4:21 - https://youtu.be/od440tpfodY?t=261

You can click in a search box and type a few characters. The search box will then show all the possible names for species they have genomes for. There are lot, suggesting this is a very comprehensive data store for genomes, probably all the ones they have sequenced.

This suggests we could create a plug-in that would let people visualize all these genomes in IGB, or in some other externally managed and released software, just by clicking a button on the site. We could write a proposal to do this, working with others of similar mindset.

32:34 - https://youtu.be/od440tpfodY?t=1954

Can look at an exon-viewer (IGB) style visualization of gene models - indicates exonic and other notable regions using background shading. We could use this to sanity-check the IGB visualization, as both use the same technique to show the same things.

34:07 - https://youtu.be/od440tpfodY?t=2047

Explains how "deflines" are created for genome annotations!

This is important because we are trying currently to create "deflines" for the latest tomato genome assembly's annotations (called "SL5") because these new annotations include splice variants, and we are trying to use the pollen data to detect alternative splicing in pollen tubes undergoing heat stress in vitro and semi in vivo (in dissected ovaries). See: IGBF-3229 issue where we are trying to transfer deflines, called "descriptions" from SL4 to SL5 annotations, using a mapping file provided by the SL5 annotation creators.

Is SL5 in the JGI database?

Answering the above question: No. The most up-to-date version is SL4.

To learn about what resources Phytozome provides for their genome archive, I downloaded a "zip" file with all available data for SL4. It included the following files - see screenshot.

I looked at the "annotation info" file. It contains the following fields:

• locusName transcriptName peptideName Pfam Panther ec KOG KO GO Best-hit-arabi-name Best-hit-arabi-defline Best-hit-clamy-name Best-hit-clamy-defline Best-hit-rice-name Best-hit-rice-defline

This is hugely useful because these data could be added to the description field in IGB's BED14 field 14, making the genes findable in IGB by searchable annotation.

I will contact JGI and ask them to include SL5 in their annotation pipeline!

Sent to Phytozome contact:

Hello,

I am a long-time user of Phytozome and have very much appreciated this wonderful resource you've provided for so many years.

I'm writing now with a question:

Would you be able to add the newest tomato genome assembly to the Phytozome system - Solanum lycopersicum SL5.0?

The paper associated with this new release is here: https://www.nature.com/articles/s41586-022-04808-9, and the data are available from the Sol Genomics ftp site from here: https://solgenomics.net/ftp/genomes/TGG/.

The authors released a "GFF" file containing gene models, but the gene models currently lack "deflines" and functional annotations, except for Gene Ontology assignments performed by the authors. If you were able to annotate these new gene models using your standard pipeline, creating the "annotation_info.txt" file for these new models, it would help my research a lot!

I am interested in this because I work with an NSF-funded project led by Mark Johnson of Brown University. The abstract for the project is available online here: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1939255.

This project investigates the effects of heat stress on pollen function in diverse tomato varieties, including both thermo-tolerant and heat-sensitive varieties. We are hoping to use the new gene models and the genome assembly to study how heat stresses affect splicing patterns in pollen and other tomato organs and tissues.

Warm regards,

Ann Loraine