ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases.

ABSTRACT:

Background

During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates.

Results

Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and mos

SUBMITTER: Bellemain E 

PROVIDER: S-EPMC2909996 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature