Finding orthologes for specific loci - Question

[vcastroagudin]

Hello, I am new to OrthoFinder and I have a question. I want to find orthologues in other species of a selected group of genes in the species I am working with but I am not sure how to do this. For example, could I just have an initial file (hand-curated file) only with the proteins of the genes I am interested in and blast them against the complete proteome of the other species?

What happens if I want to find orthologues of loci that are non-coding RNAs?

Thank you advance,

Vanina

[davidemms]

Hi Vanina

Is it a species with a sequenced genome? OrthoFinder uses the variation in sequence evolution rates across the genome to help with orthologue identification and so needs the complete set of genes in each species. It may seem like overkill but I would suggest running OrthoFinder with the default settings using your query species and target species plus four other species. It will be pretty quick (a few hours if you only have a single core, faster otherwise) so it won't really matter that you only need to know the orthologues for just a small group of genes. I would suggest an ideal input would be:

• query species, A
• species you want to know orthologues in, B
• a species a bit more closely related to A than B, and similarly, one more closely related to B
• two outgroup species

Obviously it doesn't have to be exactly that, but it's a good model to aim for. Try and get a file with one transcript per gene as that is better for accuracy and runtime. There's a guide here: https://davidemms.github.io/orthofinder_tutorials/running-an-example-orthofinder-analysis.html

All the best David

[davidemms]

For ncRNA I've just submitted an update to github which will allow you to do that. You'll need to download the source code from the github master branch (green button on the OrthoFinder page). The input needs to be entirely DNA and you need to put the option "--dna". You'll also need to have the BLAST executables downloaded and in your system path.

[vcastroagudin]

Thank you!!!

On Thu, Sep 17, 2020 at 5:53 AM David Emms notifications@github.com wrote:

For ncRNA I've just submitted an update to github which will allow you to do that. You'll need to download the source code from the github master branch (green button on the OrthoFinder page). The input needs to be entirely DNA and you need to put the option "--dna". You'll also need to have the BLAST executables downloaded and in your system path.

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-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

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