Local Synteny Analysis with Uncharacterized Genes

Question

[snaledale]

Howdy!

Is anyone familiar with running synteny analysis on uncharacterized genes? I am trying to run a local synteny analysis between two closely related species to support the absence of an orthologous gene from one of the species. I am using genes from the reference genomes on NCBI for both species, which were generated via computational annotation. I've selected 10 upstream and 10 downstream genes from my gene of interest for the analysis. The genomes themselves are very high quality, but I'm exploring non-model species so there are many genes that haven't been validated yet and are still uncharacterized, thus making my synteny analysis difficult when I don't know who is who.

For those uncharacterized genes, I tried blastn against the whole NCBI database to try to figure out there identity, but it didn't work for all of them. Does anyone have suggestions on how to find their identity? I was thinking of making a big gene tree with all the genes for both species to see if those uncharacterized gene group with a gene from the other species which has been characterized, but does that make sense or is there a better way?

Thanks in advance!

[GenoMax]

Prior thread with some tools: Software recommendations for synteny analysis

SynTracker described in: https://www.nature.com/articles/s41587-024-02276-2 available from https://github.com/leylabmpi/SynTracker

In case your genomes are available here there is CGV at NCBI: https://www.ncbi.nlm.nih.gov/cgv/

Answer 1

[Philipp Bayer]

For gene clusters of this smaller size I'd recommend clinker

There are some nice automated visualisation tools in-built. As input it takes one genbank or gff file per species with your ~20 genes.

[Joe]

+1 for clinker, came here to make the same suggestion