Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences

Phytophthora Root and Crown Rot of Lavender: New Host-Pathogen Relationships Involving Six Species of Phytophthora and Three Species of Lavandula

Phytophthora root and crown rot has become a major threat to the lavender industry worldwide. Isolations from symptomatic plants between 2015 and 2019 revealed a number of potential causal agents in the United States. In this study, we tested nine species of Phytophthora and four species of Lavandula and used Koch's Postulates to prove pathogenicity for six new host-pathogen relationships and confirm two pathogenic relationships for the first time in the United States. A total of 10 experiments were conducted with each consisting of two independent trials. Only host-pathogen combinations that occurred in the field were evaluated. All isolates used in these experiments were recovered from diseased lavender plants or, for one isolate, soil associated with a diseased plant sent to our lab or the Clemson University Plant and Pest Diagnostic Clinic for diagnosis. Experiments were conducted over 3 years, 2017 to 2019, in a research greenhouse under relatively uniform environmental conditions following a standard protocol. Plants were evaluated weekly for foliage symptom severity, and, at the end of each trial, plants were scored for final foliage symptom severity and root rot severity, area under the disease progress curve was calculated, fresh plant mass was weighed, and isolation of pathogens from roots was attempted. These studies successfully demonstrated for the first time pathogenicity of Phytophthora nicotianae, P. palmivora, and P. cinnamomi to hybrid lavender (Lavandula × intermedia), P. nicotianae to sweet lavender (L. heterophylla), and P. cryptogea and P. drechsleri to English lavender (L. angustifolia). In addition, a soil isolate of P. tropicalis was shown to be potentially pathogenic to L. × intermedia. Our results also documented for the first time in the United States pathogenicity of P. palmivora and P. citrophthora to L. angustifolia. We were not able to confirm pathogenicity for three host-pathogen relationships: P. megasperma on English lavender, P. cactorum on hybrid lavender, and P. nicotianae on Spanish lavender (L. stoechas). Results from this study expand the list of Phytophthora species causing root rot on lavender (Lavandula species) in the United States and elsewhere.

A Survey of Phytophthora spp. in Eastern Indian Nurseries and Their Sensitivity to Six Oomycete-Targeted Commercial Fungicides

A survey of the flori-horticultural nurseries in eastern India found Phytophthora nicotianae to be the most widespread Phytophthora species associated with different foliar symptoms of nursery plants and identified the presence of P. palmivora in eastern Indian nurseries for the first time. The survey also led to the first worldwide finding of P. nicotianae on Dipteracanthus prostratus (Poir.) Nees; Ocimum tenuiflorum L. (syn. Ocimum sanctum L.); Philodendron xanadu Croat, Mayo & J. Boos; and Pyrostegia venusta (Ker-Gawl.) Miers and P. palmivora on Episcia cupreata (Hook.) Hanst., as well as the first report from India of P. nicotianae on Spathiphyllum wallisii Regel; Anthurium andraeanum Linden ex André; and Adenium obesum (Forsk.) Roem. & Schult. Sensitivity to commercial fungicides Glazer 35WS, Rallis India (metalaxyl, FRAC code 4); Ridomil Gold, Syngenta (mefenoxam + mancozeb); Revus, Syngenta (mandipropamid, FRAC code 40); Aliette Bayer (fosetyl-Al, FRAC code 33); Acrobat, BASF (dimethomorph, FRAC code 40); and Amistar, Syngenta (azoxystrobin, FRAC code 11) was analyzed, showing EC50 values ranging from 0.75 to 16.39 ppm, 0.74 to 1.45 ppm, 2.43 to 17.21 ppm, 63.81 to 327.31 ppm, 8.88 to 174.69 ppm, and 0.1 to 1.13 ppm, respectively, with no cross-resistance of the isolates to the fungicides. The baseline information produced about these Phytophthora spp. from ornamental and horticultural host associations could help prevent the pathogens from becoming primary drivers of new disease outbreaks and their large-scale distribution beyond their natural endemic ranges.

Phytophthora × cambivora as a Major Factor Inciting the Decline of European Beech in a Stand within the Southernmost Limit of Its Natural Range in Europe

The objective of this study was to investigate the role of the oomycete Phytophthora× cambivora in the decline affecting European beech (Fagus sylvatica) in the Nebrodi Regional Park (Sicily, southern Italy). In a survey of a beech forest stand in the heart of the park, Phytophthora× cambivora was the sole Phytophthora species recovered from the rhizosphere soil and fine roots of trees. Both A1 and A2 mating type isolates were found. Direct isolation from the stem bark of trees showing severe decline symptoms and bleeding stem cankers yielded exclusively P. gonapodyides, usually considered as an opportunistic pathogen. The mean inoculum density of P.× cambivora in the rhizosphere soil, as determined using the soil dilution plating method and expressed in terms of colony forming units (cfus) per gm of soil, the isolation frequency using leaf baiting, and the percentage of infected fibrous roots from 20 randomly selected beech trees with severe decline symptoms (50 to 100 foliage transparency classes) were 31.7 cfus, 80%, and 48.6%, respectively. These were significantly higher than the corresponding mean values of 20 asymptomatic or slightly declining trees, suggesting P.× cambivora is a major factor responsible for the decline in the surveyed stand.

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa.

Current status of Phytophthora in Australia

Among the most economically relevant and environmentally devastating diseases globally are those caused by Phytophthora species. In Australia, production losses in agriculture and forestry result from several well-known cosmopolitan Phytophthora species and infestation of natural ecosystems by Phytophthora cinnamomi have caused irretrievable loss to biodiversity especially in proteaceous dominated heathlands. For this review, all available records of Phytophthora in Australia were collated and curated, resulting in a database of 7 869 records, of which 2 957 have associated molecular data. Australian databases hold records for 99 species, of which 20 are undescribed. Eight species have no records linked to molecular data, and their presence in Australia is considered doubtful. The 99 species reside in 10 of the 12 clades recognised within the complete phylogeny of Phytophthora. The review includes discussion on each of these species' status and additional information provided for another 29 species of concern. The first species reported in Australia in 1900 was Phytophthora infestans. By 2000, 27 species were known, predominantly from agriculture. The significant increase in species reported in the subsequent 20 years has coincided with extensive surveys in natural ecosystems coupled with molecular taxonomy and the recognition of numerous new phylogenetically distinct but morphologically similar species. Routine and targeted surveys within Australian natural ecosystems have resulted in the description of 27 species since 2009. Due to the new species descriptions over the last 20 years, many older records have been reclassified based on molecular identification. The distribution of records is skewed toward regions with considerable activity in high productivity agriculture, horticulture and forestry, and native vegetation at risk from P. cinnamomi. Native and exotic hosts of different Phytophthora species are found throughout the phylogeny; however, species from clades 1, 7 and 8 are more likely to be associated with exotic hosts. One of the most difficult challenges to overcome when establishing a pest status is a lack of reliable data on the current state of a species in any given country or location. The database compiled here for Australia and the information provided for each species overcomes this challenge. This review will aid federal and state governments in risk assessments and trade negotiations by providing a comprehensive resource on the current status of Phytophthora species in Australia. Citation: Burgess TI, Edwards J, Drenth A, et al. 2021. Current status of Phytophthora in Australia. Persoonia 47: 151-177. https://doi.org/10.3767/persoonia.2021.47.05.

Phytophthora Root and Collar Rot of Paulownia, a New Disease for Europe

Paulownia species are fast growing trees native to China, which are being grown in managed plantings in several European countries for the production of wood and biomasses. In 2018, wilting, stunting, leaf yellowing, and collapse, as a consequence of root and crown rot, were observed in around 40% of trees of a 2-year-old planting of Paulownia elongata × P. fortunei in Calabria (Southern Italy). Two species of Phytophthora were consistently recovered from roots, basal stem bark, and rhizosphere soil of symptomatic trees and were identified as Ph. nicotianae and Ph. palmivora on the basis of both morphological characteristics and phylogenetic analysis of rDNA ITS sequences. Koch’s postulates were fulfilled by reproducing the symptoms on potted paulownia saplings transplanted into infested soil or stem-inoculated by wounding. Both Phytophthora species were pathogenic and caused root rot and stem cankers. Even though P. palmivora was the only species recovered from roots of naturally infected plants, in pathogenicity tests through infested soil P. nicotianae was more virulent. This is the first report of Phytophthora root and crown rot of a Paulownia species in Europe. Strategies to prevent this emerging disease include the use of healthy nursery plants, choice of well-drained soils for new plantations, and proper irrigation management.

Inhibitory Activity of Shrimp Waste Extracts on Fungal and Oomycete Plant Pathogens

(1) Background: This study was aimed at determining the in vitro inhibitory effect of new natural substances obtained by minimal processing from shrimp wastes on fungi and oomycetes in the genera Alternaria, Colletotrichum, Fusarium, Penicillium, Plenodomus and Phytophthora; the effectiveness of the substance with the highest in vitro activity in preventing citrus and apple fruit rot incited by P. digitatum and P. expansum, respectively, was also evaluated. (2) Methods: The four tested substances, water-extract, EtOAc-extract, MetOH-extract and nitric-extract, were analyzed by HPLC-ESI-MS-TOF; in vitro preliminary tests were carried out to determine the minimal inhibitory/fungicidal concentrations (MIC and MFC, respectively) of the raw dry powder, EtOAc-extract, MetOH-extract and nitric-extract for each pathogen. (3) Results: in the agar-diffusion-assay, nitric-extract showed an inhibitory effect on all pathogens, at all concentrations tested (100, 75, 50 and 25%); the maximum activity was on Plenodomus tracheiphilus, C. gloeosporioides and Ph. nicotianae; the diameters of inhibition halos were directly proportional to the extract concentration; values of MIC and MFC of this extract for all pathogens ranged from 2 to 3.5%; the highest concentrations (50 to 100%) tested in vivo were effective in preventing citrus and apple fruit molds. (4) Conclusions: This study contributes to the search for natural and ecofriendly substances for the control of pre- and post-harvest plant pathogens.

Fire Ant Venom Alkaloids: Possible Control Measure for Soilborne and Foliar Plant Pathogens

The purpose of this study was to evaluate fire ant venom alkaloids and an alarm pheromone analog against several plant pathogens, including Botrytis cinerea, Fusarium oxysporum, Phytophthora nicotianae, P. cryptogea, Pseudomonas syringae, Phytopythium citrinum, Rhizoctonia solani, Sclerotonia rolfsii, Xanthomonas axonopodis, and X. campestris. All pathogens were tested against red imported fire ant venom alkaloid extract and alarm pheromone compound for growth inhibition in in vitro assay. The venom alkaloid extract inhibited fungal and oomycete pathogens. Neither of the treatments were effective against bacterial pathogens. Three soilborne pathogens, P. nicotianae, R. solani, F. oxysporum, and one foliar pathogen, B. cinerea were selected for further in-vivo assays on impatiens (Impatiens walleriana ‘Super Elfin XP violet’). Total plant and root weight were higher in venom alkaloid treated plants compared to an inoculated control. The venom alkaloid treatment reduced damping-off, root rot severity, and pathogen recovery in soilborne pathogen inoculated plants. Similarly, venom alkaloid reduced Botrytis blight. However, higher venom rates caused foliar phytotoxicity on plants. Therefore, additional work is needed to evaluate rates of venom alkaloids or formulations to eliminate negative impacts on plants. Overall, these results suggest that red imported fire ant venom alkaloids may provide a basis for new products to control soilborne and foliar plant pathogens.

Insight into the Systematics of Microfungi Colonizing Dead Woody Twigs of Dodonaea viscosa in Honghe (China)

Members of Dodonaea are broadly distributed across subtropical and tropical areas of southwest and southern China. This host provides multiple substrates that can be richly colonized by numerous undescribed fungal species. There is a severe lack of microfungal studies on Dodonaea in China, and consequently, the diversity, phylogeny and taxonomy of these microorganisms are all largely unknown. This paper presents two new genera and four new species in three orders of Dothideomycetes gathered from dead twigs of Dodonaea viscosa in Honghe, China. All new collections were made within a selected area in Honghe from a single Dodonaea sp. This suggests high fungal diversity in the region and the existence of numerous species awaiting discovery. Multiple gene sequences (non-translated loci and protein-coding regions) were analysed with maximum likelihood and Bayesian analyses. Results from the phylogenetic analyses supported placing Haniomyces dodonaeae gen. et sp. in the Teratosphaeriaceae family. Analysis of Rhytidhysteron sequences resulted in Rhytidhysteron hongheense sp. nov., while analysed Lophiostomataceae sequences revealed Lophiomurispora hongheensis gen. et sp. nov. Finally, phylogeny based on a combined dataset of pyrenochaeta-like sequences demonstrates strong statistical support for placing Quixadomyceshongheensis sp. nov. in Parapyrenochaetaceae. Morphological and updated phylogenetic circumscriptions of the new discoveries are also discussed.

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae

Phytophthora nicotianae is highly pathogenic to Solanaceous crops and is a major problem in tobacco production. The tobacco cultivar Beihart1000-1 (BH) is resistant, whereas the Xiaohuangjin 1025 (XHJ) cultivar is susceptible to infection. Here, BH and XHJ were used as models to identify resistant and susceptible genes using RNA sequencing (RNA-seq). Roots were sampled at 0, 6, 12, 24, and 60 h post infection. In total, 23,753 and 25,187 differentially expressed genes (DEGs) were identified in BH and XHJ, respectively. By mapping upregulated DEGs to the KEGG database, changes of the rich factor of "plant pathogen interaction pathway" were corresponded to the infection process. Of all the DEGs in this pathway, 38 were specifically regulated in BH. These genes included 11 disease-resistance proteins, 3 pathogenesis-related proteins, 4 RLP/RLKs, 2 CNGCs, 7 calcium-dependent protein kinases, 4 calcium-binding proteins, 1 mitogen-activated protein kinase kinase, 1 protein EDS1L, 2 WRKY transcription factors, 1 mannosyltransferase, and 1 calmodulin-like protein. By combining the analysis of reported susceptible (S) gene homologs and DEGs in XHJ, 9 S gene homologs were identified, which included 1 calmodulin-binding transcription activator, 1 cyclic nucleotide-gated ion channel, 1 protein trichome birefringence-like protein, 1 plant UBX domain-containing protein, 1 ADP-ribosylation factor GTPase-activating protein, 2 callose synthases, and 2 cellulose synthase A catalytic subunits. qRT-PCR was used to validate the RNA-seq data. The comprehensive transcriptome dataset described here, including candidate resistant and susceptible genes, will provide a valuable resource for breeding tobacco plants resistant to P. nicotianae infections.

Diversity of Phytophthora Communities across Different Types of Mediterranean Vegetation in a Nature Reserve Area

Research Highlights: Protected natural areas are a reservoir of Phytophthora species and represent the most suitable sites to study their ecology, being less disturbed by human activities than other environments. Background and Objectives: The specific objective of this study was to correlate the diversity and distribution of Phytophthora species with the vegetation in aquatic, riparian and terrestrial habitats within a protected area in Eastern Sicily, Southern Italy. Materials and Methods: Environmental samples (water and soil) were sourced from two streams running through the reserve and six different types of vegetation, including Platano-Salicetum pedicellatae, the Sarcopoterium spinosum community, Myrto communis-Pistacietum lentisci, Pistacio-Quercetum ilicis,Oleo-Quercetum virgilianae and a gallery forest dominated by Nerium oleander (Natura 2000 classification of habitats). Phytophthora species were recovered from samples using leaf baiting and were classified on the basis of morphological characteristics and sequencing of internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA). Results: As many as 11 Phytophthora species, within five different ITS clades, were identified, including P. asparagi, P. bilorbang, P. cryptogea, P. gonapodyides, P. lacustris, P. multivora, P. nicotianae, P. oleae, P. parvispora, P. plurivora and P. syringae. No Phytophthora species were found in the Sarcopoterium spinosum comm. Phytophthora asparagi, P. lacustris and P. plurivora were the prevalent species in the other five plant communities, but only P. plurivora was present in all of them. Overall aquatic species from clade 6 (100 out of 228 isolates) were the most common; they were recovered from all five types of vegetation, streams and riparian habitats. Phytophthora populations found in the Platano-Salicetum pedicellatae and Oleo-Quercetum virgilianae show the highest diversity, while no correlation was found with the physicochemical characteristics of the soil. Conclusions: The vegetation type and the aquatic or terrestrial habitat were identified as major environmental factors correlated with the diversity of Phytophthora communities in this reserve.

Genetic Diversity and Population Structure of Pythium irregulare from Soybean and Corn Production Fields in Ohio

High levels of genetic diversity have been described within the Pythium irregulare complex from several host plants; however, little is known about the population structure in fields used for grain production. Therefore, the objective of this study was to evaluate the genetic diversity and population structure of 53 isolates baited from 28 soybean and corn production fields from 25 counties in Ohio. Genetic diversity was characterized based on sequence analysis of the internal transcribed spacer (ITS1-5.8S-ITS2) region and with 21 simple sequence repeat (SSR) markers. In addition, aggressiveness on soybean, optimum growth temperature, and sensitivity to metalaxyl fungicide were determined. ITS sequence analysis indicated that four isolates clustered with P. cryptoirregulare, whereas the remaining isolates clustered with P. irregulare that was subdivided into two groups (1 and 2). Cluster analysis of SSR data revealed a similar subdivision, which was also supported by structure analysis. The isolates from group 2 grew at a slower rate, but both groups of P. irregulare and P. cryptoirregulare recovered in this study had the same optimum growth at 27°C. Variability of aggressiveness and sensitivity toward metalaxyl fungicide was also observed among isolates within each group. The results from this study will help in the selection of isolates to be used in screening for resistance, assessment of fungicide efficacy, and disease management recommendations.

Characterization of the Black Shank Pathogen, Phytophthora nicotianae, Across North Carolina Tobacco Production Areas

Black shank disease of tobacco, caused by the oomycete Phytophthora nicotianae, is a major threat to production in the United States and tobacco-producing areas worldwide. In a statewide survey of North Carolina, the rapid shift from race 0 to race 1 was documented. Collected pathogen isolates were characterized phenotypically for mating type and mefenoxam sensitivity, and genotypically by comparing sequences from three cytoplasmic and two nuclear regions. Both the A1 and A2 mating types were found throughout the state. When both mating types were recovered from the same field, pairings of isolates yielded viable oospores, indicating for the first time the potential for sexual sporulation by P. nicotianae in natural populations. Because the loss of complete resistance required a renewed use of the fungicide mefenoxam, a subset of the survey isolates was screened for sensitivity to the fungicide. All isolates were sensitive, with a mean effective concentration to inhibit 50% of hyphal growth of 0.4 μg/ml that was similar across mating types and races. Molecular characterization of 226 isolates revealed that the pathogen exists as multiple clonal types within the state. Genetic diversity among the pathogen population and the potential for sexual recombination may help explain the ability of the pathogen to rapidly adapt to host resistance genes.

Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms

Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.

Two previously unknown Phytophthora species associated with brown rot of Pomelo (Citrus grandis) fruits in Vietnam

Two distinct Phytophthora taxa were found to be associated with brown rot of pomelo (Citrus grandis), a new disease of this ancestral Citrus species, in the Vinh Long province, Mekong River Delta area, southern Vietnam. On the basis of morphological characters and using the ITS1-5.8S-ITS2 region of the rDNA and the cytochrome oxidase subunit 1 (COI) as barcode genes, one of the two taxa was provisionally named as Phytophthora sp. prodigiosa, being closely related to but distinct from P. insolita, a species in Phytophthora Clade 9, while the other one, was closely related to but distinct from the Clade 2 species P. meadii and was informally designated as Phytophthora sp. mekongensis. Isolates of P. sp. prodigiosa and P. sp. mekongensis were also obtained from necrotic fibrous roots of Volkamer lemon (C. volkameriana) rootstocks grafted with 'King' mandarin (Citrus nobilis) and from trees of pomelo, respectively, in other provinces of the Mekong River Delta, indicating a widespread occurrence of both Phytophthora species in this citrus-growing area. Koch's postulates were fulfilled via pathogenicity tests on fruits of various Citrus species, including pomelo, grapefruit (Citrus x paradisi), sweet orange (Citrus x sinensis) and bergamot (Citrus x bergamia) as well as on the rootstock of 2-year-old trees of pomelo and sweet orange on 'Carrizo' citrange (C. sinensis 'Washington Navel' x Poncirus trifoliata). This is the first report of a Phytophthora species from Clade 2 other than P. citricola and P. citrophthora as causal agent of fruit brown rot of Citrus worldwide and the first report of P. insolita complex in Vietnam. Results indicate that likely Vietnam is still an unexplored reservoir of Phytophthora diversity.

Population Structure of Phytophthora nicotianae Reveals Host-Specific Lineages on Brinjal, Ridge Gourd, and Tomato in South India

Severe outbreaks of Phytophthora fruit rot on brinjal, ridge gourd, and tomato have been observed since 2011 in Andhra Pradesh, Karnataka, Telangana, and Tamil Nadu states of India. Therefore, 76 Phytophthora nicotianae isolates, recovered from brinjal (17), ridge gourd (40), and tomato (19) from different localities in these states during the June to December cropping season of 2012 and 2013, were characterized based on phenotypic and genotypic analyses and aggressiveness on brinjal, tomato, and ridge gourd. All brinjal and ridge gourd isolates were A2, while tomato isolates were both A1 (13) and A2 (6). All isolates were metalaxyl sensitive. In addition, isolates were genotyped for three mitochondrial (ribosomal protein L5-small subunit ribosomal RNA [rpl5-rns], small subunit ribosomal RNA-cytochrome c oxidase subunit 2 [rns-cox2], and cox2+spacer) and three nuclear loci (hypothetical protein [hyp], scp-like extracellular protein [scp], and beta-tubulin [β-tub]). All regions were polymorphic but nuclear regions were more variable than mitochondrial regions. The network analysis of genotypes using the combined dataset of three nuclear regions revealed a host-specific association. However, the network generated using mitochondrial regions limited such host-specific groupings only to brinjal isolates. P. nicotianae isolates were highly aggressive and produced significantly (P ≤ 0.01) larger lesions on their respective host of origin than on other hosts. The results indicate significant genetic variation in the population of P. nicotianae, leading to identification of host-specific lineages responsible for severe outbreaks on brinjal, ridge gourd, and tomato.

Genetic Analysis of Phytophthora nicotianae Populations from Different Hosts Using Microsatellite Markers

In all, 231 isolates of Phytophthora nicotianae representing 14 populations from different host genera, including agricultural crops (Citrus, Nicotiana, and Lycopersicon), potted ornamental species in nurseries (Lavandula, Convolvulus, Myrtus, Correa, and Ruta), and other plant genera were characterized using simple-sequence repeat markers. In total, 99 multilocus genotypes (MLG) were identified, revealing a strong association between genetic grouping and host of recovery, with most MLG being associated with a single host genus. Significant differences in the structure of populations were revealed but clonality prevailed in all populations. Isolates from Citrus were found to be genetically related regardless of their geographic origin and were characterized by high genetic uniformity and high inbreeding coefficients. Higher variability was observed for other populations and a significant geographical structuring was determined for isolates from Nicotiana. Detected differences were related to the propagation and cultivation systems of different crops. Isolates obtained from Citrus spp. are more likely to be distributed worldwide with infected plant material whereas Nicotiana and Lycopersicon spp. are propagated by seed, which would not contribute to the spread of the pathogen and result in a greater chance for geographic isolation of lineages. With regard to ornamental species in nurseries, the high genetic variation is likely the result of the admixture of diverse pathogen genotypes through the trade of infected plant material from various geographic origins, the presence of several hosts in the same nursery, and genetic recombination through sexual reproduction of this heterothallic species.

Evolutionary relationships within the Phytophthora cactorum species complex in Europe

The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of three genes (ITS region of ribosomal RNA gene, phenolic acid decarboxylase - Pheca I, and Cytochrome oxidase - Cox I), morphometric analysis and cardinal temperature data. The high proportion of clonal genotypes, low gene flow among groups, which was defined by the structure analysis, and low Nei's gene diversity confirms the homothallic life cycle of the groups. On the other hand, the ITS, Cox I and Pheca I sequence data support occasional hybridization between species. The structure K = 5 grouping revealed two groups of hybrid origin (C2 and F). While the C2 group resembles P. × serendipita, the F group includes Finnish isolates characterized by high oogonial abortion rates and slow growth. The morphological characters routinely used in identification of Phytophthora species are not useful for delimitation of species from the P. cactorum complex. Therefore, we discuss the status of P. hedraiandra as a separate species. The epitypification of P. cactorum is proposed.

Metabarcoding Analysis of Phytophthora Diversity Using Genus-Specific Primers and 454 Pyrosequencing

A metabarcoding method based on genus-specific primers and 454 pyrosequencing was utilized to investigate the genetic diversity of Phytophthora spp. in soil and root samples of potted plants, from eight nurseries. Pyrosequencing enabled the detection of 25 Phytophthora phylotypes distributed in seven different clades and provided a much higher resolution than a corresponding cloning/Sanger sequencing approach. Eleven of these phylotypes, including P. cactorum, P. citricola s.str., P. palmivora, P. palmivora-like, P. megasperma or P. gonapodyides, P. ramorum, and five putative new Phytophthora species phylogenetically related to clades 1, 2, 4, 6, and 7 were detected only with the 454 pyrosequencing approach. We also found an additional 18 novel records of a phylotype in a particular nursery that were not detected with cloning/Sanger sequencing. Several aspects confirmed the reliability of the method: (i) many identical sequence types were identified independently in different nurseries, (ii) most sequence types identified with 454 pyrosequencing were identical to those from the cloning/Sanger sequencing approach and/or perfectly matched GenBank deposited sequences, and (iii) the divergence noted between sequence types of putative new Phytophthora species and all other detected sequences was sufficient to rule out sequencing errors. The proposed method represents a powerful tool to study Phytophthora diversity providing that particular attention is paid to the analysis of 454 pyrosequencing raw read sequences and to the identification of sequence types.

Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina

Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain-containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.

The Top 10 oomycete pathogens in molecular plant pathology

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Identification and validation of polymorphic microsatellite loci for the analysis of Phytophthora nicotianae populations

A large number of SSR loci were screened in the genomic assemblies of 14 different isolates of Phytophthora nicotianae and primers were developed for amplification of 17 markers distributed among different contigs. These loci were highly polymorphic and amplified from genetically distant isolates of the pathogen. Among these, nine were further validated using a multiplexed genotyping assay with differentially labeled primers (FAM or HEX) to allow for duplex PCR amplification. The use of reverse primers with a 5' PIG tail was important to increase the quality and reliability of the analyses. A total of 46 alleles were detected in 5 tester isolates of P. nicotianae representing the breadth of diversity in the species. Furthermore, a high incidence of heterozygosity was determined with two alleles detected in 67% of the primer/isolate combinations. Three different alleles where detected for a single locus/isolate combination, indicating variation in ploidy. These markers represent a valuable new tool for the characterization of populations of P. nicotianae.

History of oilseed rape cropping and geographic origin affect the genetic structure of Plasmodiophora brassicae populations

The soilborne pathogen Plasmodiophora brassicae causes clubroot on Brassica crops, a common disease in many oilseed rape growing regions. Here, we investigate genetic diversity and geographic differentiation of P. brassicae populations from different regions in Germany. We compared three regions that differ in oilseed rape cropping history, oilseed rape acreage, and incidence of clubroot. These regions were either spatially separated or separated by the former inner German border. Plasmodiophora isolates were collected from 59 fields (29, 17, and 13 fields per region, respectively) and 174 amplified fragment length polymorphism (AFLP) markers were analyzed. Every field isolate showed a unique genotype pattern; that is, no genotype was shared among the regions and different fields. The mean gene diversity was 0.27, suggesting that P. brassicae is a genetically diverse species. The comparison of indexes (gene diversity, genotypic diversity, and linkage disequilibrium) between the regions does not support our hypotheses that cropping history, oilseed rape acreage, and incidence of clubroot affect these estimates. Principal component analysis (PCA), fixation index (FST), and generalized linear model (GLM) were suitable to specify regional differences. PCA revealed two clusters of isolates based on the geographic origin of the isolates and FST showed that these clusters were highly differentiated. Hypotheses about association of genotypes with different spatial scales were tested with GLM: the region, reflecting the cropping history, and the individual field had a significant effect on the AFLP pattern. We propose that individual field isolates represent a discrete population and that geographic differentiation results from low levels of gene flow due to the limited dispersal of this soilborne pathogen and from localized selection pressure as unifying force on the genotypes.