Citrus unshiu cv. Miyagawa Wase genome v1.0

Overview


Analysis Name	Citrus unshiu cv. Miyagawa Wase genome v1.0
Method	Illumina, PacBio (Assembly with PLATANUS)
Source	PRJDB5882
Date performed	2024-10-08

Citation: Shimizu T, Tanizawa Y, Mochizuki T, Nagasaki H, Yoshioka T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y. Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc.) Using a Hybrid Assembly Approach. Frontiers in genetics. 2017; 8:180.

Assembly Metrics

Assembly size	360 Mb
Number of scaffolds	20,876
N50	386,404 bp
Predicted transcripts	31,732
Annotated genes	25,090
Assembly BUSCO score (embryophtya_odb10)	96.2%
Annotation BUSCO score (embryophyta_odb10)	92.2%

Assembly

The Citrus unshiu cv. Miyagawa Wase genome v1.0 assembly files are available in FASTA format.

Downloads

Chromosomes (FASTA file)

Cu_MiyagawaWase_v1.fasta.gz

Gene Predictions

The Citrus unshiu cv. Miyagawa Wase v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file)	Cu_MiyagawaWase_v1.genes.gff3.gz
Protein sequences (FASTA file)	Cu_MiyagawaWase_v1.protein.fasta.gz
Transcript sequences (FASTA file)	Cu_MiyagawaWase_v1.transcript.fasta.gz

Links

JBrowse

Synteny

Functional Analysis

Functional annotation for the Citrus unshiu cv. Miyagawa Wase genome v1.0 are available for download below. The Citrus unshiu 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	Cunshiu_Miyagawa-wase_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan	Cunshiu_Miyagawa-wase_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs	Cunshiu_Miyagawa-wase_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways	Cunshiu_Miyagawa-wase_v1_KEGG-pathways.xlsx.gz

Homology

Homology of the Citrus unshiu cv. Miyagawa Wase 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 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format.

Protein Homologs

C. unshiu cv. Miyagawa Wase v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file)	Cu_MiyagawaWase.0_vs_arabidopsis.xlsx.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins with arabidopsis (Araport11) (FASTA file)	Cu_MiyagawaWase.0_vs_arabidopsis_hit.fasta.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins without arabidopsis (Araport11) (FASTA file)	Cu_MiyagawaWase.0_vs_arabidopsis_noHit.fasta.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins with SwissProt homologs (EXCEL file)	Cu_MiyagawaWase.0_vs_swissprot.xlsx.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins with SwissProt (FASTA file)	Cu_MiyagawaWase.0_vs_swissprot_hit.fasta.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins without SwissProt (FASTA file)	Cu_MiyagawaWase.0_vs_swissprot_noHit.fasta.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins with TrEMBL homologs (EXCEL file)	Cu_MiyagawaWase.0_vs_trembl.xlsx.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins with TrEMBL (FASTA file)	Cu_MiyagawaWase.0_vs_trembl_hit.fasta.gz
C. unshiu cv. Miyagawa Wase v1.0 proteins without TrEMBL (FASTA file)	Cu_MiyagawaWase.0_vs_trembl_noHit.fasta.gz