Vigna umbellata FF25 genome v1.0

Genome Overview
Analysis NameVigna umbellata FF25 genome v1.0
MethodIllumina, PacBio, Hi-C (Assembly with GCE v1.0.2, Canu v1.9)
SourceFigshare
Date performed2024-06-26

The genome was sequenced and assembled as outlined in Guan J, Zhang J. Gong, D. et al. Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding. Nat Commun 13, 5707 (2022). https://doi.org/10.1038/s41467-022-33515-2

About the assembly:

Number of scaffolds 264
Total size  476 Mb
N50 40,359,536 bp
Assembly BUSCO score (embryophyta_odb10) 97.8%
Annotation BUSCO score (embryophyta_odb10) 96.3%
Functional Analysis

Functional annotation files for the Vigna umbellata FF25 genome v1.0 are available for download below. The V. umbellata FF25 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 Vum_FF25_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Vum_FF25_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vum_FF25_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vum_FF25_v1_KEGG-pathways.xlsx.gz
Assembly

The Vigna umbellata FF25 genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes and scaffolds (FASTA file) Vum_FF25_v1.0.fasta.gz
Gene Prediction

The Vigna umbellata FF25 genome v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences  (FASTA file) Vum_FF25_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vum_FF25_v1.0.cds.fasta.gz
Genes (GFF3 file) Vum_FF25_v1.0.genes.gff3.gz
Homology

Homology of the Vigna umbellata FF25 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 FF25 genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vum_FF25_v1_vs_tair.xlsx.gz
V. angularis FF25 genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vum_FF25_v1_vs_tair_hit.fasta.gz
V. angularis FF25 genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vum_FF25_v1_vs_tair_noHit.fasta.gz
V. angularis FF25 genome v1.0 proteins with SwissProt homologs (EXCEL file) Vum_FF25_v1_vs_swissprot.xlsx.gz
V. angularis FF25 genome v1.0 proteins with SwissProt (FASTA file) Vum_FF25_v1_vs_swissprot_hit.fasta.gz
V. angularis FF25 genome v1.0 proteins without SwissProt (FASTA file) Vum_FF25_v1_vs_swissprot_noHit.fasta.gz
V. angularis FF25 genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vum_FF25_v1_vs_trembl.xlsx.gz
V. angularis FF25 genome v1.0 proteins with TrEMBL (FASTA file) Vum_FF25_v1_vs_trembl_hit.fasta.gz
V. angularis FF25 genome v1.0 proteins without TrEMBL (FASTA file) Vum_FF25_v1_vs_trembl_noHit.fasta.gz