Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case

doi:10.1073/pnas.0611691104

Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case

*Biodiversity (Mycology and Botany), Environmental Sciences, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6;
^‡Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, 3508 AD, Utrecht, The Netherlands;
^§Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada N1G 2W1; and
^¶Department of Natural History, Royal Ontario Museum, and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 2C6

Communicated by Daniel H. Janzen, University of Pennsylvania, Philadelphia, PA, January 3, 2007 (received for review September 11, 2006)

Abstract

DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or β-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.

Footnotes

^†To whom correspondence should be addressed. E-mail: seifertk{at}agr.gc.ca
Author contributions: K.A.S., R.A.S., J.R.d., and P.D.N.H. designed research; K.A.S., J.R.d., J.H., and G.L.-S. performed research; K.A.S., R.A.S., J.H., G.L.-S., and P.D.N.H. contributed new reagents/analytic tools; K.A.S., J.R.d., C.A.L., and J.-M.M. analyzed data; and K.A.S., J.R.d., and P.D.N.H. wrote the paper.
The authors declare no conflict of interest.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. EF180096–EF180449).
This article contains supporting information online at www.pnas.org/cgi/content/full/0611691104/DC1.
Abbreviation:

ITS,

internal transcribed spacer.
Freely available online through the PNAS open access option.