TreeBASE Search-Trees for study 16949

@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.} }