Citrus sinensis cv. Newhall v1.0 genome

Overview


Analysis Name	Citrus sinensis cv. Newhall v1.0 genome
Method	Illumina NovaSeq, PacBio HiFi, Hi-C (Assembly with Hifiasm v0.15.4)
Source	Zenodo
Date performed	2023-08-01

About the assembly

For this genome, please cite Gao et al, Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. This data was originally downloaded from Zenodo.

Assembly metrics

Assembly size	685 Mb
Number of scaffolds	1013
N50	32,860,738 bp
Predicted transcripts	46,670
Annotated genes	46,670
Assembly BUSCO score (embryophyta_odb10)	99.0%
Annotation BUSCO score (embryophyta_odb10)	96.4%

Assembly

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

Downloads

Chromosomes (FASTA file)	Csinensis_Newhall_v1.0.fasta.gz
Repeats (GFF3 file)	Csinensis_Newhall_v1.0.repeats.gff3.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Csinensis_Newhall_v1.0.proteins.fasta.gz
CDS (FASTA file)	Csinensis_Newhall_v1.0.cds.fasta.gz
Genes (GFF3 file)	Csinensis_Newhall_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus sinensis Newhall 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_Newhall_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan	Csinensis_Newhall_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Csinensis_Newhall_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Csinensis_Newhall_v1.0_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus sinensis 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

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