Genome Annotation for the M82 Tomato Genome Assembly (SollycM82_v1)

February 17, 2023- The Buell Lab at the University of Georgia is pleased to make available an updated set of genome annotation for the M82 tomato cultivar (SollycM82_v1). We generated transcript and functional annotations for the published, updated long-read assembly of the M82 genome (Alonge et al. 2022 Genome Biology) using mRNA-seq and Oxford Nanopore full-length cDNA libraries.

Note: the previous M82 assembly and annotation can be found HERE.

JBrowse Genome Browser

• Genome browser for the SollycM82_v1 assembly and annotation- COMING SOON

Genome Assembly:

• SollycM82_v1.asm.fa.gz - Genome assembly for M82 - v1
• SollycM82_v1.asm.hm.fa.gz - Masked genome assembly for M82 - v1
• SollycM82_v1.asm.sm.fa.gz - Soft masked genome assembly for M82 - v1

Genome Annotation:

• High Confidence Gene Model Set
• SollycM82_v1.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of the high confidence gene models
• SollycM82_v1.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of the high confidence gene models
• SollycM82_v1.hc_gene_models.pep.fa.gz - Protein sequences of the high confidence gene models
• SollycM82_v1.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.

• SollycM82_v1.hc_gene_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the the representative high confidence gene models
• SollycM82_v1.hc_gene_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative high confidence gene models
• SollycM82_v1.hc_gene_models.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• SollycM82_v1.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.

• SollycM82_v1.working_models.cdna.fa.gz - Transcript sequences (cDNA) of the working gene models
• SollycM82_v1.working_models.cds.fa.gz - Coding sequences (CDS) of the working gene models
• SollycM82_v1.working_models.pep.fa.gz - Protein sequences of the working gene models
• SollycM82_v1.working_models.gff3.gz - Working gene models annotation in GFF3 format
• SollycM82_v1.functional_annotation.txt.gz - Functional annotation for the working gene models


• Representative Working Gene Model Set

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

• SollycM82_v1.working_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the representative working gene models
• SollycM82_v1.working_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative working gene models
• SollycM82_v1.working_models.repr.pep.fa.gz - Protein sequences of the representative working gene models