DNA barcoding Marine Bacteria

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Permalink Reply by Vijaykumar Yogesh Muley on December 9, 2011 at 2:33am

16S rRNA sequence is the most stable element in prokaryotic organisms and widely used for phylogenetic or diversity studies. You can use rpoB or some other genes such as Gyrase but analysis become tricky due to frequent horizontal transfer. Furthermore, prokaryotic genomes are dynamically rearranged in the course of evolution which can relieve functional or evolutionary constraints on genes that are shuffled within genome sequence. So when researcher use ropB like genes in such analysis they most often complement with analysis of other genes. 

  So I think its better to stick with 16S rRNA gene.

Permalink Reply by Prasanna Kumar on December 9, 2011 at 5:10am

@ Dear Vijaykumar Yogesh

Its nice to see your reply. For past few years many papers have produced enough evidence to reject 16s rRNA as taxonomic marker, as it has less variations within species. Variations within multiple 16s gene copies occurring within bacterium was published. Different copies 16s rRNA gene sequences extracted from single bacterial cell of Staphylococcus sp. shared 5% variations. After analyzing set of 16 protein coding genes, majority of manuscripts concluded that rpoB could be an alternative. I have discussed the problem and compared rpoB, 16S genes in Pseudomonas spp. @ http://connect.barcodeoflife.net/group/problemsindnabarcoding/forum... . Though horizontal gene transfer is frequent, not all genes are transferable (http://www.ccdb.ca/pa/ge/research/domains-of-life/archea-and-bacteria). rpoB occurring as a single copy gene could be an ideal candidate is my point of view. One could recommend Multilocus gene sequencing for evolutionary analysis but this single gene copy is enough for identifying bacteria.

Using rpoB for identifying bacterial pathogens is a common practice in medical microbiology.

So I think its better to adopt rpoB gene for DNA barcoding bacteria. 

Enclos: I have enclosed a phylogram drawn using 16S and rpoB gene sequences of 20 P.fluorescence strains isolated around the world from rice field to deep sea environment (extracted form NCBI). 

Thanks for sharing your opinion again.

Cheers..

Attachments:

• phylogram.tif, 54 KB

Permalink Reply by Vijaykumar Yogesh Muley on December 9, 2011 at 6:22am

Dear Prasanna Kumar,

I was talking about generalized approach and certainly my comments would be wrong in case of within species variations. As shown in figure attached herewith, Variations among species are evident using rpoB as compared to 16S rRNA sequences. Just think about diversity analyses which include number of distantly related species, in those cases your phylogenetic tree constructed using rpoB can be less informative than the 16S rRNA based. Regarding common practice of rpoB gene as a marker, I have very strong evidence that function of rpoB gene can be substituted by other proteins. So selection pressure on this gene in those bacteria is little bit relaxed. Hence more changes can occur in sequences. This observation is based on analysis of 565 organisms, so it is less likely wrong. So after going through your reply I am confused bit about usage of both genes :-)