Which sequences have to be used for prediction of orthologs, CDS or assembled contigs for phylogenomics study ?

Question

[sunnykevin97]

HI,

I mainly work with whole genome data of non-model organisms.

For phylotranscriptomics study, generally extracting the CDS from assembled contigs, and further predicting Orthologs.

I went through some of the phylogenomics articles, they said, once you get denovo genome assemblies, the next step  is the ortholog prediction in phylogenomics study.

My question is do I have to use assembled contigs or CDS for ortholog prediction ?

Any suggestions.

Answer 1

[lieven.sterck]

Orthology is an "evolutionary feature" of genes so you should have to go for the CDS (or the protein to be exact). Of course if you have genome available you will have a much more comprehensive set of all possible genes/proteins for a species so your analysis will be more robust.