Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina) - PubMed (original) (raw)

Comparative Study

Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina)

Bryn T M Dentinger et al. PLoS One. 2011.

Abstract

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (~450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp) at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Positions of the four most successful PCR primers and introns encountered in mushroom cytochrome oxidase I (COI) genes relative to COI exon regions of Agrocybe aegerita (GenBank Accession AF010257).

Figure 2

Figure 2. PhyML phylogram of 167 partial COI (left) and PhyML or Neighbor-joining distance phylograms of full and partial ITS (right) sequences from ∼100 species of mushrooms.

Thickened lines represent branches that received ≥0.95 aLRT. Stars indicate COI sequences with an intron in the barcode region. Superscript numbers next to stars correspond to the position of the intron (Fig. 1). Branching for ITS sequences reflect ML- or NJ-based analysis of contigs formed using Sequencher; branching is absent where inter-specific distances are greater than the 20% cutoff value used in the Sequencher contig assembly. Letters at nodes in the genus Pluteus represent the phylogenetic species (reciprocally monophyletic with posterior probability of ≥0.95) of the Pluteus cervinus complex.

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