Pisum sativum cv. Zhongwan6 genome v1.0

Genome Overview
Analysis NamePisum sativum cv. Zhongwan6 genome v1.0
MethodIllumina NovaSeq, HiSeq and PacBio Sequel (Assembly with Canu and Pilon)
SourcePeaZW6 assembly
Date performed2023-05-02

 

The citation is: Yang, T., Liu, R., Luo, Y. et al. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet 54, 1553–1563 (2022). https://doi.org/10.1038/s41588-022-01172-2

About the assembly uploaded into PCD:

Number of scaffolds 1,581
Total size  3.80 Gb
N50 523,395,090 bp
Assembly BUSCO score (embryophyta_odb10) 96.2%
Annotation BUSCO score (embryophyta_odb10) 98.7%
Functional Analysis

Functional annotation files for the Pisum sativum Zhongwan6 genome v1.0 are available for download below. The Pisum sativum Zhongwan6 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 ps_zw6_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan ps_zw6_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs ps_zw6_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways ps_zw6_v1_KEGG-pathways.xlsx.gz

 

Assembly

The Pisum sativum Zhongwan6 genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (FASTA file) Psativum_Zhongwan6_v1.0.chr.fasta.gz
Chromosomes and scaffolds (FASTA file) Psativum_Zhongwan6_v1.0.fasta.gz

 

Gene Prediction

The Pisum sativum Zhongwan6 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Psativum_Zhongwan6_v1.0.proteins.fasta.gz
CDS  (FASTA file) Psativum_Zhongwan6_v1.0.cds.fasta.gz
Genes (GFF3 file) Pisum_sativum_Zhongwan6_v1.0.genes.gff3.gz

 

Homology

Homology of the Pisum sativum Zhongwan6 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

G.arboreum Zhongwan6 genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) ps_zw6_v1_vs_tair.xlsx.gz
G.arboreum Zhongwan6 genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) ps_zw6_v1_vs_tair_hit.fasta.gz
G.arboreum Zhongwan6 genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) ps_zw6_v1_vs_tair_noHit.fasta.gz
G.arboreum Zhongwan6 genome v1.0 proteins with SwissProt homologs (EXCEL file) ps_zw6_v1_vs_swissprot.xlsx.gz
G.arboreum Zhongwan6 genome v1.0 proteins with SwissProt (FASTA file) ps_zw6_v1_vs_swissprot_hit.fasta.gz
G.arboreum Zhongwan6 genome v1.0 proteins without SwissProt (FASTA file) ps_zw6_v1_vs_swissprot_noHit.fasta.gz
G.arboreum Zhongwan6 genome v1.0 proteins with TrEMBL homologs (EXCEL file) ps_zw6_v1_vs_trembl.xlsx.gz
G.arboreum Zhongwan6 genome v1.0 proteins with TrEMBL (FASTA file) ps_zw6_v1_vs_trembl_hit.fasta.gz
G.arboreum Zhongwan6 genome v1.0 proteins without TrEMBL (FASTA file) ps_zw6_v1_vs_trembl_noHit.fasta.gz