Cicer arietinum CDC Frontier NCBI RefSeq v1

Genome Overview
Analysis NameCicer arietinum CDC Frontier NCBI RefSeq v1
MethodIllumina (Assembly with SOAPdenovo)
SourceGCF_000331145.1
Date performed2024-01-04

The genome was sequenced and assembled as outlined in Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo MC, Thudi M, Gowda CL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature biotechnology. 2013 Mar; 31(3):240-6.

The RefSeq annotation was performed by NCBI.

About the assembly:

Number of scaffolds 7,127
Total size  531 Mb
N50 39,989,001 bp
Assembly BUSCO score (embryophyta_odb10) NA*
Annotation BUSCO score (embryophyta_odb10) 99.7%

* When we ran BUSCO in genome mode on the assembly fasta file with the embryophyta_odb10 and eukaryota_odb10 datasets, the BUSCO jobs failed because Augustus could not find any matching genes

Functional Analysis

Functional annotation files for the Cicer arietinum CDC Frontier NCBI genome v1.0 are available for download below. The Cicer arietinum CDC Frontier NCBI 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 Ca_CDCfrontier_NCBI_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Ca_CDCfrontier_NCBI_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Ca_CDCfrontier_NCBI_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Ca_CDCfrontier_NCBI_v1_KEGG-pathways.xlsx.gz
Assembly
Assembly: 

The Cicer arietinum CDC frontier NCBI RefSeq v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes and scaffolds (FASTA file) Ca_CDCfrontier_NCBI_v1.0.fasta.gz
Gene Prediction
Gene Prediction: 

The Cicer arietinum CDC frontier NCBI RefSeq v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences  (FASTA file) Ca_CDCfrontier_NCBI_v1.0.proteins.fasta.gz
CDS  (FASTA file) Ca_CDCfrontier_NCBI_v1.0.cds.fasta.gz
Genes (GFF3 file) Ca_CDCfrontier_NCBI_v1.0.genes.gff3.gz
Homology
Homology: 

Homology of the Cicer arietinum CDC Frontier NCBI 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 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

C. arietinum CDC Frontier NCBI genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Ca_CDCfrontier_NCBI_v1_vs_tair.xlsx.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_tair_hit.fasta.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_tair_noHit.fasta.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins with SwissProt homologs (EXCEL file) Ca_CDCfrontier_NCBI_v1_vs_swissprot.xlsx.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins with SwissProt (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_swissprot_hit.fasta.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins without SwissProt (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_swissprot_noHit.fasta.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins with TrEMBL homologs (EXCEL file) Ca_CDCfrontier_NCBI_v1_vs_trembl.xlsx.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins with TrEMBL (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_trembl_hit.fasta.gz
C. arietinum CDC Frontier NCBI genome v1.0 proteins without TrEMBL (FASTA file) Ca_CDCfrontier_NCBI_v1_vs_trembl_noHit.fasta.gz