Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci.
Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Young-Joon
YJ
Choi
Division of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
Gordon
G
Beakes
135 Brodrick Road, Eastbourne, BN22 9RA, UK.
Sally
S
Glockling
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Julia
J
Kruse
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Bora
B
Nam
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Lisa
L
Nigrelli
Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.|Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Population Genetics, University of Duesseldorf, Universtitätsstr. 1, D-40225, Duesseldorf, Germany.
Sebastian
S
Ploch
Division of Environmental Science and Ecological Engineering, Korea University, 136-701, Seoul, South Korea.
Hyeon-Dong
HD
Shin
Plant Pathology Herbarium, Biosecurity Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, 4001, Queensland, Australia.
Roger G
RG
Shivas
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Sabine
S
Telle
Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria.|Department of Forest and Soil Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Peter Jordan-Straße 82, 1190, Wien, Austria.
Hermann
H
Voglmayr
Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438, Frankfurt am Main, Germany.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.|Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany.|Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
Marco
M
Thines
D019295:Computational Biology / Q000379:methods*; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D014644:Genetic Variation; D009868:Oomycetes / Q000145:classification* / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
D021903:DNA, Ribosomal Spacer; D003576:Electron Transport Complex IV
barcoding; cytochrome oxidase, herbarium specimen; mtDNA; oomycete-specific primers