I am interested to make a phylogentic tree as a requirment to prove my putative novel bacterial species. I would like to know if I should only take the Type-strain 16S RNA sequence of my related bacterial strains or any other 16sRNA sequence is ok to use?
Which 16sRNA sequence is best to use to create an authentic and acceptable phylogentic tree?
regards,
Timsy
Hi Timsy,
First of all, I would say that any 16S sequence of bacteria related to your putative new species would add more information to your gene tree. Therefore, in addition to type-strains, I would try to add as many sequences as you can find (obviously, somehow related to your focus).
Additionally, depending on the bacteria you are working on, you might want to add more genes? 16S is quite diverse and might indeed give you an idea of the variation happening (or not happening) between your new species and what is already described. However, in order to better understand the relationships between different bacterial species (for a proper phylogeny) you might want to include more markers.
Hope this helps!
Francesco
Genes/sequences with potentially useful phylogenetic information include: 16S rRNA, 23S rRNA, 16S-23S intergenic spacer region, 5S rRNA, SSU-rRNA, atpA, atpD, cbbL, clpA, clpX, cpn60, dnaJ, dnaK, erp, flaB, ftsZ, glnA, glnII, gltA, groEL, gyrA, gyrB, hsp60, hsp65, metG, mip, nifH, nifS, nox, ompA, oppA2, ospC, panC, pepX, pheS, pyrG, recA, recG, ribC, rplB, rpnB, rpoB, rpoD, rrf-rrl intergenic spacer, rrs, secA, sod4, sodA, ssrA, thrC, tuf, uvrA.
Yes, also convenient to add nearest Genbank neighbor. Make sure you mark which one's a NN and which one a TS
Submit the sequence of 16S rRNA gene of certain bacteria to gene bank and use Basic Local Search Tool programme and Clusta 1X programme to elucidate the phylogenetic tree and pairwise similarity
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