Phylogenetic relationships of Pythium species based on ITS and 5.8S sequences of the ribosomal DNA

Abstract

The sequences of ITS regions in 30 species and two groups of the genus Pythium were resolved. In the phylogenetic trees, the species were generally divided into two clusters, referred to here as the F and S groups. The species in the two groups correspond in terms of their sporangial morphology, with the F group being filamentous/Iobulate and the S group being spherical. Genetic divergence within the F group was lower than that within the S group. Other morphological characteristics such as oogonial structure and sexual nature appeared to be unrelated to the groupings in these trees. An alignment analysis revealed common sequences to all the species and arrangements specific to each F or S group. It was found that the ITS region was a good target in designing species-specific primers for the identification and detection of Pythium species. In the tree based on 5.8S rDNA sequences, oomycetes are distantly related to other fungi but separated from algae in Chromista. Key WordsChromista; internal transcribed spacer; phylogeny; Pythium; 5.8S rDNA.Pythium is a large genus of the class Oomycetes including more than 80 species (van der Plaats-Niterink, 1981 ), some of which are important plant pathogens with worldwide distribution. The taxonomy of this genus is mainly based on the morphology of reproductive structures such as the oogonium, oospore, antheridium, and sporangium. Since Matthews (1931) and Sideris (1932) proposed the first keys for Pythium spp., several keys have been published as new species have been described. Researchers providing systematic taxonomy in the genus are Middleton (1943), Waterhouse (1967), and van der Plaats-Niterink (1981). Hendrix and Papa (1974) introduced the concept of 'species complexes' in relation to taxonomy of the genus Pythium. This is an arrangement in which the species of Pythium are lumped into 15 species groups based on their morphological characteristics. In the taxonomic keys for Pythium, the size of each structure and common morphological characteristics are taken as criteria, including: (1) the presence of sexual reproductive structures -homothallic or heterothallic; (2) the sporangial morphology-spherical, filamentous or Iobulate; (3) the oogonial wall charactersmooth or ornamental; (4) the oospore character-plerotic or aplerotic; and (5) the antheridial charactermonoclinous or diclinous, However, each author regarded different characteristics as more important. For example, Middleton (1943) used the sporangial morphology at the first branch, whereas Waterhouse (1967) frequently utilized the reproductive structure size in the separaCorresponding author. E-mail: kageyama(~cc.gifu-u.ac.jp tion of species. Van der Plaats-Niterink (1981) regarded the presence of reproductive structures and the oogonial wall character as more important criteria. These differences in the interpretation of the taxonomic value of each character have resulted in a confusing taxonomic system for the Pythium species. It is therefore necessary to determine which morphological characteristic is the ...

Pythium recalcitranssp. nov. revealed by multigene phylogenetic analysis

“…The molecular phylogenies presented here for the genus Pythium support the recent studies correlating molecular clusters with subgroups defined on sporangial form (Briard et al 1995, Matsumoto et al 1999, Martin and Tooley 2000, Lévesque and de Cock 2004, Villa et al 2006. Based on these results and on our analysis it seems that the classification of oomycetes needs to be revised.…”

Oligonucleotide Array for Identification and Detection of Pythium Species

“…However, there is considerable overlap in the dimensions and shapes of microscopic structures among species and a high potential for errors in identification (11,13). In addition, some important taxonomic characteristics, such as ornamentation of oogonia and heterothallism, appear to have been acquired or lost repeatedly through evolution (33,35). These factors are compounded by a declining number of taxonomists who are capable of identifying fungi to the species level (5).…”

Molecular characterisation, pathogenesis and fungicide sensitivity ofPythiumspp. from table beet (Beta vulgarisvar.vulgaris) grown in the Lockyer Valley, Queensland

“…The ITS region, encompassing the ITS I and ITS II and 5.8S rDNA, is a useful target for characterisation as it is highly conserved within species but has sufficient sequence divergence to enable taxonomic designations to be made between species (Lévesque and de Cock 2004). Although other genes have been the subject of analysis of Pythium spp., most studies have focussed on the ITS region of rDNA, whether it be for the purposes of characterising populations or for the development of diagnostic assays (Matsumoto et al 1999;Paulitz and Adams 2003;Wang and Chang 2003;Wang and White 1997;Weiland and Sundsbak 2000).…”

“…In contrast, DNA-based methods are often rapid and unambiguous, and in many cases do not rely on the culture and propagation of the suspected pathogen. In most of these studies, detection and identification has been based on polymerase chain reaction (PCR) amplification of the internal transcribed spacer (ITS) region of the genomic sequence encoding rRNA genes (rDNA), including one or more of ITS I, ITS II and 5.8S rDNA (Lévesque et al 1998;Matsumoto et al 1999;Moorman et al 2002;Wang and White 1997;Weiland and Sundsbak 2000). Subsequent characterisation of Pythium isolates has been based on RFLP and/or DNA sequence analyses of the PCR amplified region or by hybridisation of the target DNA to arrays of the corresponding region from a range of oömycetes.…”