Taxonomy, DNA barcoding and phylogeny of three new species of <I>Pythium</I> from Canada

Abstract

Three new species of Pythium, namely, P. oopapillum, P. emineosum and P. camurandrum are presented in this paper based on morphological descriptions and molecular phylogenetic characterisation. These new species were isolated from various ecological regions in Canada. They have unique morphological features in the genus Pythium, and form distinct clades in maximum parsimony analyses, which are also supported by maximum likelihood phylogeny using general time reversible model (GTR), and Bayesian inference (BI) phylogeny using Markov Chain Monte Carlo (MCMC) analysis methods. A comparative study of the new species with closely related taxa, their clade positions, and morphological features are described in this paper.

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

“…Few Pythium genes are involved in the metabolism of xyloglucan, xylan, mannose, and cutin. In fact, the variable distribution of these genes in different species of Pythium coincides with the polyphyletic nature of the genus [14], [15], [18]. Genes related to the oomycete cell wall metabolism are predominant in all CAZyomes, but differential expansion of some classes of genes was observed in the genomes of oomycetes.…”

“…1 and Table S1). Pyve is closely related to Phytophthora species [18] and Pyar and Pyap are part of a separate clade of Pythium species (Fig. 1).…”

“…However, molecular studies indicate that the genus-level taxonomy of some of the clades is questionable [14], [16], [17]. For example, species belonging to clade K fit better in the description of the new genus Phytopythium than Pythium [15], [18], [19] and further taxonomic revisions within the genus are likely to be necessary [20]. Pythium spp.…”

Pythium cederbergensesp. nov. and related taxa fromPythiumclade G associated with the South African indigenous plantAspalathus linearis(rooibos)

“…To address such problems, Taylor et al (2000) proposed the use of multiple genes in an approach called genealogical concordance phylogenetic species recognition (GCPSR) whereby phylogenetic species are recognized based on the concordance of multigene phylogenies. Aside from ITS, other gene regions that have been used to a limited extent for species recognition in Pythium include COX1, COX2 and btubulin (Martin 2000;Garzó n et al 2005Garzó n et al , 2007Villa et al 2006;Belbahri et al 2008;Moralejo et al 2008;Bala et al 2010;Robideau et al 2011;Spies et al 2011a, b). Of these, the ITS and mitochondrial COX2 regions have proven useful in several taxonomic studies (Matsumoto et al 1999, Martin 2000, Lévesque and de Cock 2004, whereas COX1 and the ITS regions are now recognized Pythium DNA bar-coding regions (Bala et al 2011, Robideau et al 2011.…”

An annotated checklist ofPythiumspecies from Iran

“…However, there have not been sufficient variation in ITS region in some morphologically distinct species (Levesque and De Cock 2004;Long et al 2010) and intra-specific heterogeneity of ITS sequences in some species (Kageyama et al 2007;Belbahri et al 2008;McLeod et al 2009;Senda et al 2009). Bala et al (2010) pointed out that ITS region and cytochrome c oxidase subunit 1 (COXI) gene could provide good species recognition and have widely been used as DNA barcodes for the species identification in the genus Pythium. Therefore, Pythium species can be accurately identified by the combination of morphological characteristics and DNA sequence data (Nechwatal et al 2005;Garzon et al 2007;Moralejo et al 2008;Uzuhashi et al 2009).…”