The 16S rRNA gene is used for phylogenetic studies between different species of bacteria and archaea. What sort of genes that are used to study phylogeny within the strains/subspecies of bacteria?
HI, maybe you can try to reconstruct phylogeny from concatenated multiple genes...
The gyrB gene is widely used for the phylogeny of the strains/subspecies of bacteria at present. The other single housekeeping gene, such as rpoD, rpoB, recA, mutL, etc, is also used in related studies.
Compared with the single housekeeping gene described above, the Multilocus Sequence Analysis based on five to seven housekeeping genes is currently an effective, straightforward, reproducible and comparable tool to explore the phylogeny of the strains/subspecies of bacteria at present.
In my opinion, you would better to read the more review about the aspect.
Good luck to you.
Hi Aqleem,
I think the threshold has been past where doing whole genome sequencing, or using available genome sequences,are the route to go. Cost wise this often ends up being less expensive than sequencing multiple independent genes. Also, there is a good tool that extracts 107 essential core bacterial genes from the genomes and performs phylogenetic analysis. The reference (see link below) and software are both free to down load.
http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2015-0175#.WBi3IfkrK70
Genome, 2016, 59(10): 783-791, 10.1139/gen-2015-0175
Regards,
Frank
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