Can recombination take place in bacterial protein coding gene?

Question

[Rui]

Hello everyone,

I am trying to learn the selective pressure of a bacterial metal resistance gene. It seems to be a good idea to screen for recombinant sequences before conducting selection inference for viral genomes, however, I am not sure if the same applies to bacterial genes (rather than genomes), can recombination occur in bacterial genes, and is it necessary to filter out recombinant sequences?

Thank you for any insights!

Rui

Answer 1

[Istvan Albert]

When genomes recombine any region may be altered.

https://en.wikipedia.org/wiki/Bacterial_recombination

What is or isn't necessary to identify is a part of defining and refining your research question.

As far as I know in most bacterial studies people do not actively look for recombination events, thus I don't believe that it is a process that is routinely performed. I general I don't think filtering these sequences out (as in removing them) would be the correct action anyway.

[Rui]

Thank you Dr.Albert. By reading a bit further, it seems part of the reason why removing the recombinant sequences is not advisable is because it’s difficult to distinguish whether the novel sequence is due to the recombination process or selective forces exerted on it, which might affect the inference later.

But another paper also mentioned that evolutionary inference can be misled if recombination is not taken into consideration, because recombinant sequences cannot be explained by the same phylogenetic tree as the original sequences. (Kosakovsky Pond, 2006)

Two claims seem to be conflicting with each other.

Didelot, X., & Maiden, M. C. (2010). Impact of recombination on bacterial evolution. Trends in microbiology, 18(7), 315-322.

Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. (2006). GARD: a genetic algorithm for recombination detection. Bioinformatics, 22(24), 3096-3098.

[Istvan Albert]

Evolutionary inference is a complex topic with countless pitfalls and potential issues that can crop up.

What I was referring to when advising against removal was to not treat that as a "routine" screening. When one has good reasons and reliable data that indicates recombination events then perhaps you could use different genes and even point out the differences. There are very fast aligners and tree builders available, thus you can generate trees and explore multiple genes in parallel.