Citrus limon cv. Eureka genome v1.0

Overview
Analysis NameCitrus limon cv. Eureka genome v1.0
MethodPacBio, ONT, Hi-C, Illumina (Assembly with Hifiasm, minimap2)
SourceNGDC-CNCB Genome Warehouse
Date performed2023-04-28

About the assembly

For this genome, please cite Bao et al, A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance.  This data was downloaded from the Genome Warehouse website, genome accession number GWHCBFQ00000000.1.  The listed Biosample cultivar designation is Eureka.  This is a haplotype assembly, both haplotypes are included in this assembly and metrics.

Assembly metrics

Assembly size 633 Mb
Number of scaffolds 18
N50 35,596,939 bp
Predicted transcripts 62,633
Annotated genes 56,667
Assembly BUSCO score (embryophyta_odb10) 99.1%
Annotation BUSCO score (embryophyta_odb10) 97.8%
Assembly

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

Downloads

Chromosomes (FASTA file) Citrus_limon_Eureka_v1.0.fasta.gz

 

Gene Predictions

The Citrus limon Eureka v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences (FASTA file) Citrus_limon_Eureka_v1.0.proteins.fasta.gz
RNA sequences (FASTA file) Citrus_limon_Eureka_v1.0.RNA.fasta.gz
Genes (GFF3 file) Citrus_limon_Eureka_v1.0.genes.gff3.gz

 

Functional Analysis
Functional Analysis: 

Functional annotation for the Citrus limon Eureka Genome v1.0 are available for download below. The Citrus limon Eureka 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 Citrus_limon_Eureka_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan Citrus_limon_Eureka_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Citrus_limon_Eureka_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Citrus_limon_Eureka_v1.0_KEGG-pathways.xlsx.gz

 

Homology
Homology: 

Homology of the Citrus limon Eureka 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-9 was 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 limon v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Citrus_limon_Eureka_v1.0_vs_arabidopsis.xlsx.gz
Citrus limon v1.0 proteins with arabidopsis (Araport11) (FASTA file) Citrus_limon_Eureka_v1.0_vs_arabidopsis_hit.fasta.gz
Citrus limon v1.0 proteins without arabidopsis (Araport11) (FASTA file) Citrus_limon_Eureka_v1.0_vs_arabidopsis_noHit.fasta.gz
Citrus limon v1.0 proteins with SwissProt homologs (EXCEL file) Citrus_limon_Eureka_v1.0_vs_swissprot.xlsx.gz
Citrus limon v1.0 proteins with SwissProt (FASTA file) Citrus_limon_Eureka_v1.0_vs_swissprot_hit.fasta.gz
Citrus limon v1.0 proteins without SwissProt (FASTA file) Citrus_limon_Eureka_v1.0_vs_swissprot_noHit.fasta.gz
Citrus limon v1.0 proteins with TrEMBL homologs (EXCEL file) Citrus_limon_Eureka_v1.0_vs_trembl.xlsx.gz
Citrus limon v1.0 proteins with TrEMBL (FASTA file) Citrus_limon_Eureka_v1.0_vs_trembl_hit.fasta.gz
Citrus limon v1.0 proteins without TrEMBL (FASTA file) Citrus_limon_Eureka_v1.0_vs_trembl_noHit.fasta.gz