Genome Assembly and Annotation for Diploid Potato 'Jan' v1.1

January 23, 2025 - The paper "Jan and mini-Jan, a model system for potato functional genomics describing the development of Jan and mini-Jan and their role as a model system for potato functional genomicshas now been published in the Plant Biotechnology Journal.

October 1, 2024 - The chromosome scale genome assembly and genome annotation of the diploid potato 'Jan' v1.1 is now available. Jan was developed as a model system for potato functional genomics by Dr. Jiming Jiang at Michigan State University.

JBrowse Genome Browser

• Genome browser for the diploid potato 'Jan' (v1.1) assembly and annotation

Genome Assembly:

• jan_v1.1.asm.fa.gz - Genome assembly for diploid potato 'Jan' v1.1
• jan_v1.1.asm.sm.fa.gz - Soft masked genome assembly for diploid potato 'Jan' v1.1

Genome Annotation:

• High Confidence Gene Model Set
• jan_v1.1.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of high confidence gene models
• jan_v1.1.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of high confidence gene models
• jan_v1.1.hc_gene_models.pep.fa.gz - Protein sequences of high confidence gene models
• jan_v1.1.hc_gene_models.gff3.gz - High confidence gene models annotation in GFF3 format


• Representative High Confidence Gene Model Set

High confidence representative gene models are a subset of the high confidence gene model set. Each representative gene model is the isoform with the longest CDS at each locus.

• jan_v1.1.hc_gene_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the representative high confidence gene models
• jan_v1.1.hc_gene_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative high confidence gene models
• jan_v1.1.hc_gene_models.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• jan_v1.1.hc_gene_models.repr.gff3.gz - Representative high confidence gene models annotation in GFF3 format


• Working Gene Model Set

The set of working gene models contains all loci and isoforms from the annotation pipeline and may include artifacts such as partial gene models.

• jan_v1.1.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• jan_v1.1.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• jan_v1.1.working_models.pep.fa.gz - Protein sequences of working gene models
• jan_v1.1.working_models.gff3.gz - Working gene models annotation in GFF3 format
• jan_v1.1.functional_annotation.txt.gz - Functional annotation for the working gene models