Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci

Choi, Young Joon and Kruse, Julia and Nam, Bora and Nigrelli, Lisa and Telle, Sabine and Thines, Marco and Ploch, Sebastian and Beakes, Gordon and Glockling, Sally and Shin, Hyeon Dong and Shivas, Roger G. and Voglmayr, Hermann (2015) Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. Molecular Ecology Resources, 15 (6). pp. 1275-1288. ISSN 1755-098X

Abstract

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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Additional Information: Files associated with this item cannot be displayed due to copyright restrictions.
Faculty / Department / School: No Faculty
Date Deposited: 16 May 2017 22:56
Last Modified: 16 May 2017 23:37
Uncontrolled Keywords: Barcoding; Cytochrome oxidase; Herbarium specimen; MtDNA; Oomycete-specific primers; Computational Biology; DNA Barcoding, Taxonomic; DNA, Ribosomal Spacer; Electron Transport Complex IV; Genetic Variation; Oomycetes; Polymerase Chain Reaction; Sequence Analysis, DNA; GENETICS AND MOLECULAR BIOLOGY; MOLECULAR GENETICS; Molecular Biology Techniques; GENETICS AND MOLECULAR BIOLOGY; EUKARYOTIC GENETICS; Myxomycete and Fungal Genetics;
Fields of Research : 06 Biological Sciences > 0607 Plant Biology > 060704 Plant Pathology
06 Biological Sciences > 0607 Plant Biology > 060702 Plant Cell and Molecular Biology
Socio-Economic Objective: D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960413 Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments
Identification Number or DOI: 10.1111/1755-0998.12398
URI: http://eprints.usq.edu.au/id/eprint/31323

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