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Phylogenetic analysis of 58 Pythium and 17 Phytophthora isolates based on partial b-tubulin gene sequences using PAUP. Numbers on the branches represent bootstrap values obtained from 1000 replications (only values greater than 50% are shown).
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Fifty-eight isolates representing 39 Pythium species and 17 isolates representing nine Phytophthora species were chosen to investigate intra- and intergeneric relationships with sequence analysis of three genomic areas. The internal transcribed spacer regions (ITS1 and ITS2), including the 5.8S gene of the ribosomal DNA were PCR amplified with the...
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... in the ITS region, gaps were not observed in the 563 bp cox II sequence alignments. Of the 249 variable characters in the alignment of the cox II gene 180 (72.3%) parsimony informative characters were used for the phylogenetic analyses. The remaining 69 uninformative characters were excluded for the parsimony analysis. The strict consensus tree is shown (FIG. 3). Bootstrap supports of more than 50% are ...
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... the cox II gene there were no gaps in the alignment of the 658 bp of the partial b-tubulin gene sequence. A total of 224 variable characters were found, and of these 203 were parsimony informative and included in the phylogenetic analyses. The strict consensus tree with the bootstrap values on its nodes is provided (FIG. ...
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Phylogenetic relationships among 50 Phytophthora species and between Phytophthora and other oomycetes were examined on the basis of the ITS sequences of genomic rDNA. Phytophthora grouped with Pythium, Peronospora, and Halophytophthora, distant from genera in the Saprolegniales. Albugo was intermediate between these two groups. Unlike Pythium, Phyt...
A description is given of Pythium litorale sp. nov., a new species from reed stands in Germany. Pythium litorale was among the most abundant species when the oomycete community of littoral soils of Lake Constance was studied. It was consistently isolated from flooded as well as from drier reed sites. The species is characterized by subglobose, papi...
Citations
... The ITS regions of the rDNA and mitochondrial cytochrome c oxidase subunit II (cox2) were amplified by PCR as described by Oliveira et al. (2014) for ITS and Salmaninezhad and Mostowfizadeh-Ghalamfarsa (2019) for cox2. The amplicons were then sequenced using, respectively, ITS1/ITS4 primer pairs (White et al. 1990) and FM66/FM58 (Villa et al. 2006) and electrophoretic capillary separation in an ABI 3500 Genetic Analyzer (Thermo Fisher Scientific, Waltham, MA, USA) at the Biosciences Center's Multiuser Platform for DNA Sequencing, Federal University of Pernambuco, Recife, Brazil. The generated sequences were deposited in GenBank (ITS: OQ845776; cox2: OQ851471). ...
In February 2021, damping off and collar and root rot on coriander (Coriandrum sativum L.) became widespread in the
municipality of Vitória da Conquista, Bahia, Brazil. An oomycete was isolated from root and collar segments of affected
seedlings and caused the same symptoms in inoculated seedlings. Based on morphological features and DNA sequences
from the ITS and cox2 region, the pathogen was identified as Pythium aphanidermatum. To the best of our knowledge,
this is the first report of the occurrence of P. aphanidermatum on coriander plants in Brazil.
... While pathogen identity was not confirmed in this study by isolations or molecular identification of the pathogen which provides more precise evaluations (Brasier et al. 2004;Villa et al. 2006), the utilized tests are verified by the manufacturer as well as other published studies to be specific for detecting the Phytophthora genus (Lane et al. 2007;Vannini et al. 2013;Parke et al. 2019). However, another sister genus of Phytophthora might also interfere with the results obtained (i.e. ...
... Nuclear ribosomal DNA internal transcribed spacer (ITS) and genes coding for subunit 2 of β-tubulin (β-TUB II), elongation factor 1-α (EF1α) and glycerol-3phosphate dehydrogenase (GPDH) are frequently considered for fungal identification at the genus and species level and to explain the evolutionary relationships among species [14][15][16][17]. These molecular markers have also been used in various studies to highlight intraspecific variability [18][19][20][21][22][23][24][25][26][27][28]. For these reasons, one of the aims of this study was to evaluate the genetic variability amongst 47 isolates of C. camelliae from 13 worldwide localities by comparing the nucleotide sequences related to these regions. ...
Ciborinia camelliae Kohn is the causal agent of camellia flower blight. The fungus infects only the flowers of camellias. C. camelliae isolates obtained from symptomatic samples, collected in 13 different localities worldwide, were characterized by Multi-Locus Sequence Typing (MLST) using the following: (i) a nuclear ribosomal DNA internal transcribed spacer; (ii) subunit 2 of β-tubulin (β-TUB II), (iii) elongation factor 1-α (EF1α); and (iv) glycerol-3-phosphate dehydrogenase (GPDH). The variability of the strains was assessed using a universally primed–polymerase chain reaction (UP-PCR) with six universal primers. Gene sequence comparison showed high similarity among all the European strains and highlighted the diversity of the New Zealand and Chinese representative strains. The profiles obtained by UP-PCR confirmed the significant diversity of extra-European strains and identified subgroups within the European population. The presence of shared genetic profiles obtained from strains isolated in different countries (New Zealand and France) suggests the movement of strains from one location to another, which is probably due to the exchange of infected plant material. Moreover, our study shows the overall high intraspecific variability of C. camelliae, which is likely due to the sexual reproduction of the fungus, suggesting the risk of emergence of new pathotypes adapting to novel camellia varieties.
... These phylogenies consider both morphological and physiological traits as well as nucleotide sequence data. In addition to the originallyused Internal Transcribed Spacer (ITS) region sequence data from other DNA regions including mitochondrially encoded cytochrome oxidase, cox I and II (Martin and Tooley, 2003;Robideau et al., 2011) and b-tubulin (Villa et al., 2006) are now used. Rigorous databases for this information have also been established to guide accurate species identifications for Phytophthora at least (e.g. ...
Monitoring oomycete populations and communities in bodies of water is vital in developing our understanding of this important group of fungus-like protists that contains many serious pathogens of both crops and wild plants. The methodologies involved in monitoring oomycetes are often presented as a developmental hierarchy, progressing from ‘traditional’ culture-based techniques through immunological techniques and basic PCR to qPCR and metagenomics. Here, techniques are assessed according to the roles they can perform in relation to four stages of the monitoring process: capture, detection and identification, viability determination, and quantification. Possible synergies are then considered for the combined use of different techniques in addressing the various needs relating to different questions asked of monitoring, with an emphasis on the continuing value of cultural and immunodiagnostic procedures. Additionally, the exciting future presented by the ongoing development and improvement of metabarcoding and the use of high throughput sequencing techniques in the measurement and monitoring of oomycete inoculum to determine and mitigate plant disease risks is addressed.
... KEYWORDS: Pythium spp., chromista, oomycetes, soilborne phytopathogens, pathosystem. permitindo uma identificação mais rápida, precisa e confiável (MARTIN 2000;VILLA et al. 2006;RO-BIDEAU et al. 2011). Apesar desse avanço, a taxonomia de Pythium ainda permanece um desafio. ...
... O gene da citocromo oxidase II (cox II) tem sido útil na exploração das relações entre organismos semelhantes, especialmente ao nível de taxa subgenéricos ou inferiores (VILLA et al. 2006). O gene β-tubulina codifica uma de duas famílias conservadas de tubulinas, os blocos constituintes dos microtubulos que fazem parte da constituição do citoesqueleto e flagelos das células eucarióticas. ...
... Ao todo, 11 clados menores foram reconhecidos (A-K), que frequentemente se correlacionavam com o hospe-deiro, e muitas vezes com um subconjunto de caracteres morfológicos, mas muitos caracteres usados nas descrições das espécies, como a posição do anterídio, não se correlacionaram com a filogenia (LÉ-VESQUE & DE COCK 2004). Villa et al. (2006), ao analisarem sequências nucleotídicas das regiões gênicas ITS, Cox II e β-tubulina de isolados de Pythium e Phytophthora, distinguiram quatro clados, os quais foram condizentes com a morfologia dos esporângios. ...
Pythium is one of the microorganisms of greatest agricultural interest in the world. Most of the species of this genus are natural inhabitants of the soil with a high capacity for surviving even in the absence of hosts, either as saprophytes or by means of resistance structures. Pythium species can cause plant diseases, such as seedling damping off and leaf blights, as well as root, stem, branch and fruit rots. Several environmental factors differentially modulate the behavior of Pythium species, especially humidity, temperature and soil pH. Most species of this genus are polyphagous and produce resistance structures, what makes difficult to manage the diseases they cause. In this sense, management should be based mainly on the adoption of preventive measures, in order to create a less favorable environment for spread, establishment, multiplication and infection. The genus Pythium was created by Pringsheim in 1858. Since then, much has been added in terms of knowledge about the etiology, epidemiology and management of the diseases caused by this pathogen. With the development and improvement of molecular biology techniques, there was an astonishing advance in understanding the biology, physiology and genetic variability of the genus and its species, which contributed to the phylogenetic studies involving Pythium spp. The demand for new research in these areas of study will always be in vogue, as organisms are subject to constant evolutionary processes. This review presents the state of the art on the advances in studies involving the genus Pythium with a view to fostering new lines of research aimed at the ultimate goal of controlling the diseases caused by this pathogenic oomycete.
... Advances in molecular techniques have enabled more in-depth examinations of phylogenetic relationships within various groups of microorganisms including oomycetes [45,46]. Among the available genetic markers used for oomycete phylogeny, the rapidly evolving, non-coding internal transcribed spacer region (ITS 1 and ITS 2) of ribosomal DNA has been one of the most common choices for high sequence variability and availability of primers [47,48]. ...
The oomycete genus Phytophthora includes many plant pathogens important in agricultural and environmental systems. Natural interspecific hybridization has been reported several times in Phytophthora, and although the fundamental processes of interspecific hybridization and the consequences of subsequent ecological distribution are poorly understood, reports suggest some hybrids can infect a broader host range and display enhanced virulence compared to the putative parental species. During a survey carried out at the University of Aberdeen in 2014–2015, of oomycetes present in ornamental plants purchased via the internet, a batch of oomycete isolates remained unidentified, showing, in some isolates, features generally related to hybridization. The aim of this study was to determine whether hybridization events had occurred between endemic and introduced oomycetes, probably/possibly facilitated through the international plant trade. The list of isolates examined included a putative hybrid closely related to Phytophthora cryptogea. The putative hybrid isolate was further characterized, and pathogenicity were tests carried out on Eucalyptus globulus, using an isolate of P. cryptogea as a positive control. Cloning of ITS, COXI and β-tubulin genes resulted in different sequence versions of the putative hybrid isolate; after mapping and a polymorphism position comparison, it was concluded that the studied isolate contained genetic information from P. cryptogea, P. erythroseptica, P. kelmanii, P. sansomeana and Phytopythium chamaehyphon. A PCR-RFLP assay, a NEBcutter analysis and flow cytometry analysis (genomes ranged between 0.168 to 0.269 pg/2C) added further evidence of the hybrid nature of this isolate. The putative hybrid presented complex growing patterns ranging from rosaceous to chrysanthemum-like and had an optimum growth temperature of 25 °C. Although the putative hybrid produced visible symptoms of disease on E. globulus seedlings, assessment of the relative susceptibility of E. globulus to P. cryptogea and the putative hybrid indicated that P. cryptogea was significantly more virulent than the putative hybrid, based on mortality, disease severity and foliar symptoms.
... They also argued J. Fungi 2023, 9,517 2 of 23 that paraphyletic jumps, such as the emergence of descendants with a new lifestyle (the DMs) from an ancestral and evolutionary successful, cohesive genus (Phytophthora), should be considered a normal feature of evolution. Unlike Phytophthora, the genus Pythium was, in multigene phylogenetic analyses, shown to be polyphyletic [10,12,[17][18][19] and, consequently, divided into Pythium sensu stricto and four new genera, i.e., Phytopythium (syn. Ovatisporangium), Elongisporangium, Globisporangium and Pilasporangium [20][21][22][23]. ...
During a survey of Phytophthora diversity in Panama, fast-growing oomycete isolates were obtained from naturally fallen leaves of an unidentified tree species in a tropical cloud forest. Phylogenetic analyses of sequences from the nuclear ITS, LSU and ßtub loci and the mitochondrial cox1 and cox2 genes revealed that they belong to a new species of a new genus, officially described here as Synchrospora gen. nov., which resided as a basal genus within the Peronosporaceae. The type species S. medusiformis has unique morphological characteristics. The sporangiophores show determinate growth, multifurcating at the end, forming a stunted, candelabra-like apex from which multiple (8 to >100) long, curved pedicels are growing simultaneously in a medusa-like way. The caducous papillate sporangia mature and are shed synchronously. The breeding system is homothallic, hence more inbreeding than outcrossing, with smooth-walled oogonia, plerotic oospores and paragynous antheridia. Optimum and maximum temperatures for growth are 22.5 and 25–27.5 °C, consistent with its natural cloud forest habitat. It is concluded that S. medusiformis as adapted to a lifestyle as a canopy-dwelling leaf pathogen in tropical cloud forests. More oomycete explorations in the canopies of tropical rainforests and cloud forests are needed to elucidate the diversity, host associations and ecological roles of oomycetes and, in particular, S. medusiformis and possibly other Synchrospora taxa in this as yet under-explored habitat.
... Phytopythium is a recently established genus between Phytophthora and Pythium in terms of age, with similar characteristics. The sporangia of Phytopythium are more similar to those of Phytophthora, and the mode of discharge of zoospores, zoospores being created in the vesicle, is similar to that of Pythium [20][21][22]. The classification of taxa in the genus Pythium was revised on the basis of morphological differences in sporangia and the phylogenetic analysis of the LSU rDNA and coxI mDNA regions, from which four new genera were established: Ovatisporangium, Globisporangium, Elongisporangium, and Pilasporangium [23]. ...
As a famous street tree, camphor (Cinnamomum camphora) is widely planted worldwide. However, in recent years, camphor with root rot was observed in Anhui Province, China. Based on morphological characterization, thirty virulent isolates were identified as Phytopythium species. Phylogenetic analysis of combined ITS, LSU rDNA, β-tubulin, coxI, and coxII sequences assigned the isolates to Phytopythium vexans. Koch’s postulates were fulfilled in the greenhouse, and the pathogenicity of P. vexans was determined by root inoculation tests on 2-year-old camphor seedlings; the symptoms of indoor inoculation were consistent with those in the field. P. vexans can grow at 15–30 °C, with an optimal growth temperature of 25–30 °C. The results of fungicide sensitivity experiments indicated that P. vexans was the most sensitive to metalaxyl hymexazol, which may be a useful idea for the future prevention and control management of P.vexans. This study provided the first step for further research on P. vexans as a pathogen of camphor, and provided a theoretical basis for future control strategies.
... ITS sequences and the Cox1 gene have become powerful tools to identify Pythium species [13,17]. Therefore, a phylogenetic analysis was inferred from the combined ITS and Cox1 dataset to explore the relationships of uncertain species within taxa in Pythium. ...
... Maximum parsimony (MP) analysis was applied to the combined datasets of ITS and Cox1 sequences. Two isolates of Saprolegnia parasitica Coker were used as outgroups [17]. The tree-construction procedure was performed in PAUP* version 4.0b10 [18]. ...
Two new species of Globisporangium, G. pengfuense and G. tenuihyphum, that were isolated from soybean in China are described and illustrated based on their morphological characters and molecular evidence. The characteristics of G. pengfuense include globose to sub-globose sporangia that are: catenulate, terminal, occasionally with apical papillae or intercalary, smooth oogonia, mostly monoclinous, occasionally diclinous antheridia, fist-shaped to crook-necked, with straight or curved antheridial cells, and plerotic or nearly plerotic with thin-walled oospores (0.5–1.0 µm). Globisporangium tenuihyphum differs from other species in this genus by its relatively narrow hyphae that are: mostly sub-globose to globose, occasionally ovoid-obpyriform sporangia, smooth oogonia, monoclinous antheridia, subclavate, falcate or semicircular to subcircular antheridial cells, and with aplerotic oospores. Phylogenetically, data from the combined internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (Cox1) sequences support the designation of G. pengfuense and G. tenuihyphum as two distinct species of Globisporangium (Pythium sensu lato clades G and J). In addition, the two new species were compared to closely related Globisporangium species, to delineate their phylogenetic positions and morphological features.
... There were no phylogenetic relationships among isolates by host or geographic region of origin (Figs 1 and 2). The topology of the phylogenetic tree of the genus Pythium showed a division of species into 11 distinct clades, named as A to K, that correspond to the sporangium morphology: a monophyletic group composed of species with filamentous sporangia and another monophyletic group formed by clades containing species with globose sporangia as previously mentioned by Matsumoto et al. (2000), L evesque and de Cock (2004) and Villa et al. (2006). The K clade is phylogenetically more distant from the other clades and the species from this clade were transferred to the genus Phytopythium (Bala et al. 2010b;de Cock et al. 2015;Jesus et al. 2016). ...
This study aimed to identify Pythium and Phytopythium species from weeds collected in vegetable fields and test their pathogenicity. Weeds with symptoms of damping‐off, root rot, or wilt were sampled in the Brazilian states of Ceará, Goiás and Pernambuco, as well as in the Distrito Federal, for isolation and identification of the causal agents. Once isolated, colonies with typical Pythium and Phytopythium characteristics grew in selective V8 medium. Procedures for species identification included morphology and amplification of the ITS and Cox II regions, which were compared with reference sequences available at GenBank. The phylogenetic relationships among the isolates and pathogenicity to their original hosts were evaluated. Six Pythium species were identified: P. aphanidermatum, P. oopapillum, P. orthogonon, P. ultimum var. ultimum, P. myriotylum and P. sylvaticum, and two species of Phytopythium, Phy. chamaehyphon and Phy. oedochilum. In the pathogenicity tests, the ten weed hosts showed symptoms of damping‐off or root rot after inoculation, with exception of Portulaca oleraceae in which none of the isolates was pathogenic. Therefore, common weeds in vegetable fields areas can host different Pythium and Phytopythium species and play an important role in the epidemiology of vegetable diseases, in particular on pathogen survival and population increase.
