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Citation for Study 16949

Citation title: "Towards a universal barcode of oomycetes ? a comparison of the cox1 and cox2 loci ".

Study name: "Towards a universal barcode of oomycetes ? a comparison of the cox1 and cox2 loci ".

This study is part of submission 16949 (Status: Published).

Citation

Choi Y., Beakes G., Glockling S., Kruse J., Nam B., Nigrelli L., Ploch S., Shin H., Shivas R.G., Telle S., Voglmayr H., & Thines M. 2015. Towards a universal barcode of oomycetes ? a comparison of the cox1 and cox2 loci. Molecular Ecology Resources, .

Authors

• Choi Y. (submitter)
• Beakes G.
• Glockling S.
• Kruse J.
• Nam B.
• Nigrelli L. +49 69 7542 1834
• Ploch S. +49 69 75421834
• Shin H.
• Shivas R.G.
• Telle S.
• Voglmayr H.
• Thines M. +496975421833

Abstract

Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide, and include several devastating plant pathogens, e.g. 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 for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine whether cox1 or cox2 is better suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three of these. 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 none for cox1. In addition, cox2 yielded higher species identification success, and interspecific divergence and lower intraspecific divergence than cox1. Therefore, cox2 is suggested as partner DNA barcode with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.

Keywords

barcoding; cytochrome oxidase, herbarium specimen; mtDNA; oomycete-specific primers

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16949
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24087,
  	 author = {Youngjoon  Choi and Gordon W.  Beakes and Sally  Glockling and Julia  Kruse and Bora  Nam and Lisa  Nigrelli and Sebastian  Ploch and Hyeon-Dong   Shin and Roger G Shivas and Sabine  Telle and Hermann  Voglmayr and Marco  Thines},
  	 title = {Towards a universal barcode of oomycetes ? a comparison of the cox1 and cox2 loci },
  	 year = {2015},
  	 keywords = {barcoding; cytochrome oxidase, herbarium specimen; mtDNA; oomycete-specific primers},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Ecology Resources},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide, and include several devastating plant pathogens, e.g. 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 for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine whether cox1 or cox2 is better suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three of these. 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 none for cox1. In addition, cox2 yielded higher species identification success, and interspecific divergence and lower intraspecific divergence than cox1. Therefore, cox2 is suggested as partner DNA barcode with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24087
  AU  - Choi,Youngjoon 
  AU  - Beakes,Gordon W. 
  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 
  T1  - Towards a universal barcode of oomycetes ? a comparison of the cox1 and cox2 loci 
  PY  - 2015
  KW  - barcoding; cytochrome oxidase
  KW  - herbarium specimen; mtDNA; oomycete-specific primers
  UR  - http://dx.doi.org/
  N2  - Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide, and include several devastating plant pathogens, e.g. 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 for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine whether cox1 or cox2 is better suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three of these. 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 none for cox1. In addition, cox2 yielded higher species identification success, and interspecific divergence and lower intraspecific divergence than cox1. Therefore, cox2 is suggested as partner DNA barcode with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.
  L3  - 
  JF  - Molecular Ecology Resources
  VL  - 
  IS  - 
  ER  -