Gene to use for phylogenic analysis

Question

[uttkarsh]

I am trying to perform phylogenetic analysis using data from NCBI of Acinetobacter baumannii; I am not able to figure out which gene should I use to compare the molecular evolution of the bacteria

[Ram]

None of the tags you used are relevant to the question you asked - they broadly describe the entire field of bioinformatics. I've fixed it this time, please use more relevant tags in the future.

Answer 1

[dthorbur]

This question is hard to answer without much context, but there are some generalisations that might be useful.

Ultimately, the answer is "it depends". If you are using single locus phylogenetics, then 16S rRNA gene is probably the most commonly used in bacterial phylogenetics and taxonomy. However, this locus evolves relatively slowly, so it might not be useful if you are trying to build a phylogeny of species/strains with low evolutionary time to the last common ancestor. There are numerous housekeeping gene loci that are used in phylogenetics, so looking through the literature for similar studies is the best way to identify good candidates.

If you have the computational power and data resources, whole genome phylogenetics is considerably more powerful, but a compromise could be analysing multiple loci in a single analysis. Generally speaking, the more core genes you add, the more robust your analysis will be.