Because 16S sequencing relies on PCR amplification of the 16S gene
, it is subject to the inherent biases of PCR.
This is interesting, as the most abundant rRNA 16S gene
sequences also clustered close to this organism (Figure 4).
This was especially important in the case of the 16S gene
, which presented a large number of gaps when comparing sequences of the most divergent species.
We conducted a nucleotide BLAST search (BLASTn) of the unknown frog 16S gene
A simple algorithm for specific differentiation at subspecies level with single rDNA 16S gene
digestions for K.
In vitro amplification of the sequences belonging to the rRNA 16S gene
was conducted on the thermal cycler (Thermal Cycler, Veriti[R] 96-Well--Applied Biosystems).
More than 170 zebra mussel bacterial 16S gene
sequences were checked for similarity to 16S sequences contained in the Ribosomal Database Project and BLAST public databases.
rDNA 16S gene
amplification from Klebsiella genus species were performed under the following reaction conditions: Klebrib-1 (5'-GTAATGTCTGGG AAACTGCC-3') [0.5 [micro]M] and Klebrib-2A (3'-CCACC TTCCTCCAGTTTATC-5') [0.5 [micro]M] Taq polymerase [0.25U], MgCl [1.5 mM], dNTPs [0.2 mM], PCR buffer [1X] and DNA sample [10 ng/[micro]l], adjusted to a final volume of 50 [micro]l.
Amplification primers 5'-CCTAACACATGCAAGTCGARCG-3' (forward) and 5'-CGTAT-TACCGCGGCTGCT-3' (reverse), both from Eurogentec (Seraing, Belgium) were used in a standard polymerase chain reaction (PCR) to generate a 490-bp fragment from the 5' end of the 16S gene
. The PCR (25 [micro]L) consisted of 1 [micro]L DNA, 0.5 [micro]mol/L of both PCR primers, 1.5 mmol/L Mg[Cl.sub.2], 0.2 mmol/L dNTP, and 1 U FastStart Taq DNA polymerase (Roche Diagnostics, Almere, the Netherlands) in 1 x reaction buffer.
anthracis had an identical 16S gene
sequence, designated type 6; 16S type 10 was seen in all B.
However, despite the similarities, the 16S gene
sequence of M175 differed from M.
According to the results from the BLAST search (Table III), the sequences of COI and 16S genes
for the AF matched Diporochaeta sp., because the only a few studies have been published concerning DNA in E.