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Towards a universal barcode of oomycetes – a comparison of the cox 1 and cox 2 loci
Author(s) -
Choi YoungJoon,
Beakes Gordon,
Glockling Sally,
Kruse Julia,
Nam Bora,
Nigrelli Lisa,
Ploch Sebastian,
Shin HyeonDong,
Shivas Roger G.,
Telle Sabine,
Voglmayr Hermann,
Thines Marco
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12398
Subject(s) - biology , oomycete , dna barcoding , herbarium , phylogenetics , phytophthora infestans , genetics , barcode , evolutionary biology , gene , botany , computer science , operating system
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 ( cox 2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox 1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA . The cox 1 locus has been used in some studies of Pythium and Phytophthora , but has rarely been used for other oomycetes, as amplification success of cox 1 varies with different lineages and sample ages. To determine which out of cox 1 or cox 2 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 cox 2 successfully amplified all oomycete genera tested, while cox 1 failed to amplify three genera. In addition, cox 2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding‐type material. Sequence data for several historic type specimens exist for cox 2, but there are none for cox 1. In addition, cox 2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox 1. Therefore, cox 2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox 1. 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.