title: DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer.
abstract: Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.
authors.affiliation: Biology Department, Carleton University, 1125 Colonel By Dr., Ottawa, Ontario, Canada.
authors.forename: Gregg P
authors.initials: GP
authors.lastname: Robideau
authors.forename: Arthur W A M
authors.initials: AW
authors.lastname: De Cock
authors.forename: Michael D
authors.initials: MD
authors.lastname: Coffey
authors.forename: Hermann
authors.initials: H
authors.lastname: Voglmayr
authors.forename: Henk
authors.initials: H
authors.lastname: Brouwer
authors.forename: Kanak
authors.initials: K
authors.lastname: Bala
authors.forename: David W
authors.initials: DW
authors.lastname: Chitty
authors.forename: Nicole
authors.initials: N
authors.lastname: Désaulniers
authors.forename: Quinn A
authors.initials: QA
authors.lastname: Eggertson
authors.forename: Claire M M
authors.initials: CM
authors.lastname: Gachon
authors.forename: Chia-Hui
authors.initials: CH
authors.lastname: Hu
authors.forename: Frithjof C
authors.initials: FC
authors.lastname: Küpper
authors.forename: Tara L
authors.initials: TL
authors.lastname: Rintoul
authors.forename: Ehab
authors.initials: E
authors.lastname: Sarhan
authors.forename: Els C P
authors.initials: EC
authors.lastname: Verstappen
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Peter J M
authors.initials: PJ
authors.lastname: Bonants
authors.forename: Jean B
authors.initials: JB
authors.lastname: Ristaino
authors.forename: C André
authors.initials: CA
authors.lastname: Lévesque
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D003576:Electron Transport Complex IV / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009868:Oomycetes / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D021903:DNA, Ribosomal Spacer; D003576:Electron Transport Complex IV