Hi,
If it is possible to do both then both is better. If not i would choose 16s with sequecning forward and reversed the fragment and always by inserting the fragment first in a plasmid and then sequencing using a plasmid (like T7 and SP6 primers) pair of primers.
Cheers
From my knowledge, the best marker to use is the 16S rRNA gene because apart from having the advantage of enabling the identification of hard to cultivate/culture microorganisms, this gene fragment is highly conservative at the species level and as a result speciation is good. However, for identification of subspecies and strains, it is not recommended.
Hi Aloo,
For the identification of subspecies and strain which primer set is most appropriate for this.
Dear Ganshyam Prajapat,
To detect the presence of cyanobacteria a region of the 16S rRNA gene was amplified by PCR using bacterial-specific primers CYA359F 5'- GGG GAA TYT TCC GCA ATG GG-3' and CYA781R (a) 5'- GAC TAC TGG GGT ATC TAA TCC CAT T -3' and CYA781R (b) 5'- GAC TAC AGG GGT ATC TAA TCC CTT T - 3' (Nubel et al. 1997).
Best regards
Genomic DNA can be isolated from the cyanobacterial cultures using MiniPrep Bacterial Genomic DNA method (Ausubel, 1999) . The forward primer CY106F (5’-CGG ACG GGT GAG TAA CGC GTG A-3’) and reverse primer CY781R {equimolar mixture of CY781R(A) 5’-GAC TAC TGG GGT ATC TAA TCC CAT T-3’ and CY781R(B) 5’-GAC TAC AGG GGT ATC TAA TCC CTT T-3’} can be used for amplification of a fragment of the 16S rRNA gene from the isolated DNA (Nubel, 1997).
I have same question Which primer set or which gene primer is more useful for molecular level identification of cyanobacteria ?currently i am usinf ITS and IGS primers
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