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 language | English |
|---|---|
| Pages (from-to) | 1275-1288 |
| Number of pages | 14 |
| Journal | Molecular Ecology Resources |
| Volume | 15 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - 2015 Nov 1 |
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Keywords
- Barcoding
- Cytochrome oxidase
- Herbarium specimen
- MtDNA
- Oomycete-specific primers
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Biotechnology
- Genetics
Cite this
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 journal › Article
}
TY - JOUR
T1 - Towards a universal barcode of oomycetes - a comparison of the cox1 and cox2 loci
AU - Choi, Young Joon
AU - Beakes, Gordon
AU - Glockling, Sally
AU - Kruse, Julia
AU - Nam, Bora
AU - Nigrelli, Lisa
AU - Ploch, Sebastian
AU - Shin, Hyeon-Dong
AU - Shivas, Roger G.
AU - Telle, Sabine
AU - Voglmayr, Hermann
AU - Thines, Marco
PY - 2015/11/1
Y1 - 2015/11/1
N2 - 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.
AB - 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.
KW - Barcoding
KW - Cytochrome oxidase
KW - Herbarium specimen
KW - MtDNA
KW - Oomycete-specific primers
UR - http://www.scopus.com/inward/record.url?scp=84932599026&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84932599026&partnerID=8YFLogxK
U2 - 10.1111/1755-0998.12398
DO - 10.1111/1755-0998.12398
M3 - Article
C2 - 25728598
AN - SCOPUS:84932599026
VL - 15
SP - 1275
EP - 1288
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
SN - 1755-098X
IS - 6
ER -