High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples

By Hirokazu Toju, Akifumi S. Tanabe, Satoshi Yamamoto, Hirotoshi Sato. PLoS ONE, 2012

1,140 citations recorded by the source corpus.

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.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6e22612bc22dc48cb47dfc4bb41c7bf8974c9b75

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

In Molecular Biology

In Plant Science

Citations in the corpus

Effects of plant community history, soil legacy and plant diversity on soil microbial communities (2020, background): “…primer pair ITS1-F_KYO2 (5’-TAGAGGAAGTAAAAGTCGTAA) and ITS2_KYO2 (5’-TTYRCTRCGTTCTTCATC) to amplify the internal transcribed spacer subregion 1 (ITS1, Toju et al. 2012) and the primer pair S-D-Bact-0341-b-S-17 (5’-CCTACGGGNGGCWGCAG) and S-D-Bact-0785-a-A-21 (5’-GACTACHVGGGTATCTAATCC) to amplify…”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “…the most important factors determining the DNA sequences obtained, and several studies have been conducted using both in silico and experimental approaches to adequately design appropriate primers for use in metabarcoding analyses (Bokulich and Mills, 2013; Stielow et al., 2015; Toju et al., 2012).”