Fortunella hindsii S3y-45 genome v2.0 | Citrus Genome Database

Overview


Analysis Name	Fortunella hindsii S3y-45 genome v2.0
Method	PacBio, Illumina, Hi-C (Assembly with Canu, Smartdenovo)
Source	Huazhong Agriculture University
Date performed	2023-05-10

About the assembly

For this genome, please cite Wang et al, Structural variation and parallel evolution of apomixis in citrus during domestication and diversification. This data was downloaded from the Citrus Pan-Genome to Breeding Database website. The manuscript identifies accession S3y-45 as the sample that was sequenced and this is an improved version of the previous assembly.

Assembly metrics

Assembly size	324 Mb
Number of scaffolds	10
N50	32,266,151 bp
Predicted transcripts	32,563
Annotated genes	32,563
Assembly BUSCO score (embryophyta_odb10)	98.9%
Annotation BUSCO score (embryophyta_odb10)	97.7%

Assembly

The Fortunella hindsii S3y-45 v2.0 genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file)

Fhindsii_S3y-45_v2.0.fasta.gz

Gene Predictions

The Fortunella hindsii S3y-45 v2.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences (FASTA file)	Fhindsii_S3y-45_v2.0.proteins.fasta.gz
CDS (FASTA file)	Fhindsii_S3y-45_v2.0.cds.fasta.gz
Genes (GFF3 file)	Fhindsii_S3y-45_v2.0.genes.gff3.gz

Links

BLAST

JBrowse

Synteny Viewer

Functional Analysis

Functional annotation for the Fortunella hindsii S3y-45 genome v2.0 are available for download below. The Fortunella hindsii S3y-45 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	Fh_S3y-45_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan	Fh_S3y-45_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Fh_S3y-45_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Fh_S3y-45_v2.0_KEGG-pathways.xlsx.gz

Homology

Homology of the Fortunella hindsii S3y-45 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^-9was used for the NCBI nr (Release 2021-09) and 1e^-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.

Protein Homologs

F. hindsii S3y-45 v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Fh_S3y-45_v2.0_vs_arabidopsis.xlsx.gz
F. hindsii S3y-45 v2.0 proteins with arabidopsis (Araport11) (FASTA file)	Fh_S3y-45_v2.0_vs_arabidopsis_hit.fasta.gz
F. hindsii S3y-45 v2.0 proteins without arabidopsis (Araport11) (FASTA file)	Fh_S3y-45_v2.0_vs_arabidopsis_noHit.fasta.gz
F. hindsii S3y-45 v2.0 proteins with SwissProt homologs (EXCEL file)	Fh_S3y-45_v2.0_vs_swissprot.xlsx.gz
F. hindsii S3y-45 v2.0 proteins with SwissProt (FASTA file)	Fh_S3y-45_v2.0_vs_swissprot_hit.fasta.gz
F. hindsii S3y-45 v2.0 proteins without SwissProt (FASTA file)	Fh_S3y-45_v2.0_vs_swissprot_noHit.fasta.gz
F. hindsii S3y-45 v2.0 proteins with TrEMBL homologs (EXCEL file)	Fh_S3y-45_v2.0_vs_trembl.xlsx.gz
F. hindsii S3y-45 v2.0 proteins with TrEMBL (FASTA file)	Fh_S3y-45_v2.0_vs_trembl_hit.fasta.gz
F. hindsii S3y-45 v2.0 proteins without TrEMBL (FASTA file)	Fh_S3y-45_v2.0_vs_trembl_noHit.fasta.gz