Citrus hongheensis cv. HH genome v1.0 | Citrus Genome Database

Overview


Analysis Name	Citrus hongheensis cv. HH genome v1.0
Method	Nanopore, PacBio, 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 PRJNA783764 and the assembly accession number is GCA_030448925.1. The listed BioSample isolate designation is HH.

Assembly metrics

Assembly size	355 Mb
Number of scaffolds	653
N50	2,606,256 bp
Predicted transcripts	47,000
Annotated genes	30,525
Assembly BUSCO score (embryophyta_odb10)	98.9%
Annotation BUSCO score (embryophyta_odb10)	96.2%

Assembly

The Citrus hongheensis cv. HH genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Ch_HH_v1.0.fasta.gz

Gene Predictions

The Citrus hongheensis cv. HH genome v1.0 gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (FASTA file)	Ch_HH_v1.0.proteins.fasta.gz
CDS (FASTA file)	Ch_HH_v1.0.cds.fasta.gz
Gene sequences (FASTA file)	Ch_HH_v1.0.genes.fasta.gz
Genes (GFF3 file)	Ch_HH_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus hongheensis cv. HH genome v1.0 are available for download below. The Citrus hongheensis 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	Ch_HH_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Ch_HH_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Ch_HH_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Ch_HH_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus hongheensis cv. HH 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. hongheensis cv. HH v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Ch_HH_v1.0_vs_arabidopsis.xlsx.gz
C. hongheensis cv. HH v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Ch_HH_v1.0_vs_arabidopsis_hit.fasta.gz
C. hongheensis cv. HH v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Ch_HH_v1.0_vs_arabidopsis_noHit.fasta.gz
C. hongheensis cv. HH v1.0 proteins with SwissProt homologs (EXCEL file)	Ch_HH_v1.0_vs_swissprot.xlsx.gz
C. hongheensis cv. HH v1.0 proteins with SwissProt (FASTA file)	Ch_HH_v1.0_vs_swissprot_hit.fasta.gz
C. hongheensis cv. HH v1.0 proteins without SwissProt (FASTA file)	Ch_HH_v1.0_vs_swissprot_noHit.fasta.gz
C. hongheensis cv. HH v1.0 proteins with TrEMBL homologs (EXCEL file)	Ch_HH_v1.0_vs_trembl.xlsx.gz
C. hongheensis cv. HH v1.0 proteins with TrEMBL (FASTA file)	Ch_HH_v1.0_vs_trembl_hit.fasta.gz
C. hongheensis cv. HH v1.0 proteins without TrEMBL (FASTA file)	Ch_HH_v1.0_vs_trembl_noHit.fasta.gz