Citrus ichangensis cv. ZGYCC v2.0 genome

Overview


Analysis Name	Citrus ichangensis cv. ZGYCC v2.0 genome
Method	PacBio, Nanopore, Illumina (Assembly with SMARTdenovo, miniasm, NextDenovo)
Source	Huazhong Agriculture University
Date performed	2023-12-21

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 PRJNA321657 and the assembly accession number is GCA_030448935.1. The listed BioSample isolate designation is ZGYCC.

Assembly metrics

Assembly size	365 Mb
Number of scaffolds	506
N50	5,250,823 bp
Predicted transcripts	47,961
Annotated genes	29,451
Assembly BUSCO score (embryophyta_odb10)	99.0%
Annotation BUSCO score (embryophyta_odb10)	96.5%

Assembly

The Citrus ichangensis cv. ZGYCC genome v2.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Ci_ZGYCC_v2.0.fasta.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Ci_ZGYCC_v2.0.proteins.fasta.gz
Gene sequences (FASTA file)	Ci_ZGYCC_v2.0.genes.fasta.gz
CDS (FASTA file)	Ci_ZGYCC_v2.0.cds.fasta.gz
Genes (GFF3 file)	Ci_ZGYCC_v2.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus ichangensis ZGYCC genome v2.0 are available for download below. The Citrus ichangensis genome v2.0 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	Ci_ZGYCC_v2_genes2GO.xlsx.gz
IPR assignments from InterProScan	Ci_ZGYCC_v2_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Ci_ZGYCC_v2_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Ci_ZGYCC_v2_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus ichangensis genome v2.0 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 ZGYCC v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Ci_ZGYCC_v2.0_vs_arabidopsis.xlsx.gz
C. ichangensis ZGYCC v2.0 proteins with arabidopsis (Araport11) (FASTA file)	Ci_ZGYCC_v2.0_vs_arabidopsis_hit.fasta.gz
C. ichangensis ZGYCC v2.0 proteins without arabidopsis (Araport11) (FASTA file)	Ci_ZGYCC_v2.0_vs_arabidopsis_noHit.fasta.gz
C. ichangensis ZGYCC v2.0 proteins with SwissProt homologs (EXCEL file)	Ci_ZGYCC_v2.0_vs_swissprot.xlsx.gz
C. ichangensis ZGYCC v2.0 proteins with SwissProt (FASTA file)	Ci_ZGYCC_v2.0_vs_swissprot_hit.fasta.gz
C. ichangensis ZGYCC v2.0 proteins without SwissProt (FASTA file)	Ci_ZGYCC_v2.0_vs_swissprot_noHit.fasta.gz
C. ichangensis ZGYCC v2.0 proteins with TrEMBL homologs (EXCEL file)	Ci_ZGYCC_v2.0_vs_trembl.xlsx.gz
C. ichangensis ZGYCC v2.0 proteins with TrEMBL (FASTA file)	Ci_ZGYCC_v2.0_vs_trembl_hit.fasta.gz
C. ichangensis ZGYCC v2.0 proteins without TrEMBL (FASTA file)	Ci_ZGYCC_v2.0_vs_trembl_noHit.fasta.gz