Genome Annotation (UGA-v1) for the M82 Tomato Genome Assembly

January 26, 2022 - The Buell Lab at the University of Georgia is pleased to make available an updated set of genome annotation (UGA-v1) for the M82 tomato cultivar. We generated transcript and functional annotations for the previously published long-read assembly of the M82 genome (Alonge et al. 2019 Genome Biology) using mRNA-seq and Oxford Nanopore full-length cDNA libraries. The annotation can also be viewed on a Jbrowse genome browser or search on the SpudDB BLAST server.

JBrowse Genome Browser

• Genome browser for the M82 Tomato UGA-v1 annotation

• M82 Tomato - High Confidence Gene Model Set - UGA-v1
• M82.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of high confidence gene models
• M82.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of high confidence gene models
• M82.hc_gene_models.pep.fa.gz - Protein sequences of high confidence gene models
• M82.hc_gene_models.gff3.gz - High confidence gene models annotation in GFF3 format


• M82 Tomato - Representative High Confidence Gene Model Set - UGA-v1

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.

• M82.hc_gene_models.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• M82.hc_gene_models.repr.gff3.gz - Representative high confidence gene models annotation in GFF3 format


• M82 Tomato - Working Gene Model Set - UGA-v1

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

• M82.working_models.cdna.fa.gz - Transcript sequences (cDNA) of working gene models
• M82.working_models.cds.fa.gz - Coding sequences (CDS) of working gene models
• M82.working_models.pep.fa.gz - Protein sequences of working gene models
• M82.working_models.gff3.gz - Working gene models annotation in GFF3 format
• M82.working_models.func_anno.txt.gz - Functional annotation for the working gene models