Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Dr., Ottawa, ON K1S 5B6, Canada.
Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada.
Mol Phylogenet Evol. 2014 Oct;79:279-91. doi: 10.1016/j.ympev.2014.04.009. Epub 2014 Apr 16.
Oomycete systematics has traditionally been reliant on ribosomal RNA and mitochondrial cytochrome oxidase sequences. Here we report the use of two single-copy protein-coding flagellar genes, PF16 and OCM1, in oomycete systematics, showing their utility in phylogenetic reconstruction and species identification. Applying a recently proposed mutation-selection model of codon substitution, the phylogenetic relationships inferred by flagellar genes are largely in agreement with the current views of oomycete evolution, whereas nucleotide- and amino acid-level models produce biologically implausible reconstructions. Interesting parallels exist between the phylogeny inferred from the flagellar genes and zoospore ontology, providing external support for the tree obtained using the codon model. The resolution achieved for species identification is ample using PF16, and quite robust using OCM1, and the described PCR primers are able to amplify both genes for a range of oomycete genera. Altogether, when analyzed with a rich codon substitution model, these flagellar genes provide useful markers for the oomycete molecular toolbox.
卵菌系统学传统上依赖核糖体 RNA 和线粒体细胞色素氧化酶序列。在这里，我们报告了在卵菌系统学中使用两个单拷贝的蛋白编码鞭毛基因 PF16 和 OCM1，展示了它们在系统发育重建和物种鉴定中的应用。应用最近提出的密码子替换突变-选择模型，鞭毛基因推断的系统发育关系与卵菌进化的当前观点基本一致，而核苷酸和氨基酸水平模型产生了不合理的重建。从鞭毛基因推断出的系统发育与游动孢子本体论之间存在有趣的相似之处，为使用密码子模型获得的树提供了外部支持。使用 PF16 进行物种鉴定的分辨率足够高，使用 OCM1 则相当稳健，并且描述的 PCR 引物能够扩增一系列卵菌属的这两个基因。总的来说，当用丰富的密码子替换模型进行分析时，这些鞭毛基因为卵菌分子工具包提供了有用的标记。
