Phylogenetic Relationships among Phytophthora Species Inferred from Sequence Analysis of Mitochondrially Encoded Cytochrome Oxidase I and II Genes

Martin, Frank N.; Tooley, Paul W.

doi:10.2307/3762038

Cited by 187 publications

(170 citation statements)

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“…Moreover, because the gene is encoded in mitochondria, it may clarify phylogenic relationships among the species in relation to another genetic background. In species of both Pythium and Phytophthora, sequence analyses of the COX II gene corroborates findings from sequence analysis of the ITS region (Martin 2000;Martin and Tooley 2003).…”

Section: Introductionsupporting

confidence: 77%

Phylogenetic and morphological analyses of Pythium graminicola and related species

et al. 2005

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Isolates of Pythium graminicola and related species were differentiated using restriction fragment length polymorphism (RFLP) analyses of the internal transcribed spacer (ITS) regions of rDNA and the cytochrome c oxidase subunit II (COX II) gene. These sequences were used in subsequent phylogenetic analyses. Finally, the phylogenetic placement of species was compared to that determined from morphological characteristics. The 62 isolates tested were divided into seven groups, A-G, based on RFLP analysis of the rDNA-ITS region. In the RFLP analysis of the COX II gene, isolates were divided into groups similar to those based on ITS-RFLP. Groups A and B were each separated into two additional subgroups. Grouping of isolates based on RFLP analyses agreed with the morphological differentiation. Groups A, B, D, E, F, and G were identified as P. graminicola, P. arrhenomanes, P. aphanidermatum, P. myriotylum, P. torulosum, and P. vanterpoolii, respectively. Group C was closely related to group B based on phylogenetic analysis of the rDNA-ITS region and the COX II gene and is similar to P. arrhenomanes. Each of the other species occupied their own individual clades. Although P. arrhenomanes is morphologically similar to P. graminicola, our phylogenetic analyses revealed that it was evolutionarily distant from P. graminicola and more closely related to P. vanterpoolii. Our analysis also revealed that P. torulosum with smaller oogonia is more closely related to P. myriotylum with large oogonia than to P. vanterpoolii, which forms smaller oogonia and is morphologically similar to P. torulosum. P. aphanidermatum with large oogonia and aplerotic oospores was not related to the morphologically similar species P. myriotylum. Results suggest that P. graminicola and related species are phylogenetically distinct, and molecular analyses, in addition to morphological analyses, are necessary for the accurate taxonomic placement of species in this complex.

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Section: Introductionsupporting

confidence: 77%

Phylogenetic and morphological analyses of Pythium graminicola and related species

et al. 2005

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“…The mitochondrial cytochrome oxidase c subunit I gene (coxI) was amplified for all isolates with primers FM84 and FM83 (Martin and Tooley 2003) to screen for various groupings or species. In addition, the internal transcribed spacers (ITS1-5.8S-1TS2) region of the nuc rDNA (ITS) was amplified for representative isolates in each group, with the ITS6 and ITS4 primers (White et al 1990, Cooke et al 2000.…”

Section: Methodsmentioning

confidence: 99%

“…PCR mixtures contained 13 PCR reaction buffer (Roche Diagnostics, Mannheim, Germany), 2 mM MgCl 2 (Roche Diagnostics, Mannheim, Germany), 2.5 units FastStart Taq DNA polymerase (Roche Diagnostics, Mannheim, Germany), 200 mM of each dNTP, 0.45 mM of each primer, 2 mL template DNA (20-50 ng) and sterile water to a final volume of 25 mL and were performed in a 2720 thermal-cycler (Applied Biosystems, Foster City, California). PCR conditions were the same as those used in previous studies for ITS (Cooke et al 2000, Martin andTooley 2003). All DNA and PCR samples were electrophoretically analyzed on a 1.5 % agarose gel using gel red (Biotium, Hayward, California) as fluorescent dye and viewed under UV illumination.…”

Section: Methodsmentioning

confidence: 99%

MultiplePhytophthoraspecies associated with a single riparian ecosystem in South Africa

Nagel¹,

Slippers²,

Wingfield

et al. 2015

Mycologia

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The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke's ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally.

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“…Ten clades were proposed for genus Phytophthora after phylogenetic analyses of mitochondrial and nuclear DNA sequences (Cooke et al 2000, Martin and Tooley 2003, Kroon et al 2004, Villa et al 2006, Blair et al 2008, Robideau et al 2011. By taking advantage of the phylogenetic analyses, many new species have been separated from some well known species complexes.…”

Section: Introductionmentioning

confidence: 99%

A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov.

2014

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A previously unknown Phytophthora species was isolated from irrigation water in Virginia, USA. This novel species produces abundant noncaducous and nonpapillate sporangia in soil water extract solution. It sometimes produces chlamydospores and hyphal swellings in aged cultures and in Petri's solution. This species has optimum vegetative growth at 30 C and grows well at 35 C. The lowest and highest temperatures for growth are 5 and 40 C. All isolates examined in this study are compatibility type A1 and produce mostly plerotic oospores when paired with an A2 mating-type tester of P. cinnamomi. Sequence analyses of the rDNA internal transcribed spacer (ITS) regions and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene placed this species in clade 9 of the genus Phytophthora. These characteristics support the description of this taxon as a new species for which we propose the name P. hydrogena sp. nov. Further phylogenetic and physiological investigations of clade 9 species revealed a high-temperature tolerant cluster including P. hydrogena, P. aquimorbida, P. hydropathica, P. irrigata, P. chrysanthemi, P. insolita, P. polonica and P. parsiana. These species all grow well at 35 C. The monophyly of the species in this heat-tolerant cluster except P. insolita and P. polonica is highly supported by the maximum-likelihood analyses of the ITS and cox 1 sequences.

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Phylogenetic Relationships among Phytophthora Species Inferred from Sequence Analysis of Mitochondrially Encoded Cytochrome Oxidase I and II Genes

Cited by 187 publications

References 0 publications

Phylogenetic and morphological analyses of Pythium graminicola and related species

Phylogenetic and morphological analyses of Pythium graminicola and related species

MultiplePhytophthoraspecies associated with a single riparian ecosystem in South Africa

A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov.

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