Citrus maxima Cupi Majiayou v1.0 genome

Overview


Analysis Name	Citrus maxima Cupi Majiayou v1.0 genome
Method	Illumina, Nanopore (Assembly with NECAT)
Source	Huazhong Agriculture University
Date performed	2023-05-10

About the assembly

For this genome, please cite Lu et al, The high-quality genome of pummelo provides insights into the tissue-specific regulation of citric acid and anthocyanin during domestication. This data was originally downloaded from the Citrus Pan-Genome to Breeding Database website (Citrus grandis (L.) Osbeck.cv.'Cupi Majiayou' v1.0).

Assembly metrics

Assembly size	368 Mb
Number of scaffolds	10
N50	38,734,001 bp
Predicted transcripts	44,021
Annotated genes	26,988
Assembly BUSCO score (embryophyta_odb10)	98.2%
Annotation BUSCO score (embryophyta_odb10)	92.5%

Assembly

The Citrus maxima genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file)

Cm_CupiMajiayou_v1.0.fasta.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Cm_CupiMajiayou_v1.0.proteins.fasta.gz
CDS (FASTA file)	Cm_CupiMajiayou_v1.0.cds.fasta.gz
Gene sequences (FASTA file)	Cm_CupiMajiayou_v1.0.genes.fasta.gz
Genes (GFF3 file)	Cm_CupiMajiayou_v1.0.genes.gff3.gz

Links

BLAST

JBrowse

Synteny Viewer

Functional Analysis

Functional annotation for the Citrus maxima 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	CMJ_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan	CMJ_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	CMJ_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	CMJ_v1.0_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus maxima 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^-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

Citrus maxima v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	CMJ_v1.0_vs_arabidopsis.xlsx.gz
Citrus maxima v1.0 proteins with arabidopsis (Araport11) (FASTA file)	CMJ_v1.0_vs_arabidopsis_hit.fasta.gz
Citrus maxima v1.0 proteins without arabidopsis (Araport11) (FASTA file)	CMJ_v1.0_vs_arabidopsis_noHit.fasta.gz
Citrus maxima v1.0 proteins with SwissProt homologs (EXCEL file)	CMJ_v1.0_vs_swissprot.xlsx.gz
Citrus maxima v1.0 proteins with SwissProt (FASTA file)	CMJ_v1.0_vs_swissprot_hit.fasta.gz
Citrus maxima v1.0 proteins without SwissProt (FASTA file)	CMJ_v1.0_vs_swissprot_noHit.fasta.gz
Citrus maxima v1.0 proteins with TrEMBL homologs (EXCEL file)	CMJ_v1.0_vs_trembl.xlsx.gz
Citrus maxima v1.0 proteins with TrEMBL (FASTA file)	CMJ_v1.0_vs_trembl_hit.fasta.gz
Citrus maxima v1.0 proteins without TrEMBL (FASTA file)	CMJ_v1.0_vs_trembl_noHit.fasta.gz