High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples

PLoS One. 2012;7(7):e40863. doi: 10.1371/journal.pone.0040863. Epub 2012 Jul 12.


The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ascomycota / classification*
  • Ascomycota / genetics*
  • Base Pair Mismatch
  • Base Sequence
  • Basidiomycota / classification*
  • Basidiomycota / genetics*
  • Cell Nucleus / genetics
  • Computational Biology
  • DNA Primers / metabolism*
  • DNA, Fungal / genetics*
  • DNA, Intergenic / genetics*
  • Environmental Microbiology
  • Mycological Typing Techniques
  • Nucleic Acid Renaturation / genetics
  • Plants / genetics
  • Polymerase Chain Reaction
  • RNA, Ribosomal / genetics
  • Temperature


  • DNA Primers
  • DNA, Fungal
  • DNA, Intergenic
  • RNA, Ribosomal