Citrus mangshanensis cv. MSYG genome v1.0

Overview


Analysis Name	Citrus mangshanensis cv. MSYG genome v1.0
Method	Illumina, PacBio, Nanopore (Assembly with SMARTdenovo, miniasm, NextDenovo)
Source	Huazhong Agriculture University
Date performed	2023-12-21

About the assembly

For this genome, please cite Huang et al, Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. This data was originally downloaded from the Citrus Pan-genome to Breeding Database. This data is also on NCBI under BioProject PRJNA782799 and the assembly accession number is GCA_030449895.1. The listed BioSample isolate designation is MSYG.

Assembly metrics

Assembly size	371 Mb
Number of scaffolds	376
N50	3,582,878 bp
Predicted transcripts	45,056
Annotated genes	28,131
Assembly BUSCO score (embryophyta_odb10)	99.0%
Annotation BUSCO score (embryophyta_odb10)	96.5%

Assembly

The Citrus mangshanensis cv. MSYG genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Cman_MSYG_v1.0.fasta.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Cman_MSYG_v1.0.proteins.fasta.gz
CDS (FASTA file)	Cman_MSYG_v1.0.cds.fasta.gz
Gene (FASTA file)	Cman_MSYG_v1.0.gene.fasta.gz
Genes (GFF3 file)	Cman_MSYG_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Functional Analysis

Functional annotation for the Citrus mangshanensis cv. MSYG genome v1.0 are available for download below. The Citrus mangshanensis 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	Cman_MSYG_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cman_MSYG_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cman_MSYG_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cman_MSYG_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus mangshanensis cv. MSYG 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. mangshanensis cv. MSYG v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cman_MSYG_v1.0_vs_arabidopsis.xlsx.gz
C. mangshanensis cv. MSYG v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cman_MSYG_v1.0_vs_arabidopsis_hit.fasta.gz
C. mangshanensis cv. MSYG v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cman_MSYG_v1.0_vs_arabidopsis_noHit.fasta.gz
C. mangshanensis cv. MSYG v1.0 proteins with SwissProt homologs (EXCEL file)	Cman_MSYG_v1.0_vs_swissprot.xlsx.gz
C. mangshanensis cv. MSYG v1.0 proteins with SwissProt (FASTA file)	Cman_MSYG_v1.0_vs_swissprot_hit.fasta.gz
C. mangshanensis cv. MSYG v1.0 proteins without SwissProt (FASTA file)	Cman_MSYG_v1.0_vs_swissprot_noHit.fasta.gz
C. mangshanensis cv. MSYG v1.0 proteins with TrEMBL homologs (EXCEL file)	Cman_MSYG_v1.0_vs_trembl.xlsx.gz
C. mangshanensis cv. MSYG v1.0 proteins with TrEMBL (FASTA file)	Cman_MSYG_v1.0_vs_trembl_hit.fasta.gz
C. mangshanensis cv. MSYG v1.0 proteins without TrEMBL (FASTA file)	Cman_MSYG_v1.0_vs_trembl_noHit.fasta.gz