Resource for recent 16S rRNA phylogenetic of Archaea

Question

[kz0004]

Hey,

does someone know a good and reliable database or website regarding the recent phylogenetics "status quo", including recent studies on that particular topic? I mean the "tree of life"-website is a good resource for eucaryotic data, but not so good in anything else. The taxonomy website of NCBI is recently quite helpful, but maybe you guys know a better resource.

Thank you!

Kilian

[kz0004]

Thank you, Josh Herr. I actually looked for different sources in the net, but couldn't find anything but papers. The last good archaeal paper was from 2011 & 2012.

Brochier-Armanet, C., Forterre, P., & Gribaldo, S. (2011). Phylogeny and evolution of the Archaea: one hundred genomes later. Current opinion in microbiology, 14(3), 274-281.

Gribaldo, S., & Brochier-Armanet, C. (2012). Time for order in microbial systematics. Trends in microbiology, 20(5), 209-210.

My professor recommended me the tree of life resource, cause the last time, when he worked on phylogenetics this page was a good one. Here is the link: http://tolweb.org/tree/

I've ask that question because I want to compare a specific enzyme sequence which I can find in all families throughout the Archaea, but I don't know for sure, if I have all families together. I probably also have to take some families out, cause they don't align well up to this point.

[Josh Herr]

I'm not aware of any more recent studies to compare the newest (and there are a lot) Archaeal genomes.

Sounds like you are trying to gather a list of Archaea to search for the presence of a specific gene region. You can wait forever to get a definitive list of the Archaea and the taxonomy is always going to be in constant flux. If I were you, I would just choose (NCBI list is a good place to start) or make a list of the Archaeal genomes you want to include in your study and work from there -- don't add or allow for changes in the future. Search for your gene of interest and report your list of genomes you searched in your publication.

As far as a phylogeny, the Tree of Life project has a good Archaeal component -- maybe use that for inspiration?!

Answer 1

[Josh Herr]

This is an poorly worded question that shows you haven't really attempted to do any investigation yourself.

There are numerous resources for 16S data -- I think the best resource is the greengenes database, but Silva also has some utility.

I do not know what you are referring to regarding the "tree of life" website -- can you provide a link or some information on this reference? I would disagree completely with you -- I think the majority of our amplicon information is focused on "Prokaryotes" (that term isn't really used anymore) rather than Eukaryotes -- but certainly more concentrated in the bacteria versus archaea. There is still information on Archaea in greengenes, for example, even though not all 16S primers work reliably well for Archaea. The Archaeal genome browser is quite good. NCBI taxonomy is a fairly good resource.

Are you looking for a paper or something else? Have you attempted to conduct a literature search using Google Scholar or another search tool?