Murraya paniculata cv. JLX genome v1.0

Overview


Analysis Name	Murraya paniculata cv. JLX genome v1.0
Method	PacBio, Nanopore (Assembled with SMARTdenovo, miniasm)
Source	Huazhong Agriculture University
Date performed	2024-01-22

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 PRJNA695120 and the assembly accession number is GCA_030449075.1. The listed BioSample isolate designation is JLX.

Assembly metrics

Assembly size	218 Mb
Number of scaffolds	260
N50	2,450,840 bp
Predicted transcripts	33,550
Annotated genes	22,856
Assembly BUSCO score (embryophyta_odb10)	98.6%
Annotation BUSCO score (embryophyta_odb10)	94.5%

Assembly

The Murraya paniculata cv. JLX genome v1.0 assembly files are available in GFF3 and FASTA format.

Downloads

Chromosomes (FASTA file)

Mp_JLX_v1.0.fasta.gz

Gene Predictions

The Murraya paniculata cv. JLX v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Protein sequences (FASTA file)	Mp_JLX_v1.0.proteins.fasta.gz
Gene sequences (FASTA file)	Mp_JLX_v1.0.genes.fasta.gz
CDS (FASTA file)	Mp_JLX_v1.0.cds.fasta.gz
Genes (GFF3 file)	Mp_JLX_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotation for the Murraya paniculata cv. JLX genome v1.0 are available for download below. The M. paniculata cv. JLX 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	Mp_JLX_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Mp_JLX_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Mp_JLX_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Mp_JLX_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Murraya paniculata cv. JLX 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

M. paniculata cv. JLX v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Mp_JLX_v1.0_vs_arabidopsis.xlsx.gz
M. paniculata cv. JLX v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Mp_JLX_v1.0_vs_arabidopsis_hit.fasta.gz
M. paniculata cv. JLX v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Mp_JLX_v1.0_vs_arabidopsis_noHit.fasta.gz
M. paniculata cv. JLX v1.0 proteins with SwissProt homologs (EXCEL file)	Mp_JLX_v1.0_vs_swissprot.xlsx.gz
M. paniculata cv. JLX v1.0 proteins with SwissProt (FASTA file)	Mp_JLX_v1.0_vs_swissprot_hit.fasta.gz
M. paniculata cv. JLX v1.0 proteins without SwissProt (FASTA file)	Mp_JLX_v1.0_vs_swissprot_noHit.fasta.gz
M. paniculata cv. JLX v1.0 proteins with TrEMBL homologs (EXCEL file)	Mp_JLX_v1.0_vs_trembl.xlsx.gz
M. paniculata cv. JLX v1.0 proteins with TrEMBL (FASTA file)	Mp_JLX_v1.0_vs_trembl_hit.fasta.gz
M. paniculata cv. JLX v1.0 proteins without TrEMBL (FASTA file)	Mp_JLX_v1.0_vs_trembl_noHit.fasta.gz