Citrus sinensis cv. Gannanzao v1.0 genome

Overview


Analysis Name	Citrus sinensis cv. Gannanzao v1.0 genome
Method	Illumina NovaSeq 6000, PacBio HiFi, Hi-C (Assembled with Hifisam v0.15.4, LAchesis)
Source	Zenodo
Date performed	2023-12-14

About the assembly

For this genome, please cite Xiong et al, Chromosome-Level Genome Assembly of Navel orange cv. Gannanzao (Citrus sinensis Osbeck cv. Gannanzao). This data was originally downloaded from Zenodo.

Assembly metrics

Assembly size	335 Mb
Number of scaffolds	187
N50	31,863,774 bp
Predicted transcripts	23,037
Annotated genes	23,037
Assembly BUSCO score (embryophyta_odb10)	97.4%
Annotation BUSCO score (embryophyta_odb10)	91.7%

Assembly

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

Downloads

Chromosomes (FASTA file)	Cs_Gannanzao_v1.0.fasta.gz
Repeats (GFF3 file)	Cs_Gannanzao_v1.0.repeats.gff3.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Cs_Gannanzao_v1.0.proteins.fasta.gz
CDS (FASTA file)	Cs_Gannanzao_v1.0.cds.fasta.gz
Genes (GFF3 file)	Cs_Gannanzao_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus sinensis cv. Gannanzao 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	Cs_Gannanzao_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cs_Gannanzao_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cs_Gannanzao_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cs_Gannanzao_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus sinensis cv. Gannanzao 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. Gannanzao v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cs_Newhall_v1.0_vs_arabidopsis.xlsx.gz
C. sinensis cv. Gannanzao v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cs_Newhall_v1.0_vs_arabidopsis_hit.fasta.gz
C. sinensis cv. Gannanzao v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cs_Newhall_v1.0_vs_arabidopsis_noHit.fasta.gz
C. sinensis cv. Gannanzao v1.0 proteins with SwissProt homologs (EXCEL file)	Cs_Newhall_v1.0_vs_swissprot.xlsx.gz
C. sinensis cv. Gannanzao v1.0 proteins with SwissProt (FASTA file)	Cs_Newhall_v1.0_vs_swissprot_hit.fasta.gz
C. sinensis cv. Gannanzao v1.0 proteins without SwissProt (FASTA file)	Cs_Newhall_v1.0_vs_swissprot_noHit.fasta.gz
C. sinensis cv. Gannanzao v1.0 proteins with TrEMBL homologs (EXCEL file)	Cs_Newhall_v1.0_vs_trembl.xlsx.gz
C. sinensis cv. Gannanzao v1.0 proteins with TrEMBL (FASTA file)	Cs_Newhall_v1.0_vs_trembl_hit.fasta.gz
C. sinensis cv. Gannanzao v1.0 proteins without TrEMBL (FASTA file)	Cs_Newhall_v1.0_vs_trembl_noHit.fasta.gz