Vicia sativa cv. Studenica genome v1.0

Genome Overview
Analysis NameVicia sativa cv. Studenica genome v1.0
MethodNanopore, Illumina, CHiCAGO, Hi_C (assembled with Canu, Pilon)
SourceGigaDB
Date performed2023-06-12

The genome was sequenced and assembled as outlined in Xi H, Nguyen V, Ward C, Liu Z, Searle IR. Chromosome-level assembly of the common vetch (Vicia sativa) reference genome. GigaByte (Hong Kong, China). 2022; 2022:gigabyte38.

About the assembly:

Number of scaffolds 18
Total size  1.65 Gb
N50 290,752,327 bp
Assembly BUSCO score (embryophyta_odb10) 98.3%
Annotation BUSCO score (embryophyta_odb10) 96.6%
Functional Analysis

Functional annotation files for the Vicia sativa Studenica genome v1.0 are available for download below. The Vicia sativa Studenica 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 Vs_Studenica_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Vs_Studenica_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vs_Studenica_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vs_Studenica_v1_KEGG-pathways.xlsx.gz

 

Assembly
Assembly: 

The Vicia sativa Studenica genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes and scaffolds (FASTA file) Vs_Studenica_v1.0.fasta.gz
Repeat (GFF3 file) Vs_Studenica_v1.0.repeat.gff3.gz

 

Gene Prediction
Gene Prediction: 

The Vicia sativa Studenica v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences  (FASTA file) Vs_Studenica_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vs_Studenica_v1.0.cds.fasta.gz
Genes (GFF3 file) Vs_Studenica_v1.0.genes.gff3.gz

 

Homology
Homology: 

Homology of the Vicia sativa Studenica 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), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

V.sativa Studenica genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vs_Studenica_v1_vs_tair.xlsx.gz
V.sativa Studenica genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vs_Studenica_v1_vs_tair_hit.fasta.gz
V.sativa Studenica genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vs_Studenica_v1_vs_tair_noHit.fasta.gz
V.sativa Studenica genome v1.0 proteins with SwissProt homologs (EXCEL file) Vs_Studenica_v1_vs_swissprot.xlsx.gz
V.sativa Studenica genome v1.0 proteins with SwissProt (FASTA file) Vs_Studenica_v1_vs_swissprot_hit.fasta.gz
V.sativa Studenica genome v1.0 proteins without SwissProt (FASTA file) Vs_Studenica_v1_vs_swissprot_noHit.fasta.gz
V.sativa Studenica genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vs_Studenica_v1_vs_trembl.xlsx.gz
V.sativa Studenica genome v1.0 proteins with TrEMBL (FASTA file) Vs_Studenica_v1_vs_trembl_hit.fasta.gz
V.sativa Studenica genome v1.0 proteins without TrEMBL (FASTA file) Vs_Studenica_v1_vs_trembl_noHit.fasta.gz