Citrus linwuensis cv. LW genome v1.0 | Citrus Genome Database

Overview


Analysis Name	Citrus linwuensis cv. LW genome v1.0
Method	PacBio, Illumina, Oxford 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 PRJNA782869 and the assembly accession number is GCA_030444885.1. The listed BioSample isolate designation is LW.

Assembly metrics

Assembly size	393 Mb
Number of scaffolds	599
N50	4,257,099 bp
Predicted transcripts	54,459
Annotated genes	31,413
Assembly BUSCO score (embryophyta_odb10)	98.7%
Annotation BUSCO score (embryophyta_odb10)	96.5%

Assembly

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

Downloads

Chromosomes (FASTA file)

Clin_LW_v1.0.fasta.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Clin_LW_v1.0.proteins.fasta.gz
CDS (FASTA file)	Clin_LW_v1.0.cds.fasta.gz
Genes (GFF3 file)	Clin_LW_v1.0.genes.gff3.gz

Links

BLAST

JBrowse

Synteny

Functional Analysis

Functional annotation for the Citrus linwuensis LW genome v1.0 are available for download below. The Citrus linwuensis 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	Clin_LW_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Clin_LW_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Clin_LW_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Clin_LW_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus linwuensis cv. LW 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. linwuensis cv. LW proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cs_Newhall_v1.0_vs_arabidopsis.xlsx.gz
C. linwuensis cv. LW proteins with arabidopsis (Araport11) (FASTA file)	Cs_Newhall_v1.0_vs_arabidopsis_hit.fasta.gz
C. linwuensis cv. LW proteins without arabidopsis (Araport11) (FASTA file)	Cs_Newhall_v1.0_vs_arabidopsis_noHit.fasta.gz
C. linwuensis cv. LW proteins with SwissProt homologs (EXCEL file)	Cs_Newhall_v1.0_vs_swissprot.xlsx.gz
C. linwuensis cv. LW proteins with SwissProt (FASTA file)	Cs_Newhall_v1.0_vs_swissprot_hit.fasta.gz
C. linwuensis cv. LW proteins without SwissProt (FASTA file)	Cs_Newhall_v1.0_vs_swissprot_noHit.fasta.gz
C. linwuensis cv. LW proteins with TrEMBL homologs (EXCEL file)	Cs_Newhall_v1.0_vs_trembl.xlsx.gz
C. linwuensis cv. LW proteins with TrEMBL (FASTA file)	Cs_Newhall_v1.0_vs_trembl_hit.fasta.gz
C. linwuensis cv. LW proteins without TrEMBL (FASTA file)	Cs_Newhall_v1.0_vs_trembl_noHit.fasta.gz