A nomenclature for fungal PCR primers with examples from intron-containing SSU rDNA

Abstract

We present a compilation of polymerase chain reaction primers (oligonucleotides) used to amplify and sequence the small subunit of nuclear ribosomal DNA. To simplify use of these primers we designed a nomenclature that defines the location of each relative to Saccharomyces cerevisiae. With these primers we have developed strategies for selectively amplifying the diverse ribosomal DNA repeat types found in lichens; either between symbionts or between ribosomal DNA repeats (often the product of optional group I introns) within an individual fungus. A diversity of primers allows a choice of which small subunit ribosomal DNA repeat is amplified or sequenced from a complex extract such as that derived from lichens.