What is UniTato?
UniTato is a web-based service that provides access to comprehensive and accurate potato gene models. It unifies the recent potato double monoploid (DM) v4 and v6 gene models of the Buell Lab's Spud DB, and allows further community-based manual curation in a user-friendly web interface powered by Apollo, a genome annotation and editing platform.
Why use UniTato?
- UniTato contains the most up-to-date and unified potato gene models, which can help you avoid missing or wrongly annotated genes.
- UniTato allows you to browse, search, and download manually curated potato gene models.
- UniTato enables you to edit and improve the potato gene models, as well as contribute your own functional annotations and comments.
- UniTato is powered by JBrowse that supports various track formats, including GFF3, BED, and BigWig.
How to get started?
UniTato is free and easy to use. You can access the Apollo interface and start exploring the potato genome immediately:
Access the public UniTato Apollo interface.
To start contributing manual annotations, please see:
Contribute.
If you already have an account:
Login to UniTato Apollo interface.
For help with using Apollo, please see the
Apollo User Guide.
UniTato tracks
The following tracks are available for exploration in Apollo:
| Name | Description | |
|---|---|---|
| Gene models and gene model subsets | UniTato-v4v6 | DM Phureja potato unified (merged) v4 and v6 gene models (GFF) |
| DMv4 unmatching v6 | DM Phureja potato v4 gene models not matching v6 gene models (GFF), added to UniTato GFF | |
| DMv4 low confidence matches to v6 | DM Phureja potato v4 gene models matching v6 gene models with low confidence (GFF), added to UniTato GFF | |
| DMv4 high confidence matches to v6 | DM Phureja potato v4 gene models matching v6 gene models with high confidence (GFF), included in translation table | |
| Pan-transcriptome | pan-transcriptome Desiree/PW363/Rywal | Representative de-novo assembled transcripts of potato cv. Desiree, cv. Rywal and breeding clone PW363 (BAM) |
| Long-read transcriptomes | Rywal IsoSeq transcripts | cv. Rywal potato Iso-Seq reads (BAM) |
| Altus IsoSeq transcripts | cv. Altus potato Iso-Seq reads (BAM) | |
| Avenger IsoSeq transcripts | cv. Avenger potato Iso-Seq reads (BAM) | |
| Colomba IsoSeq transcripts | cv. Colomba potato Iso-Seq reads (BAM) | |
| Spunta IsoSeq transcripts | cv. Spunta potato Iso-Seq reads (BAM) | |
| PRJNA612026 ONT transcripts | potato ONT reads from SRA project PRJNA612026 (BAM) | |
| Short paired-end read transcriptomes | Phureja tuber Illumina PE | Solanum tuberosum L. Phureja Illumina NovaSeq 6000 reads (bw) |
| potato seed-tubers Illumina PE | Solanum tuberosum tuber-seeds from northern Antioquia/Cundinamarca/Boyaca (bw) | |
| Phureja DM1-3 516 R44 Illumina PE | Solanum tuberosum strain:DM1-3 516 R44 Genome sequencing and assembly (bw) | |
| Phureja pistil Illumina PE | C065 pistil transcriptome sequencing (bw) | |
| Phureja Illumina PE | Solanum phureja lines contrasting by resistant to nematode (bw) | |
| Potato landraces young leaves Illumina PE | Transcriptomes of in vitro young leaves in eleven potato landraces (bw) | |
| Phureja seed-tuber sprouts Illumina PE | RNAseq of certified, and informal potato seed tubers in the province of Antioquia (bw) | |
| Reference proteomes | Arabidopsis proteome Araport11 | Arabidopsis thaliana proteome (v. Araport11) aligned to UniTato genome using miniprot |
| Tomato proteome ITAG4.1 | Solanum lycopersicum proteome (v. ITAG 4.1) aligned to UniTato genome using miniprot | |
| Tobacco proteome NtaSR1 | Nicotiana tabacum proteome (v. SR1) aligned to UniTato genome using miniprot | |
| Benthi proteome NbeHZ1 | Nicotiana benthamiana proteome (v. HZ1) aligned to UniTato genome using miniprot |
If you make use of UnitTato, please cite:
UniTato is maintained by the National Institute of Biology. For more information, please contact us.