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Lookup NU author(s): Dr Gordon Beakes, Dr Sally Glockling
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© 2015 John Wiley & Sons Ltd. 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.
Author(s): Choi Y-J, Beakes G, Glockling S, Kruse J, Nam B, Nigrelli L, Ploch S, Shin H-D, Shivas RG, Telle S, Voglmayr H, Thines M
Publication type: Article
Publication status: Published
Journal: Molecular Ecology Resources
Year: 2015
Volume: 15
Issue: 6
Pages: 1275-1288
Print publication date: 01/11/2015
Online publication date: 24/03/2015
Acceptance date: 02/02/2015
ISSN (print): 1755-098X
ISSN (electronic): 1755-0998
Publisher: Blackwell Publishing Ltd
URL: https://doi.org/10.1111/1755-0998.12398
DOI: 10.1111/1755-0998.12398
PubMed id: 25728598
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