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Brasier C, Scanu B, Cooke D, Jung T. Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation. IMA Fungus 2022; 13:12. [PMID: 35761420 PMCID: PMC9235178 DOI: 10.1186/s43008-022-00097-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
The considerable economic and social impact of the oomycete genus Phytophthora is well known. In response to evidence that all downy mildews (DMs) reside phylogenetically within Phytophthora, rendering Phytophthora paraphyletic, a proposal has been made to split the genus into multiple new genera. We have reviewed the status of the genus and its relationship to the DMs. Despite a substantial increase in the number of described species and improvements in molecular phylogeny the Phytophthora clade structure has remained stable since first demonstrated in 2000. Currently some 200 species are distributed across twelve major clades in a relatively tight monophyletic cluster. In our assessment of 196 species for twenty morphological and behavioural criteria the clades show good biological cohesion. Saprotrophy, necrotrophy and hemi-biotrophy of woody and non-woody roots, stems and foliage occurs across the clades. Phylogenetically less related clades often show strong phenotypic and behavioural similarities and no one clade or group of clades shows the synapomorphies that might justify a unique generic status. We propose the clades arose from the migration and worldwide radiation ~ 140 Mya (million years ago) of an ancestral Gondwanan Phytophthora population, resulting in geographic isolation and clade divergence through drift on the diverging continents combined with adaptation to local hosts, climatic zones and habitats. The extraordinary flexibility of the genus may account for its global 'success'. The 20 genera of the obligately biotrophic, angiosperm-foliage specialised DMs evolved from Phytophthora at least twice via convergent evolution, making the DMs as a group polyphyletic and Phytophthora paraphyletic in cladistic terms. The long phylogenetic branches of the DMs indicate this occurred rather rapidly, via paraphyletic evolutionary 'jumps'. Such paraphyly is common in successful organisms. The proposal to divide Phytophthora appears more a device to address the issue of the convergent evolution of the DMs than the structure of Phytophthora per se. We consider it non-Darwinian, putting the emphasis on the emergent groups (the DMs) rather than the progenitor (Phytophthora) and ignoring the evolutionary processes that gave rise to the divergence. Further, the generic concept currently applied to the DMs is narrower than that between some closely related Phytophthora species. Considering the biological and structural cohesion of Phytophthora, its historic and social impacts and its importance in scientific communication and biosecurity protocol, we recommend that the current broad generic concept is retained by the scientific community.
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Affiliation(s)
- Clive Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, UK.
| | - Bruno Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100, Sassari, Italy
| | - David Cooke
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas Jung
- Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, Mendel University in Brno, 613 00, Brno, Czech Republic.
- Phytophthora Research and Consultancy, 83131, Nussdorf, Germany.
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Martin FN, Tooley PW. Phylogenetic relationships amongPhytophthoraspecies inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833112] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Paul W. Tooley
- USDA-ARS, Foreign Disease-Weed Science Research Unit, 1301 Ditto Ave., Fort Detrick, Maryland 21702
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Griffith, Shaw. Polymorphisms in phytophthora infestans: four mitochondrial haplotypes are detected after PCR amplification of DNA from pure cultures or from host lesions. Appl Environ Microbiol 1998; 64:4007-14. [PMID: 9758833 PMCID: PMC106592 DOI: 10.1128/aem.64.10.4007-4014.1998] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/1998] [Accepted: 07/21/1998] [Indexed: 11/20/2022] Open
Abstract
Four pairs of primers were designed for PCR amplification of known polymorphic regions of the mitochondrial genome of Phytophthora infestans. Digestion of the amplified products with restriction enzymes allows identification of previously identified haplotypes. Product P2 cut with MspI uniquely identifies haplotypes Ib and IIa, while types Ia and IIb are differentiated by digestion of product P4 with EcoRI. Digestion of products P1 and P3 gave results similar to that with digestion of P4, but amplification of these products was less robust. Thus, all four common haplotypes are identified by amplifying and digesting products P2 and P4. Identification of haplotypes was also possible from DNA extracted directly from small, late-blight lesions on both tomato and potato leaves, making isolation of the fungus unnecessary. A rapid and efficient method of monitoring changes in the pathogen population is facilitated. These PCR primers were also useful for differentiating other Phytophthora species.
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Affiliation(s)
- Griffith
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, Wales, United Kingdom
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Tooley PW, Bunyard BA, Carras MM, Hatziloukas E. Development of PCR primers from internal transcribed spacer region 2 for detection of Phytophthora species infecting potatoes. Appl Environ Microbiol 1997; 63:1467-75. [PMID: 9097445 PMCID: PMC168442 DOI: 10.1128/aem.63.4.1467-1475.1997] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We developed PCR primers and assay methods to detect and differentiate three Phytophthora species which infect potatoes and cause late blight (Phytophthora infestans) and pink rot (P. erythroseptica and P. nicotianae) diseases. Primers based on sequence analysis of internal transcribed spacer region 2 of ribosomal DNA produced PCR products of 456 bp (P. infestans), 136 bp (P. erythroseptica), and 455 bp (P. nicotianae) and were used to detect the pathogens in potato leaf (P. infestans) and tuber (P. infestans, P. erythroseptica, and P. nicotianae) tissue with a sensitivity of 1 to 10 pg of DNA. Leaf and tuber tissue were processed for PCR by a rapid NaOH method as well as a method based on the use of commercially available ion-exchange columns of P. infestans primers and the rapid NaOH extraction method were used to detect late blight in artificially and naturally infected tubers of potato cultivar Red LaSoda. In sampling studies, P. infestans was detected by PCR from artificially infected tubers at 4 days postinoculation, before any visible symptoms were present. The PCR assay and direct tissue extraction methods provide tools which may be used to detect Phytophthora pathogens in potato seedlots and storages and thus limit the transmission and spread of new, aggressive strains of P. infestans in U.S. potato-growing regions.
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Affiliation(s)
- P W Tooley
- USDA Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Fort Detrick, Frederick, Maryland 21702, USA
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Mochizuki T, Uehara M, Menon T, Ranganathan S. Minipreparation of total cellular DNA is useful as an alternative molecular marker of mitochondrial DNA for the identification of Trichophyton mentagrophytes and T. rubrum. Mycoses 1996; 39:31-5. [PMID: 8786754 DOI: 10.1111/j.1439-0507.1996.tb00080.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Total cellular DNA was extracted from 18 isolates of Trichophyton mentagrophytes and six isolates of unidentified Trichophyton species taken from tinea corporis, tinea cruris and tinea pedis patients by a minipreparation method. The DNA was digested with the restriction enzymes HaeIII and MspI, followed by electrophoresis on agarose gels. The restriction enzyme profiles of the DNAs were compared with those of mitochondrial (mt) DNA extracted from reference strains of T. mentagrophytes (Arthroderma simii, A. benhamiae and A. vanbreuseghemii) and T. rubrum. All 18 T. mentagrophytes isolates showed the same DNA profiles as mtDNA from A. vanbreuseghemii. The six unidentified Trichophyton isolates exhibited DNA profiles the same as that of mtDNA from T. rubrum. Consequently, these isolates were identified as T. rubrum. In conclusion, restriction enzyme analysis of total cellular DNA prepared by the minipreparation method is considered to be useful as an alternative method of mtDNA analysis and is helpful for the identification of these dermatophyte species.
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Affiliation(s)
- T Mochizuki
- Department of Dermatology, Shiga University of Medical Science, Japan
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Béatrice L, Georgios Z. Molecular systematics of the genus Pleurotus: analysis of restriction polymorphisms in ribosomal DNA. Microbiology (Reading) 1995; 141:1479-1490. [DOI: 10.1099/13500872-141-6-1479] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Part of the nuclear ribosomal DNA unit of Pleurotus cornucopiae, including most of the intergenic sequences, was used as a probe to hybridize with DNA from eleven Pleurotus taxa (29 isolates), digested with nine restriction endonucleases. For all digests, a high level of rDNA heterogeneity between and within species was detected, which is in agreement with the phenetic variability already reported in previous studies on Pleurotus taxa. Numerical analysis of the results, performed by use of two different tree-making methods, clearly distinguished among well-defined species, i.e. P. dryinus, P. eryngii and P. flabellatus, which presented large phenetic distances with the rest of the taxa tested. P. abalonus, despite morphological similarity and interfertility with P. cystidiosus, appears to be a discrete taxon. Although they showed relative affinity, P. cornucopiae, P. columbinus and P. ostreatus presented large distances among their representative isolates, supporting the idea that they correspond to distinct taxa. All strains of P. pulmonarius, P. sajor-caju and P. sapidus having small phenetic distances were closely positioned on dendrograms; in relation to results from recent interfertility and isozyme studies, these results support the common genetic background of P. pulmonarius and P. sajor-caju; the position of P. sapidus remains controversial. Furthermore, the rDNA analysis identified ten fragments suitable for species identification: eight allowed the characterization of five taxa (P. cornucopiae. P. ostreatus, P. sajor-caju, P. abalonus and P. columbinus) and two distinguished among clusters including related taxa. By a combination of just two restriction enzymes, the rDNA probe used seems to be the appropriate tool for both varietal characterization and protection of commercially valuable strains.
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Affiliation(s)
| | - Zervakis Georgios
- Laboratoire de Génétique Moléculaire et d'Amélioration des Champignons Cultivés, Université de Bordeaux II -INRA, CRA de Bordeaux, BP 81, 33883 Villenave d'Ornon Cedex, France
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A comparison of morphology, pathogenicity and restriction fragment patterns of mitochondrial DNA among isolates of Phytophthora porri Foister. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf01974386] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Ophiostoma novo-ulmi sp. nov., causative agent of current Dutch elm disease pandemics. Mycopathologia 1991. [DOI: 10.1007/bf00462219] [Citation(s) in RCA: 178] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Use of nuclear DNA restriction fragment length polymorphisms to analyze the diversity of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius. Appl Environ Microbiol 1990; 56:2453-61. [PMID: 1976300 PMCID: PMC184748 DOI: 10.1128/aem.56.8.2453-2461.1990] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recombinant DNA clones carrying high-copy or low-copy sequences from Aspergillus nidulans and Neurospora crassa were used to identify restriction fragment length polymorphisms (RFLPs) diagnostic for members of the A. flavus group: A. flavus, A. parasiticus, and A. nomius. These fungi were resolved into three distinct categories when they were grouped according to RFLP patterns. Subgroups within these categories were also evident. This limited RFLP analysis of nuclear DNA of members of the A. flavus group did not identify any RFLPs that differentiate these isolates on the basis of toxin production, but limited correlation with geographic location was observed.
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Abstract
To assess evolutionary relationships among the oomycetous fungi we have constructed a physical and genic map of the mtDNA of a broad host range strain (695T) of Phytophthora megasperma. While, like other Phytophthora species, this 43.5 kb circular genome lacks the typical oomycete large inverted repeat, a short 0.5-0.9 kb inverted repeat has been identified. Comparison of the relative order of seven genic regions with host-specific Phytophthora strains reveals both a clustering of these loci within one-third of the host-specific genomes, and two genic inversions relative to the broad host range genome. The location of the short inverted repeat suggests that at least one of the inversions is a consequence of intramolecular recombination between repeat elements.
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Affiliation(s)
- D S Shumard-Hudspeth
- Department of Biological Sciences, Northern Illinois University, DeKalb 60115-2861
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Goodwin PH, Kirkpatrick BC, Duniway JM. Identification of
Phytophthora citrophthora
with Cloned DNA Probes. Appl Environ Microbiol 1990; 56:669-74. [PMID: 16348140 PMCID: PMC183403 DOI: 10.1128/aem.56.3.669-674.1990] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two different DNA fragments, one of 2.9 kilobases and the other of 5.1 kilobases, were cloned from
Phytophthora citrophthora
and showed no homology with DNA from plants and other related fungi. These DNA probes hybridized with DNA from 12 different
P. citrophthora
isolates obtained from a variety of hosts but did not hybridize with DNA from 6
P. citrophthora
isolates obtained from cacao. Southern blot analysis revealed that the probes contained repetitive DNA, and restriction fragment length polymorphisms were identified among several
P. citrophthora
isolates. Of the isolates tested, two major groups were observed whose genetic similarity correlated with geographical distribution. One of the DNA probes was used to detect
P. citrophthora
growing from infected citrus roots incubated on semiselective medium.
P. citrophthora
was not detected by a hybridization assay of total DNA extracted directly from infected roots.
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Affiliation(s)
- P H Goodwin
- Department of Environmental Biology, University of Guelph, Guelph, Ontario NIG 2W1, Canada, and Department of Plant Pathology, University of California, Davis, California 95616
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12
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Restriction fragment length polymorphisms in Septoria tritici occur at a high frequency. Curr Genet 1990. [DOI: 10.1007/bf00312858] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Braithwaite KS, Manners JM. Human hypervariable minisatellite probes detect DNA polymorphisms in the fungus Colletotrichum gloeosporioides. Curr Genet 1989. [DOI: 10.1007/bf00340729] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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