Identify unique genes and protein families from eukaryotic genome

Question

[nazninislamnif]

I have done Assembly and annotation of a fish genome. Assembly has been done upto scaffold level. Now I want to do Phylogenetic analysis and want to discover SNP from this genome. Also want to find uniqe gene and protein families of this fish. But have no idea how can I do that? Can anyone have any idea?

[Dunois]

Take a look at OrthoFinder for the gene/protein families issue (and probably also the phylogenetics stuff).

[nazninislamnif]

I tried orthofinder. It just compare orthologs with other fish genomes. But I wanted to separate the genes responsible for adaptation and the genes which are solely unique for my species. How do I do that?

[Dunois]

OrthoFinderalready provides you the data you need, albeit somewhat indirectly.

If you look in the Comparative_Genomics_Statistics/Statistics_PerSpecies.tsv file, there should be a column indicating how many sequences from the organism you're interested in were not assigned to any orthogroups. These, I suppose, would be the genes that are unique to your species.

The corresponding sequences (or sequence headers anyway) can be found in Orthogroups/Orthogroups_UnassignedGenes.tsv. Each column in the file corresponds to a particular sample you included in the analysis.

You'll probably need to look into whatever single copy orthologs have been detected in your species by OrthoFinder in order to investigate the genes involved in adaptation. Take a look at Orthogroups/Orthogroups_SingleCopyOrthologues.txt and Single_Copy_Orthologue_Sequences/ under the OrthoFinder results directory for this.

I cannot really comment much on how you should conclude that a particular gene was responsible for adaptation to whatever event/situation, as this is outside my domain of knowledge. I can point you to a paper I found that did look at this topic (and also used OrthoFinder): Peng et. al. New insights into the evolutionary history of Megacodon: Evidence from a newly discovered species. Plant Diversity 42, 198-208 (2020). Here's the paper's DOI: https://doi.org/10.1016/j.pld.2020.05.003 .