Molecular evolution of overlapping genes

Hello everybody!

I’m interested in studying the molecular evolution of overlapping genes in viruses, do you recommend any special program or method that you might know that can be useful to analyse from a phylogenetic or any other perspective this kind of genes?. Of course I’m doing my research but I wanted to know if you have any special recomendation.

Thank you for your time

PS. I’m new in the field of molecular evolution of viruses, but I’m so exited to learn

Best wishes,

Quique

Hi.

HIV and other lentiviruses have overlapping genes. The bigger issue really is recombination. If there is no recombination, all of the genes shared the same history and have the same phylogeny. If you are interested in selection pressures on individual codons or small regions of genes/proteins, then the overlapping regions are a confounding issue, because the “silent sites” for one protein reading frame are not silent for the other reading frames.

In some of the HIV overlapping regions, only one of the two proteins produced from that region is critical for viral function, while the other one is not critical. For example, in the gag-pol overlap region the gag protein has function but that region of the gag-pol polyprotein product is cleaved off by protease and has no known function.

Are you sure all the genes shared the same history and have the same phylogeny without recombination?