Citropsis gilletiana cv. CGI genome v1.0

Overview


Analysis Name	Citropsis gilletiana cv. CGI genome v1.0
Method	Nanopore, PacBio (Assembly with SMARTdenovo, miniasm)
Source	Huazhong Agriculture University
Date performed	2024-01-22

About the assembly

For this genome, please cite Huang et al, Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. This data was originally downloaded from the Citrus Pan-genome to Breeding Database. This data is also on NCBI under BioProject PRJNA782478 and the assembly accession number is GCA_030449925.1. The listed BioSample isolate designation is CGI.

Assembly metrics

Assembly size	419 Mb
Number of scaffolds	259
N50	5,249,098 bp
Predicted transcripts	44,060
Annotated genes	28,225
Assembly BUSCO score (embryophyta_odb10)	98.2%
Annotation BUSCO score (embryophyta_odb10)	95.0%

Assembly

The Citropsis gilletiana cv. CGI genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Cig_CGI_v1.0.fasta.gz

Gene Predictions

The Citropsis gilletiana cv. ZGYCC_v2.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (FASTA file)	Cig_CGI_v1.0.proteins.fasta.gz
Gene sequences (FASTA file)	Cig_CGI_v1.0.genes.fasta.gz
CDS (FASTA file)	Cig_CGI_v1.0.cds.fasta.gz
Genes (GFF3 file)	Cig_CGI_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citropsis gilletiana CGI genome v1.0 are available for download below. The Citropsis gilletiana 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	Cig_CGI_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cig_CGI_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cig_CGI_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cig_CGI_v1.0_KEGG-pathways.xlsx.gz

Homology

Homology of the Citropsis gilletiana CGI 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. ichangensis CGI v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cig_CGI_v1.0_vs_arabidopsis.xlsx.gz
C. ichangensis CGI v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cig_CGI_v1.0_vs_arabidopsis_hit.fasta.gz
C. ichangensis CGI v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cig_CGI_v1.0_vs_arabidopsis_noHit.fasta.gz
C. ichangensis CGI v1.0 proteins with SwissProt homologs (EXCEL file)	Cig_CGI_v1.0_vs_swissprot.xlsx.gz
C. ichangensis CGI v1.0 proteins with SwissProt (FASTA file)	Cig_CGI_v1.0_vs_swissprot_hit.fasta.gz
C. ichangensis CGI v1.0 proteins without SwissProt (FASTA file)	Cig_CGI_v1.0_vs_swissprot_noHit.fasta.gz
C. ichangensis CGI v1.0 proteins with TrEMBL homologs (EXCEL file)	Cig_CGI_v1.0_vs_trembl.xlsx.gz
C. ichangensis CGI v1.0 proteins with TrEMBL (FASTA file)	Cig_CGI_v1.0_vs_trembl_hit.fasta.gz
C. ichangensis CGI v1.0 proteins without TrEMBL (FASTA file)	Cig_CGI_v1.0_vs_trembl_noHit.fasta.gz