How to find orthologus sequences between the different species of non-model organisms?

Question

[sunnykevin97]

Hi

I work with non-model organisms trying to understand the orthologs transcripts shared among the different species.

I de novo assembled the transcripts using TRINITY

Removed redundant transcripts using CDHIT

How to find the orthologs common among the species , is their any tools of interest that can do the job ?

Suggestions please.

Thanks Kevin

Answer 1

[Michael]

There is OrthoFinder. It works on predicted proteomes, so you need to get the likely coding sequences and the predicted amino-acids sequences from the transcriptome assembly. This can be done with Transdecoder.

[sunnykevin97]

Predicted ORF's using Transdecoder. Subjected the aminoacid sequences of each species into Orthofinder. I generated comparative stats about the shared orthologs among all species. How do I extract Orthology sequences ? further doing MSA alignment -> positive selection analysis (dN/dS).

Suggestions please!

[Michael]

What do you mean by "orthology sequences", consensus sequences?

Answers please! :D

[sunnykevin97]

The sequences shared among the all the nine species in my case.

I generated the alignment by performing multiple sequence alignment.

Answer 2

[lieven.sterck]

Phylogeny has been raised here already. That one is certainly capable of doing this and will even be quite robust but will also entail a lot of work as well as some knowledge on the basics of it and the data processing.

Much more straightforward (and more than enough in most cases) is to do a blast based analysis. You can either run and process the blast yourself or even run some tool that does it all for you. examples of tools: InParanoid, Orthomcl, OrthoFinder, RBH, ....

I personally suggest you first give those a try (or one/some of them) and only if that does not work out go to phylogeny.

Answer 3

[Elucidata]

If you have sequence files (preferably FASTA, even FASTQ files can be converted to FASTA) for all the organisms of your interest, you can use phylogeny tools like MEGA. MEGA X is a popular tool with several similarity functions and visualization tools that you can use for the construction of de novo phylogeny trees.

Starting from scratch can be helpful in your case if there's not a lot of prior information known about the organisms of your choice. MEGA is properly documented and has text and video tutorials too. For other tools, see this comprehensive answer.