Hi! I'm a PhD student working on insects symbionts. I have a very important query because I really don't know how to proceed with my surveys. I hope you can help me.
Well, I sequenced 16S RNA for different european insects populations and related species (by means of Illumina), and now I have a list of OTUs for Wolbachia (in every population), a very important bacteria involved on insects reproduction. I read many papers about Wolbachia strains, but those were based on Asian insects species, solely. Then, even they found two different Wolbachia strains, its probable that my populations have different strains. Indeed, I aligned the 16S sequences and constructed a neighbour-joining tree, and the result consisted in many clades, without any pattern based on insect populations. Anyway, I ordered the primers that these Asian researchers designed and I'm going to test them on my populations, but in case they don't work I will not know how to proceed and distinguish new strains, I mean, I don't know which level I need to stablish in terms of nucleotide substitutions between the 16S Wolbachia sequences and so separate strains.
Thanks in advance!