Molecular analyses of Pythium irregulare isolates from grapevines in South Africa suggest a single variable species

Spies, Chris; Mazzola, Mark; Botha, W. J.; Langenhoven, Shaun D.; Mostert, Lizel; McLeod, A.

doi:10.1016/j.funbio.2011.08.006

Cited by 27 publications

(16 citation statements)

References 70 publications

(115 reference statements)

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“…Several other species are indistinguishable even when both ITS and cox1 sequences are compared (see Text S1B of Robideau et al 2011), and many of these should probably be formally synonymized pending more thorough investigations with multiple hypervariable genes. This approach should also resolve species complexes found in the group formed by P. irregulare, P. paroecandrum, P. cylindrosporum, P. cryptoirregulare and P. mamillatum (Barr et al 1997;Matsumoto et al 2000;Garzón et al 2007;Spies et al 2011a), the varieties of P. ultimum (Barr et al 1996), and the P. vexans and P. cucurbitacearum group (Spies et al 2011b). Some species epithets have been applied to multiple phylogenetic species due to imprecise species descriptions and/or misidentifications.…”

Section: Species Identification and Numbersmentioning

confidence: 99%

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

et al. 2014

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Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineagespecific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae,

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Section: Species Identification and Numbersmentioning

confidence: 99%

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

et al. 2014

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“…This democratization of taxonomy is a positive step, especially with so many undescribed species present in the world that need to be documented, however, good science should prevail and describing a new species with a single strain that has a few base pair differences in its ITS sequence compared to an ex-type should be avoided. Spies et al (2011) clearly demonstrated that there is gene flow among some of the newly described species within the Pythium irregulare complex. If molecular phylogeny becomes the new approach to define new species, the phylogenetic species concept based on multiple gene phylogeny should be applied (Taylor et al 2000).…”

Section: New Species Discoverymentioning

confidence: 89%

Fifty years of oomycetes—from consolidation to evolutionary and genomic exploration

Lévesque

2011

Fungal Diversity

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Transformative changes in biological sciences during the past 25 years have led to many significant advances in oomycete research. Before the last half century there were some hints that the oomycetes were related to some algae but it is now definitively demonstrated that they do not share an evolutionary path with kingdom Eumycota and are instead placed in a new kingdom Straminipila. Clarifying this once and for all has created many opportunities, but the rapid expansion of the research community has caused some fragmentation, probably much more so than in other groups of fungi because of a lack of a unifying forum for the members of the community working on issues such as taxonomy or phylogeny. Prior to the advent of molecular phylogenetics, mycologists working in zoosporic fungi were examining the ultrastructure of the zoospore, mainly focussing on the flagellar apparatus, and managed to generate phylogenies or define clades of zoospore producing fungi that remained for the most part valid after the advances in molecular biology. Comprehensive molecular phylogenies that have been published for some genera of the oomycetes have helped in recognising a large number of new species and in the development of a wide range of DNA-based diagnostic tools. The number of genomes available for this group is increasing rapidly, pushing further the discoveries of novel host-parasite interaction mechanisms in oomycetes. Some important plant diseases that were believed to be under control have re-emerged and many new diseases have appeared particularly in forestry and even in mammals. The research community has been able to respond rapidly and effectively to these new challenges. New ecological roles for the oomycetes were found in the suppression of plant diseases and reduction of plant invasineness in natural ecosystems. There are still many challenges ahead in the oomycete community, probably the most pressing one is to establish a robust tree of life foundation like the Assembling the Fungal Tree of Life initiative. The oomycete research community is dynamic and has put to very good use the many new technological advances.

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“…Pythium RB I that has been described as Pythium cederbergense and Pythium RB II). Spies et al (2011c). The latter isolate is no longer available in culture because it died in storage.…”

Section: Methodsmentioning

confidence: 99%

“…Some of the Pythium clades identified by Lévesque and de Cock (2004) have been studied in more detail than others. For example, several studies are available on clade F species (Matsumoto et al 2000;Garzó n et al 2005Garzó n et al , 2007Spies et al 2011a), whereas less is known about clade G species. Clade G is small and contains only seven known species including Pythium canariense B.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2013

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The genus Pythium consists of more than 120 species and is subdivided into 11 phylogenetic clades (A-K) based on internal transcribed spacer (ITS) region sequence data. Pythium clade G contains only seven known species, with most not being well described. Our study characterized 12 Pythium isolates from Aspalathus linearis (rooibos) that fit into clade G. Phylogenetic analyses of the ITS region and a combined phylogeny of four gene regions (ITS, β-tubulin, COX1 and COX2 [cytochrome c oxidase subunits I, II]) identified five clade G subclades. The rooibos isolates formed two groups, Pythium Rooibos I (RB I) and II (RB II), that clustered into two separate clades within subclade 1. The nine Pythium RB I isolates formed a distinct clade from P. iwayamai and is described here as a new species, Pythium cederbergense sp. nov. The three Pythium RB II isolates had P. canariense and P. violae as their closest relatives and were genetically diverse, suggesting the presence of several new species or a species complex that cannot be resolved with the current data, thus precluding a species description of this group. Morphological analyses showed that P. cederbergense and Pythium RB II were indistinguishable from each other but distinct from known clade G species. Clade G studies are being hampered by imprecise morphological descriptions of P. violae, P. canariense and P. iwayamai and each species being represented by only one isolate. The P. cederbergense and Pythium RB II isolates all were nonpathogenic toward rooibos, lupin and oats seedlings. One oligonucleotide was developed for each of P. cederbergense and Pythium RB II, which was able to differentiate the isolates with DNA macro-array analyses.

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Molecular analyses of Pythium irregulare isolates from grapevines in South Africa suggest a single variable species

Cited by 27 publications

References 70 publications

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

Fifty years of oomycetes—from consolidation to evolutionary and genomic exploration

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

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