Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) genome v1.0

Overview


Analysis Name	Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) genome v1.0
Method	Illumina NovaSeq 6000, PacBio Sequel II, Hi-C (Assembly with Canu, MInimap2)
Source	Huazhong Agriculture University
Date performed	2024-01-31

About the assembly

For this genome, please cite Zheng et al, Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo. This data was originally downloaded from the Citrus Pan-genome to Breeding Database. This data is also on NCBI under BioProject PRJNA911419 and the assembly accession number is GCA_029641205.1. The listed BioSample isolate designation is HZY-T.

Assembly metrics

Assembly size	345 Mb
Number of scaffolds	10
N50	36,344,869 bp
Predicted transcripts	39,524
Annotated genes	26,926
Assembly BUSCO score (embryophyta_odb10)	99.0%
Annotation BUSCO score (embryophyta_odb10)	91.3%

Assembly

The Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Cm_HZY-T_v1.0.fasta.gz

Gene Predictions

The Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (FASTA file)	Cm_HZY-T_v1.0.proteins.fasta.gz
Gene sequences (FASTA file)	Cm_HZY-T_v1.0.genes.fasta.gz
CDS (FASTA file)	Cm_HZY-T_v1.0.cds.fasta.gz
Genes (GFF3 file)	Cm_HZY-T_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) genome v1.0 are available for download below. The Citrus maxima 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	Cm_HZY-T_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cm_HZY-T_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cm_HZY-T_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cm_HZY-T_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus maxima cv. Huazhouyou-tomentosa (HZY-T) 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. maxima cv. HZY-T v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cm_HZY-T_v1.0_vs_arabidopsis.xlsx.gz
C. maxima cv. HZY-T v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cm_HZY-T_v1.0_vs_arabidopsis_hit.fasta.gz
C. maxima cv. HZY-T v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cm_HZY-T_v1.0_vs_arabidopsis_noHit.fasta.gz
C. maxima cv. HZY-T v1.0 proteins with SwissProt homologs (EXCEL file)	Cm_HZY-T_v1.0_vs_swissprot.xlsx.gz
C. maxima cv. HZY-T v1.0 proteins with SwissProt (FASTA file)	Cm_HZY-T_v1.0_vs_swissprot_hit.fasta.gz
C. maxima cv. HZY-T v1.0 proteins without SwissProt (FASTA file)	Cm_HZY-T_v1.0_vs_swissprot_noHit.fasta.gz
C. maxima cv. HZY-T v1.0 proteins with TrEMBL homologs (EXCEL file)	Cm_HZY-T_v1.0_vs_trembl.xlsx.gz
C. maxima cv. HZY-T v1.0 proteins with TrEMBL (FASTA file)	Cm_HZY-T_v1.0_vs_trembl_hit.fasta.gz
C. maxima cv. HZY-T v1.0 proteins without TrEMBL (FASTA file)	Cm_HZY-T_v1.0_vs_trembl_noHit.fasta.gz