The primer pairs, NPR1F/NPR1R were designed from the NPR1 conserved region to amplify partial PhaNPR1 cDNA using RNA isolated from P. aphrodite subsp. formosana treated with salicylic acid.
Twelve degenerate primers (named as PERO primers) were designed on those conserved motifs to amplify DNA towards the 5'end of the targeted Prx sequences (Table 5).
As these markers were shown to be conserved enough to amplify genes across potato and tobacco populations of AG-3, we explored their potential appropriateness for phylogenetic and population genetics analyses within R. solani AG-3.
However, with the exception of our studies, very few primer sequences from rice have been shown to be conserved enough to amplify in related genera, although some amplify DNA of wheat, oat, barley, maize, sorghum, millet, sugarcane and bamboo reliably [ 27, 46].
We used degenerated primers designed in the highly conserved regions of GST to amplify the corresponding mRNA.
It can be used to amplify conserved sequences of genes from other gene families.
The common PCR primer pairs designed by our algorithm could be applied to amplify conserved sequences of genes from the same or different organisms.
The LightCycler RNA master Hybprobe kit (Roche diagnostics) was used to amplify conserved sequences within the LTR region using the primers 5'-GGCGCCACTGCTAGAGATTTT-3' and 5'-GCCTCAATAAAGCTTGCCTTGA-3' and a Taqman probe 5'-6Fam-AAGTAGTGTGTGCCCGTCTGTTRTKTGACT-Tamra-3'.
Internal PCR products for X. laevis TRPM8 and TRPM8-b were obtained using PCR primers designed to amplify conserved regions within each gene (based on rat, human, chick, and X. tropicalis genome sequences), and the resulting sequence information was used to obtain complete transcript sequences using 5' and 3' SmartRACE (Clontech).
Conserved primer sets designed to amplify yir genes across the phylogenetic tree and validated on genomic DNA were initially used (data not shown) in order to avoid any primer bias but the conserved set f1/r1 were used subsequently as the results obtained were identical.
PCR primers to amplify conserved DNA sequences of 18S rRNA genes shared by most clinically important fungi were used.
