahashi Y, Sakai H, Ariga H, Teramoto S, Shimada TL, Eun H, Muto C, Naito K, Tomooka N. Domesticating Vigna stipulacea: Chromosome-Level genome assembly reveals VsPSAT1 as a candidate gene decreasing hard-seededness. Frontiers in plant science. 2023; 14:1119625.

About the assembly:

Number of scaffolds 790
Total size  413 Mb
N50 34,378,316bp
Assembly BUSCO score (embryophyta_odb10) 98.2%
Annotation BUSCO score (embryophyta_odb10) 98.7%
Functional Analysis

Functional annotation files for the Vigna stipulacea acc. JP252948 genome v1.0 are available for download below. The V. stipulacea acc. JP252948 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 Vst_JP252948_v2_genes2GO.xlsx.gz
IPR assignments from InterProScan Vst_JP252948_v2_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vst_JP252948_v2_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vst_JP252948_v2_KEGG-pathways.xlsx.gz
Assembly

The Vigna stipulacea acc. JP252948 genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes and scaffolds (FASTA file) Vst_JP252948_v2.0.fasta.gz
Gene Prediction

The Vigna stipulacea acc. JP252948 genome v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences  (FASTA file) Vst_JP252948_v2.0.proteins.fasta.gz
CDS  (FASTA file) Vst_JP252948_v2.0.cds.fasta.gz
Genes (GFF3 file) PCD-Vst_JP252948_v2.0.genes.gff3.gz
Homology

Homology of the Vigna stipulacea acc. JP252948 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 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

V. angularis acc. JP252948 genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vst_JP252948_v2_vs_tair.xlsx.gz
V. angularis acc. JP252948 genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vst_JP252948_v2_vs_tair_hit.fasta.gz
V. angularis acc. JP252948 genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vst_JP252948_v2_vs_tair_noHit.fasta.gz
V. angularis acc. JP252948 genome v1.0 proteins with SwissProt homologs (EXCEL file) Vst_JP252948_v2_vs_swissprot.xlsx.gz
V. angularis acc. JP252948 genome v1.0 proteins with SwissProt (FASTA file) Vst_JP252948_v2_vs_swissprot_hit.fasta.gz
V. angularis acc. JP252948 genome v1.0 proteins without SwissProt (FASTA file) Vst_JP252948_v2_vs_swissprot_noHit.fasta.gz
V. angularis acc. JP252948 genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vst_JP252948_v2_vs_trembl.xlsx.gz
V. angularis acc. JP252948 genome v1.0 proteins with TrEMBL (FASTA file) Vst_JP252948_v2_vs_trembl_hit.fasta.gz
V. angularis acc. JP252948 genome v1.0 proteins without TrEMBL (FASTA file) Vst_JP252948_v2_vs_trembl_noHit.fasta.gz