Outgroup Selection In Pks Domain Phylogeny

Question

[Fungiphylogenomics]

Hi

I have generated a phylogenetic tree depicting the relationship between PKS domains of 8 fungal species. I am interested in orthologous domain comparison between species and finding gene family contraction/expansion.

What I want to know is what is the best outgroup for this? If I was doing a species tree phylogeny I would just select a fungal species that is related to but distant enough. I am not sure what domain to use for a PKS outgroup.

Answer 1

[Konrad]

For the PKS (polyketide synthase) domains that have FAS (fatty acid synthases) equivalents you could try to use the corresponding equivalents. You have to take care as the evolution of this domain group is quite complicated and it might be that your PKS and FAS domain are too close related. I did once a similar analysis for bacterial PKS domains and used maximum likelihood trees to discriminate between PKS and FAS.