Phaseolus vulgaris cv. Flavert genome v1.0

Genome Overview
Analysis NamePhaseolus vulgaris cv. Flavert genome v1.0
MethodPacBio (Assembly with Canu v2.2)
SourcePRJNA931244
Date performed2024-07-01

The genome was sequenced and assembled as outlined in Carrère S, Mayjonade B, Lalanne D, Gaillard S, Verdier J, Chen NWG. First whole genome assembly and annotation of a European common bean cultivar using PacBio HiFi and Iso-Seq data. Data in brief. 2023 Jun; 48:109182.

Assembly was downloaded from NCBI, annotation from link in manuscript.

About the assembly:

Number of scaffolds 1,231
Total size  616 Mb
N50 54,932,568 bp
Assembly BUSCO score (embryophyta_odb10) 99.0%
Annotation BUSCO score (embryophyta_odb10) 98.7%
Functional Analysis

Functional annotation files for the Phaseolus vulgaris cv. Flavert genome v1.0 are available for download below. The Phaseolus vulgaris cv. Flavert 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 Pv_Flavert_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Pv_Flavert_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Pv_Flavert_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Pv_Flavert_v1_KEGG-pathways.xlsx.gz
Assembly

The Phaseolus vulgaris cv. Flavert genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes and scaffolds (FASTA file) Pv_Flavert_v1.0.fasta.gz
Gene Prediction

The Phaseolus vulgaris cv. Flavert genome v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences  (FASTA file) Pv_Flavert_v1.0.proteins.fasta.gz
CDS  (FASTA file) Pv_Flavert_v1.0.cds.fasta.gz
Genes (GFF3 file) PCD-Pv_Flavert_v1.0.genes.gff3.gz
Homology

Homology of the Phaseolus vulgaris cv. Flavert 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 cv. Flavert genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Pv_Flavert_v1_vs_tair.xlsx.gz
V. angularis cv. Flavert genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Pv_Flavert_v1_vs_tair_hit.fasta.gz
V. angularis cv. Flavert genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Pv_Flavert_v1_vs_tair_noHit.fasta.gz
V. angularis cv. Flavert genome v1.0 proteins with SwissProt homologs (EXCEL file) Pv_Flavert_v1_vs_swissprot.xlsx.gz
V. angularis cv. Flavert genome v1.0 proteins with SwissProt (FASTA file) Pv_Flavert_v1_vs_swissprot_hit.fasta.gz
V. angularis cv. Flavert genome v1.0 proteins without SwissProt (FASTA file) Pv_Flavert_v1_vs_swissprot_noHit.fasta.gz
V. angularis cv. Flavert genome v1.0 proteins with TrEMBL homologs (EXCEL file) Pv_Flavert_v1_vs_trembl.xlsx.gz
V. angularis cv. Flavert genome v1.0 proteins with TrEMBL (FASTA file) Pv_Flavert_v1_vs_trembl_hit.fasta.gz
V. angularis cv. Flavert genome v1.0 proteins without TrEMBL (FASTA file) Pv_Flavert_v1_vs_trembl_noHit.fasta.gz