Internal transcribed spacer (ITS) is as effective as the primers used. The shortfall should be from the specificity of your ITS primers. My advice is for you to increase your primers or look for more specific amplified ITS primers for your PCR analysis in other to achieve better results
As mentioned by Dr Peter, ITS is generally used, To identify Trichoderma species at morphological level is difficult task. Try for RBP1, RBP2 ,Beta tubulin gene to reach at strain level and check by BLASTn analysis.
I'm sorry but I disagree with colleagues a bit, for strain-level identification gene sequencing (even different genes) is not the appropriate strategy, since the differences between strains are usually small marks distributed throughout the genome, and the regions used for phylogeny are not the most suitable due to conservation. The ideal is to use neutral markers, such as SNP, SSR, VNTR's etc.
You can do this by in gel analysis or even by sequencing the marker (genotype by sequencing).
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA