Citrus reticulata 'Chachi' cv. Dazhongyoushen genome v1.0

Overview


Analysis Name	Citrus reticulata 'Chachi' cv. Dazhongyoushen genome v1.0
Method	Oxford Nanopore (Assembly with NextDenovo v2.5.2)
Source	Figshare
Date performed	2024-10-30

About the assembly

For this genome, please cite Zhu C, You C, Wu P, Huang Y, Zhang R, Fan Z, Yu C, Gong J, Hu X, Zeng J, Sun X. The gap-free genome and multi-omics analysis of Citrus reticulata ‘Chachi’ reveal the dynamics of fruit flavonoid biosynthesis. Horticulture Research. 2024 Aug;11(8):uhae177. This data was originally downloaded from Figshare.

Assembly metrics

Assembly size	313 Mb
Number of scaffolds	9
N50	32,187,089 bp
Predicted transcripts	34,097
Annotated genes	34,097
Assembly BUSCO score (embryophyta_odb10)	99.2%
Annotation BUSCO score (embryophyta_odb10)	98.4%

Assembly

The Citrus reticulata 'Chachi' cv. Dazhongyoushen genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file)

Cr_Chachi_v1.chr.fasta.gz

Gene Predictions

The Citrus reticulata 'Chachi' cv. Dazhongyoushen v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file)	Cr_Chachi_v1.genes.gff3.gz
Protein sequences (FASTA file)	Cr_Chachi_v1.protein.fasta.gz
CDS (FASTA file)	Cr_Chachi_v1.cds.fasta.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus reticulata 'Chachi' cv. Dazhongyoushen genome v1.0 are available for download below. The Citrus reticulata 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	Cr_Chachi_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cr_Chachi_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cr_Chachi_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cr_Chachi_v1_KEGG-pathways.xlsx.gz

Homology

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