Citrus sinensis cv. Jinhong genome v1.0

Overview


Analysis Name	Citrus sinensis cv. Jinhong genome v1.0
Method	PacBio Sequel II, Illumina NovaSeq 6000 (Assembled with Hifiasm v0.16, Meryl v1.4, Verkko v1.3.1)
Source	Zenodo
Date performed	2024-03-19

About the assembly

For this genome, please cite Wang N, Chen P, Xu Y, Guo L, Li X, Yi H, Larkin RM, Zhou Y, Deng X, Xu Q. Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange. Horticulture research. 2024 Feb; 11(2):uhad268. This data was originally downloaded from Zenodo.

Assembly metrics

Assembly size	627 Mb
Number of scaffolds	18
N50	35,022,480 bp
Predicted transcripts	60,821
Annotated genes	60,821
Assembly BUSCO score (embryophyta_odb10)	99.1%
Annotation BUSCO score (embryophyta_odb10)	93.9%

Assembly

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

Downloads

Chromosomes (Hap A) (FASTA file)	CGD-C.sinensis_Jinhong_HapA_v1.0.a1.fasta.gz
Chromosomes (Hap B) (FASTA file)	CGD-C.sinensis_Jinhong_HapB_v1.0.a1.fasta.gz

Gene Predictions

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

Downloads

Genes (Hap A) (GFF3 file)	CGD-C.sinensis_Jinhong_HapA_v1.0.a1.genes.gff3.gz
Genes (Hap A) (GFF3 file)	CGD-C.sinensis_Jinhong_HapB_v1.0.a1.genes.gff3.gz
Protein sequences (Hap A) (FASTA file)	CGD-C.sinensis_Jinhong_HapA_v1.0.a1.protein.fasta.gz
Protein sequences (Hap B) (FASTA file)	CGD-C.sinensis_Jinhong_HapB_v1.0.a1.protein.fasta.gz
Transcript sequences (Hap A) (FASTA file)	CGD-C.sinensis_Jinhong_HapA_v1.0.a1.Transcript.fasta.gz
Transcript sequences (Hap B) (FASTA file)	CGD-C.sinensis_Jinhong_HapB_v1.0.a1.Transcript.fasta.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus sinensis cv. Jinhong genome v1.0 are available for download below. The Citrus sinensis 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	Csinensis_Jinhong_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Csinensis_Jinhong_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Csinensis_Jinhong_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Csinensis_Jinhong_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus sinensis cv. Jinhong 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. sinensis cv. Jinhong v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cs_Jinhong_v1_vs_arabidopsis.xlsx.gz
C. sinensis cv. Jinhong v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cs_Jinhong_v1_vs_arabidopsis_hit.fasta.gz
C. sinensis cv. Jinhong v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cs_Jinhong_v1_vs_arabidopsis_noHit.fasta.gz
C. sinensis cv. Jinhong v1.0 proteins with SwissProt homologs (EXCEL file)	Cs_Jinhong_v1_vs_swissprot.xlsx.gz
C. sinensis cv. Jinhong v1.0 proteins with SwissProt (FASTA file)	Cs_Jinhong_v1_vs_swissprot_hit.fasta.gz
C. sinensis cv. Jinhong v1.0 proteins without SwissProt (FASTA file)	Cs_Jinhong_v1_vs_swissprot_noHit.fasta.gz
C. sinensis cv. Jinhong v1.0 proteins with TrEMBL homologs (EXCEL file)	Cs_Jinhong_v1_vs_trembl.xlsx.gz
C. sinensis cv. Jinhong v1.0 proteins with TrEMBL (FASTA file)	Cs_Jinhong_v1_vs_trembl_hit.fasta.gz
C. sinensis cv. Jinhong v1.0 proteins without TrEMBL (FASTA file)	Cs_Jinhong_v1_vs_trembl_noHit.fasta.gz