Vicia faba inbred line Hedin/2 genome v1.0

Genome Overview
Analysis NameVicia faba inbred line Hedin/2 genome v1.0
MethodPacBio Hifi, Hi-C (Assembly with hifiasm v0.11-r302)
SourceFaba Bean Genome Consortium
Date performed2023-05-02

This assembly and annotation was downloaded from the Faba Bean Genome Consortium and the citation is: Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature. 2023 Mar 08.

About the assembly:

Number of scaffolds 3,986
Total size  11.91 Gb
N50 1,637,815,978 bp
Annotation BUSCO score (embryophyta_odb10) 96.0%
Functional Analysis

Functional annotation files for the Vicia faba Hedin/2 genome v1.0 are available for download below. The Vicia faba Hedin/2 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 Vf_Hedin2_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Vf_Hedin2_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Vf_Hedin2_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Vf_Hedin2_v1_KEGG-pathways.xlsx.gz

 

Assembly

The Vicia faba inbred line Hedin2 genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Vf_inbred_Hedin2_v1.0.fasta.gz

 

Gene Prediction

The Vicia faba inbred line Hedin2 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Vf_inbred_Hedin2_v1.0.proteins.fasta.gz
CDS  (FASTA file) Vf_inbred_Hedin2_v1.0.cds.fasta.gz
Genes (GFF3 file) Vf_inbred_Hedin2_v1.0.genes.gff3.gz

 

Homology

Homology of the Vicia faba Hedin/2 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-9 was used for the NCBI nr (Release 2021-09) and 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.faba Hedin/2 genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Vf_Hedin2_v1_vs_tair.xlsx.gz
V.faba Hedin/2 genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Vf_Hedin2_v1_vs_tair_hit.fasta.gz
V.faba Hedin/2 genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Vf_Hedin2_v1_vs_tair_noHit.fasta.gz
V.faba Hedin/2 genome v1.0 proteins with SwissProt homologs (EXCEL file) Vf_Hedin2_v1_vs_swissprot.xlsx.gz
V.faba Hedin/2 genome v1.0 proteins with SwissProt (FASTA file) Vf_Hedin2_v1_vs_swissprot_hit.fasta.gz
V.faba Hedin/2 genome v1.0 proteins without SwissProt (FASTA file) Vf_Hedin2_v1_vs_swissprot_noHit.fasta.gz
V.faba Hedin/2 genome v1.0 proteins with TrEMBL homologs (EXCEL file) Vf_Hedin2_v1_vs_trembl.xlsx.gz
V.faba Hedin/2 genome v1.0 proteins with TrEMBL (FASTA file) Vf_Hedin2_v1_vs_trembl_hit.fasta.gz
V.faba Hedin/2 genome v1.0 proteins without TrEMBL (FASTA file) Vf_Hedin2_v1_vs_trembl_noHit.fasta.gz