Citrus changshanensis cv. Huyou genome v1.0

Overview


Analysis Name	Citrus changshanensis cv. Huyou genome v1.0
Method	PacBio, Illumina, Hi-C (Assembled with Hifiasm v0.19.6)
Source	GWHEQVQ00000000.1
Date performed	2024-06-25

About the assembly

For this genome, please cite Miao C, Wu Y, Wang L, Zhao S, Grierson D, Xu C, Chen W, Chen K. Haplotype-resolved chromosome-level genome assembly of Huyou (Citrus changshanensis). Scientific data. 2024 Jun 07; 11(1):605. This data was originally downloaded from Genome Warehouse.

Assembly metrics

Assembly size	340 Mb
Number of scaffolds	31
N50	30,365,619 bp
Predicted transcripts	29,754
Annotated genes	29,754
Assembly BUSCO score (embryophyta_odb10)	98.5%
Annotation BUSCO score (embryophyta_odb10)	94.6%

Assembly

The Citrus changshanensis cv. Huyou genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (HAP1 FASTA file)

Ccha_Huyou_v1.cch.fasta.gz

Gene Predictions

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

Downloads

Genes (GFF3 file)	Ccha_Huyou_v1.cch.genes.gff3.gz
Protein sequences (FASTA file)	Ccha_Huyou_v1.cch.protein.fasta.gz
Transcript sequences (FASTA file)	Ccha_Huyou_v1.cch.transcript.fasta.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus changshanensis cv. Huyou genome v1.0 are available for download below. The Citrus changshanensis 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	Citrus_changshanensis_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Citrus_changshanensis_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Citrus_changshanensis_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Citrus_changshanensis_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus changshanensis cv. Huyou 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 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format.

Protein Homologs

C. changshanensis cv. Huyou v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Ccha_Huyou_v1.0_vs_arabidopsis.xlsx.gz
C. changshanensis cv. Huyou v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Ccha_Huyou_v1.0_vs_arabidopsis_hit.fasta.gz
C. changshanensis cv. Huyou v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Ccha_Huyou_v1.0_vs_arabidopsis_noHit.fasta.gz
C. changshanensis cv. Huyou v1.0 proteins with SwissProt homologs (EXCEL file)	Ccha_Huyou_v1.0_vs_swissprot.xlsx.gz
C. changshanensis cv. Huyou v1.0 proteins with SwissProt (FASTA file)	Ccha_Huyou_v1.0_vs_swissprot_hit.fasta.gz
C. changshanensis cv. Huyou v1.0 proteins without SwissProt (FASTA file)	Ccha_Huyou_v1.0_vs_swissprot_noHit.fasta.gz
C. changshanensis cv. Huyou v1.0 proteins with TrEMBL homologs (EXCEL file)	Ccha_Huyou_v1.0_vs_trembl.xlsx.gz
C. changshanensis cv. Huyou v1.0 proteins with TrEMBL (FASTA file)	Ccha_Huyou_v1.0_vs_trembl_hit.fasta.gz
C. changshanensis cv. Huyou v1.0 proteins without TrEMBL (FASTA file)	Ccha_Huyou_v1.0_vs_trembl_noHit.fasta.gz