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