Hello,
I am getting confused with the 16S marker and would need help.
I saw that the 16S rDNA is mostly used in bacteria research and is the component of the 30S small subunit of a prokaryotic ribosome, 18S for eucaryotes. So why is it also used for animal phylogenetics (e.g. fish) ?
Also just to be sure, from what I read, 16S rDNA is maternally inherited and non coding, right ? I have many stop codons in my sequences, whatever the reading frame used..
If someone can help me I would be very grateful !
Hello Lola,
You are right in everything you just said. The 16S rDNA gene encodes the small subunit RNA of the ribosome (ssu_rRNA) in prokaryotes, while the 18S do the same in eukaryotes. However, eukaryotes are composed by more complex cells that includes organelles. One of those is the mitochondria, which has its own genome and synthesize its own proteins, so it needs ribosomes, hence it needs ssu_rRNA. Now, according to the endosymbiotic theory (or symbiogenesis), mitochondria has bacterial origins (in fact the eukaryotic cell was the product of the endosymbiosis of bacteria within archaea -- see attached publications for more details), and that is the reason why mitochondria has a prokaryotic ssu_rRNA (i.e. 16S). This subunit is purely RNA -- it does not encode any protein, which is the reason it can has stop codons within because it is never interpreted in terms of codons.. it is just not translated, it is simply folded as RNA and used as such as part of the ribosome complex.
And yes, only the egg cell has mitchondria, not the sperm cell.
Relevant scientific literature:
Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013). An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504, 231-236.
Martin, W., Roettger, M., Kloesges, T., Thiergart, T., Woehle, C., Gould, S., & Dagan, T. (2012). Modern endosymbiotic theory: Getting lateral gene transfer into the equation. Endocytobiosis & Cell Research, 23.
I hope that helps. Best regards.
For eucaryote projects (phylogenetics) the gold standard marker proposed some time ago was the cytochrome oxidase COI gene. You can take a look at the "The Fish Barcode of Life Initiative (FISH-BOL)" project where you can find different tools (primers, databases, etc).
http://www.fishbol.org/enabling_tools.php
Best regards
Dear Lola,
16S rDNA is widely used in phylogenetic inferences in invertebrates. It depends on your organisms and scope. In earthworms it is a quite sensitive marker on genus level. In fish it is also used and you can find several papers like this http://www.tandfonline.com/doi/abs/10.3109/19401736.2013.815168?journalCode=imdn20
However, even on genus level nowadays the multilocus approach prevails.
Regards,
Csaba
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