Citrus limon cv. Xiangshui genome v1.0

Overview


Analysis Name	Citrus limon cv. Xiangshui genome v1.0
Method	PacBio, Illumina HiSeq (Assembly with Canu and Pilon)
Source	CNCB Genome Warehouse
Date performed	2024-02-01

About the assembly

For this genome, please cite Yu et al, The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis. This data was originally downloaded from the CNCB Genome Warehouse (GWHCBFU00000000). The raw read data is on NCBI under BioProject PRJNA793193. The listed BioSample isolate designation is Xiangshui.

Assembly metrics

Assembly size	365 Mb
Number of scaffolds	64
N50	38,658,008 bp
Predicted transcripts	25,682
Annotated genes	27,521
Assembly BUSCO score (embryophyta_odb10)	97.9%
Annotation BUSCO score (embryophyta_odb10)	87.4%

Assembly

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

Downloads

Chromosomes (FASTA file)

Cl_Xiangshui_v1.0.fasta.gz

Gene Predictions

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

Downloads

Protein sequences (FASTA file)	Cl_Xiangshui_v1.0.proteins.fasta.gz
CDS (FASTA file)	Cl_Xiangshui_v1.0.cds.fasta.gz
Genes (GFF3 file)	Cl_Xiangshui_v1.0.genes.gff3.gz

Links

JBrowse

BLAST

Synteny

Functional Analysis

Functional annotations for the Citrus limon cv. Xiangshui genome v1.0 are available for download below. The Citrus limon 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	Cl_Xiangshui_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cl_Xiangshui_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cl_Xiangshui_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cl_Xiangshui_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus limon cv. Xiangshui 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. limon cv. Xiangshui v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cl_Xiangshui_v1.0_vs_arabidopsis.xlsx.gz
C. limon cv. Xiangshui v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cl_Xiangshui_v1.0_vs_arabidopsis_hit.fasta.gz
C. limon cv. Xiangshui v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cl_Xiangshui_v1.0_vs_arabidopsis_noHit.fasta.gz
C. limon cv. Xiangshui v1.0 proteins with SwissProt homologs (EXCEL file)	Cl_Xiangshui_v1.0_vs_swissprot.xlsx.gz
C. limon cv. Xiangshui v1.0 proteins with SwissProt (FASTA file)	Cl_Xiangshui_v1.0_vs_swissprot_hit.fasta.gz
C. limon cv. Xiangshui v1.0 proteins without SwissProt (FASTA file)	Cl_Xiangshui_v1.0_vs_swissprot_noHit.fasta.gz
C. limon cv. Xiangshui v1.0 proteins with TrEMBL homologs (EXCEL file)	Cl_Xiangshui_v1.0_vs_trembl.xlsx.gz
C. limon cv. Xiangshui v1.0 proteins with TrEMBL (FASTA file)	Cl_Xiangshui_v1.0_vs_trembl_hit.fasta.gz
C. limon cv. Xiangshui v1.0 proteins without TrEMBL (FASTA file)	Cl_Xiangshui_v1.0_vs_trembl_noHit.fasta.gz