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

Young Joon Choi, Gordon Beakes, Sally Glockling, Julia Kruse, Bora Nam, Lisa Nigrelli, Sebastian Ploch, Hyeon-Dong Shin, Roger G. Shivas, Sabine Telle, Hermann Voglmayr, Marco Thines

Research output: Contribution to journalArticle

58 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1275-1288
Number of pages14
JournalMolecular Ecology Resources
Volume15
Issue number6
DOIs
Publication statusPublished - 2015 Nov 1

Fingerprint

Oomycetes
barcoding
loci
gene
herbarium
DNA barcoding
Phytophthora infestans
Ribosomal DNA
herbaria
divergence
Genes
DNA
genes
Pythium
type specimen
Phytophthora
eukaryote
Polymerase Chain Reaction
potato
cytochrome

Keywords

  • Barcoding
  • Cytochrome oxidase
  • Herbarium specimen
  • MtDNA
  • Oomycete-specific primers

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Genetics

Cite this

Choi, Y. J., Beakes, G., Glockling, S., Kruse, J., Nam, B., Nigrelli, L., ... Thines, M. (2015). Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. Molecular Ecology Resources, 15(6), 1275-1288. https://doi.org/10.1111/1755-0998.12398

Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. / Choi, Young Joon; Beakes, Gordon; Glockling, Sally; Kruse, Julia; Nam, Bora; Nigrelli, Lisa; Ploch, Sebastian; Shin, Hyeon-Dong; Shivas, Roger G.; Telle, Sabine; Voglmayr, Hermann; Thines, Marco.

In: Molecular Ecology Resources, Vol. 15, No. 6, 01.11.2015, p. 1275-1288.

Research output: Contribution to journalArticle

Choi, YJ, Beakes, G, Glockling, S, Kruse, J, Nam, B, Nigrelli, L, Ploch, S, Shin, H-D, Shivas, RG, Telle, S, Voglmayr, H & Thines, M 2015, 'Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci', Molecular Ecology Resources, vol. 15, no. 6, pp. 1275-1288. https://doi.org/10.1111/1755-0998.12398
Choi YJ, Beakes G, Glockling S, Kruse J, Nam B, Nigrelli L et al. Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. Molecular Ecology Resources. 2015 Nov 1;15(6):1275-1288. https://doi.org/10.1111/1755-0998.12398
Choi, Young Joon ; Beakes, Gordon ; Glockling, Sally ; Kruse, Julia ; Nam, Bora ; Nigrelli, Lisa ; Ploch, Sebastian ; Shin, Hyeon-Dong ; Shivas, Roger G. ; Telle, Sabine ; Voglmayr, Hermann ; Thines, Marco. / Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci. In: Molecular Ecology Resources. 2015 ; Vol. 15, No. 6. pp. 1275-1288.
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