Publications by authors named "Marc A Cubeta"

36 Publications

Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type.

G3 (Bethesda) 2021 Feb;11(2)

Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA.

Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was characterized. Biotrophic effectors allow the pathogen to avoid recognition by the host plant and evade or mitigate host defense responses during the early stages of fruit infection. Following locule colonization, necrotizing effectors promote the mummification of host tissues. Potential biotrophic effectors utilized by Mvc include chorismate mutase for reducing host salicylate and necrotrophic effectors include necrosis-inducing proteins and hydrolytic enzymes for macerating host tissue. The MAT locus sequences indicate the potential for homothallism in the reference genome, but a deletion allele of the MAT locus, characterized in a second isolate, indicates heterothallism. Further research is needed to verify the roles of individual effectors in virulence and to determine the role of the MAT locus in outcrossing and population genotypic diversity.
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http://dx.doi.org/10.1093/g3journal/jkaa052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022979PMC
February 2021

Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood.

Phytopathology 2021 Jan 12;111(1):184-193. Epub 2020 Nov 12.

Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD.

Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species has remained genetically isolated from its European-limited sister species , while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 isolates from four continents and 1,017 SNPs in 13 isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation.
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http://dx.doi.org/10.1094/PHYTO-06-20-0219-FIDOI Listing
January 2021

One Clonal Lineage of Is Primarily Responsible for the Boxwood Blight Epidemic in the United States.

Phytopathology 2020 Nov 7;110(11):1845-1853. Epub 2020 Oct 7.

U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705.

Boxwood blight caused by and is destroying cultivated and native boxwood worldwide, with profound negative economic impacts on the horticulture industry. First documented in the United States in 2011, the disease has now occurred in 30 states. Previous research showed that global populations prior to 2014 had a clonal structure, and only the idiomorph was observed. In this study, we examined genetic diversity and population structure in the United States after 2014, following the expansion of the disease across the country over the past 5 years. Two hundred eighteen isolates from 21 states were genotyped by sequencing 11 simple sequence repeat (SSR) loci and by idiomorph typing. All isolates presented -specific alleles, indicating that is still absent in the U.S. states sampled. The presence of only the idiomorph and gametic linkage disequilibrium suggests the prevalence of asexual reproduction. The contemporary population is characterized by a clonal structure and composed of 13 multilocus genotypes (SSR-MLGs) unevenly distributed across the United States. These SSR-MLGs grouped into two clonal lineages (CLs). The predominant lineage CL2 (93% of isolates) is the primary contributor to U.S. disease expansion. The contemporary U.S. population is not geographically subdivided and not genetically differentiated from the U.S. population prior to 2014, but is significantly differentiated from the main European population, which is largely composed of CL1. Our findings provide insights into the boxwood blight epidemic that are critical for disease management and breeding of resistant boxwood cultivars.
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http://dx.doi.org/10.1094/PHYTO-04-20-0130-RDOI Listing
November 2020

Identification and characterization of as the causal agent of Septoria leaf spot disease of stevia in North Carolina.

Mycologia 2019 May-Jun;111(3):456-465. Epub 2019 Apr 15.

b Department of Entomology and Plant Pathology , North Carolina State University , Raleigh , North Carolina 27695.

Stevia () is an emerging perennial crop in the southeastern United States. A Septoria leaf spot disease of stevia was first identified on field plantings in Japan in 1978. The pathogen was named based on a morphological characterization. In 2015, a species of with morphological characters of was isolated from field and greenhouse-grown stevia plants with leaf spot symptoms in North Carolina. In this study, 12 isolates obtained from diseased stevia plants in 2015 and 2016 were characterized and compared with reference strains of . Comparisons were based on conidial and pycnidial morphology and multilocus sequence analysis of actin (), β-tubulin (), calmodulin (), nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2 = ITS), nuc rDNA 28S subunit (28S), RNA polymerase II second largest subunit (), and translation elongation factor-1α (). Measurements of conidia and pycnidia from symptomatic field leaves and 12 pure cultures grown on nutrient medium were consistent with those previously reported for ex-type strains of . North Carolina strains formed a well-supported monophyletic group with ex-type strains of . This study represents the first genetic characterization of in the United States and provides an experimental framework to elucidate the genetic diversity and disease ecology of field populations of .
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http://dx.doi.org/10.1080/00275514.2019.1584503DOI Listing
April 2020

, Causal Agent of a New Foliar Blight Disease of .

Plant Dis 2019 Jun 8;103(6):1337-1346. Epub 2019 Apr 8.

1 Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705.

Woody plants of the Buxaceae, including species of , , and , are widely grown evergreen shrubs and groundcovers. Severe leaf spot symptoms were observed on at the U.S. National Arboretum in Washington, DC, in 2016. Affected plants were growing adjacent to exhibiting Volutella blight symptoms. Fungi isolated from both hosts were identical based on morphology and multilocus phylogenetic analysis and were identified as (Nectriaceae, Hypocreales), causal agent of Volutella blight of species. Pathogenicity tests established that isolated from both hosts caused disease symptoms on and , but not on . Artificial inoculations with , causal agent of Volutella blight of , did not result in disease on or . Wounding enhanced infection by and on all hosts tested but was not required for disease development. Genome assemblies were generated for the Buxaceae pathogens that cause Volutella diseases: , . , and ; these ranged in size from 25.7 to 28.5 Mb. To our knowledge, this foliar blight of represents a new disease for this host and is capable of causing considerable damage to infected plants.
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http://dx.doi.org/10.1094/PDIS-09-18-1676-REDOI Listing
June 2019

Multi-locus DNA sequence analysis, antifungal agent susceptibility, and fungal keratitis outcome in horses from Southeastern United States.

PLoS One 2019 28;14(3):e0214214. Epub 2019 Mar 28.

Department of Clinical Sciences, NC State University, Raleigh, NC, United States of America.

Morphological characterization and multi-locus DNA sequence analysis of fungal isolates obtained from 32 clinical cases of equine fungal keratitis (FK) was performed to identify species and determine associations with antifungal susceptibility, response to therapy and clinical outcome. Two species of Aspergillus (A. flavus and A. fumigatus) and three species of Fusarium (F. falciforme, F. keratoplasticum, and F. proliferatum) were the most common fungi isolated and identified from FK horses. Most (91%) equine FK Fusarium nested within the Fusarium solani species complex (FSSC) with nine genetically diverse strains/lineages, while 83% of equine FK Aspergillus nested within the A. flavus clade with three genetically diverse lineages. Fungal species and evolutionary lineage were not associated with clinical outcome. However, species of equine FK Fusarium were more likely (p = 0.045) to be associated with stromal keratitis. Species of Aspergillus were more susceptible to voriconazole and terbinafine than species of Fusarium, while species of Fusarium were more susceptible to thiabendazole than species of Aspergillus. At the species level, A. fumigatus and A. flavus were more susceptible to voriconazole and terbinafine than F. falciforme. Natamycin susceptibility was higher for F. falciforme and A. fumigatus compared to A. flavus. Furthermore, F. falciforme was more susceptible to thiabendazole than A. flavus and A. fumigatus. These observed associations of antifungal sensitivity to natamycin, terbinafine, and thiabendazole demonstrate the importance of fungal identification to the species rather than genus level. The results of this study suggest that treatment of equine FK with antifungal agents requires accurate fungal species identification.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214214PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438541PMC
December 2019

Thermal sensitivity of Calonectria henricotiae and Calonectria pseudonaviculata conidia and microsclerotia.

Mycologia 2018 May-Jun;110(3):546-558. Epub 2018 Jul 3.

a Center For Integrated Fungal Research, Department of Entomology and Plant Pathology , North Carolina State University, 851 Main Campus Drive , Raleigh , North Carolina 27606.

Knowledge of the thermal sensitivity of conidia and microsclerotia is useful for developing plant disease management approaches that deploy heat to inactivate infectious vegetative propagules of fungal pathogens. For boxwood blight disease, heat treatment of cuttings that harbor conidia and microsclerotia would provide a useful management tool for suppressing the pathogenic activity of Calonectria pseudonaviculata (present in the United States) and C. henricotiae (a quarantine pathogen not present in the United States). In this study, we investigated the thermal sensitivity of conidia and microsclerotia of the boxwood blight pathogens C. henricotiae and C. pseudonaviculata treated in water at 45, 47.5, 50, 52.5, and 55 C. For conidia, as time of exposure increased at each temperature, the proportion of germinated conidia decreased. The predicted time required to inactivate 90% of C. pseudonaviculata conidia (LD) decreased as water temperature increased from 45 to 55 C and ranged from 35.4 to 5.6 min, respectively. Inactivation of conidia was dependent on isolate, species of Calonectria, and length of exposure at each temperature tested. Microsclerotia of C. henricotiae and C. pseudonaviculata displayed reduced germination with increasing exposure and higher temperatures of hot water. Microsclerotia of C. henricotiae were significantly more resistant to heat treatment than C. pseudonaviculata at 47.5 and 50 C, whereas microsclerotia of both species were rapidly killed at 55 C.
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http://dx.doi.org/10.1080/00275514.2018.1465778DOI Listing
July 2019

Fine-Scale Genetic Structure and Reproductive Biology of the Blueberry Pathogen Monilinia vaccinii-corymbosi.

Phytopathology 2017 02 30;107(2):231-239. Epub 2016 Nov 30.

Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695.

The fungus Monilinia vaccinii-corymbosi, a pathogen of Vaccinium spp., requires asexual and sexual spore production to complete its life cycle. A recent study found population structuring of M. vaccinii-corymbosi over a broad spatial scale in the United States. In this study, we examined fine-scale genetic structuring, temporal dynamics, and reproductive biology within a 125-by-132-m blueberry plot from 2010 to 2012. In total, 395 isolates of M. vaccinii-corymbosi were sampled from infected shoots and fruit to examine their multilocus haplotype (MLH) using microsatellite markers. The MLH of 190 single-ascospore isolates from 21 apothecia was also determined. Little to no genetic differentiation and unrestricted gene flow were detected among four sampled time points and between infected tissue types. Discriminant analysis of principal components suggested genetic structuring within the field, with at least K = 3 genetically distinct clusters maintained over four sampled time points. Single-ascospore progeny from eight apothecia had identical MLH and at least two distinct MLH were detected from 13 apothecia. Tests for linkage disequilibrium suggested that genetically diverse ascospore progeny were the product of recombination. This study supports the idea that the fine-scale dynamics of M. vaccinii-corymbosi may be complex, with genetic structuring, inbreeding, and outcrossing detected in the study area.
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http://dx.doi.org/10.1094/PHYTO-02-16-0093-RDOI Listing
February 2017

Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales.

Fungal Biol 2016 Apr 29;120(4):603-619. Epub 2016 Jan 29.

Department of Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Campus Box 7251, Raleigh, NC 27695, USA.

Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets were analysed individually and combined using Maximum Parsimony, Maximum Likelihood, and Bayesian Phylogenetic Inference methods. All analyses supported the monophyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. This analysis coupled with analyses of a larger sample of 165 rpb2 sequences of fungi in the Cantharellales supported a sister relationship between the Botryobasidiaceae and Ceratobasidiaceae and a sister relationship of the Tulasnellaceae with the rest of the Cantharellales. The inclusion of additional sequence data did not clarify incongruences observed in previous studies of Rhizoctonia fungi in the Cantharellales based on analyses of a single or multiple genes. The diversity of ecological and morphological characters associated with these fungi requires further investigation on character evolution for re-evaluating homologous and homoplasious characters.
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http://dx.doi.org/10.1016/j.funbio.2016.01.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013834PMC
April 2016

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.

BMC Genomics 2015 Aug 22;16:630. Epub 2015 Aug 22.

Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.

Background: Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq.

Results: Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation.

Conclusions: This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.
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http://dx.doi.org/10.1186/s12864-015-1758-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4546130PMC
August 2015

Characterization and colonization of endomycorrhizal Rhizoctonia fungi in the medicinal herb Anoectochilus formosanus (Orchidaceae).

Mycorrhiza 2015 Aug 11;25(6):431-45. Epub 2015 Jan 11.

Department of Plant Pathology, National Chung Hsing University, No. 250, Kuo-Kuang Road, Taichung, Taiwan.

The medicinal effects and techniques for cultivating Anoectochilus formosanus are well-documented, but little is known about the mycorrhizal fungi associated with A. formosanus. Rhizoctonia (Thanatephorus) anastomosis group 6 (AG-6) was the most common species isolated from fungal pelotons in native A. formosanus and represented 67% of the sample. Rhizoctonia (Ceratobasidium) AG-G, P, and R were also isolated and represent the first occurrence in the Orchidaceae. Isolates of AG-6, AG-R, and AG-P in clade I increased seed germination 44-91% and promoted protocorm growth from phases III to VI compared to asymbiotic treatments and isolates of AG-G in clade II and Tulasnella species in clade III. All isolates in clades I to III formed fungal pelotons in tissue-cultured seedlings of A. formosanus, which exhibited significantly greater growth than nonmycorrhizal seedlings. An analysis of the relative effect of treatment ([Formula: see text]) showed that the low level of colonization ([Formula: see text]) by isolates in clade I resulted in a significant increase in seedling growth compared to isolates in clades II (0.63-0.82) and III (0.63-0.75). There was also a negative correlation (r = -0.8801) with fresh plant weight and fungal colonization. Our results suggest that isolates in clade I may represent an important group associated with native populations of A. formosanus and can vary in their ability to establish a symbiotic association with A. formosanus. The results presented here are potentially useful for advancing research on the medicinal properties, production, and conservation of A. formosanus in diverse ecosystems.
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http://dx.doi.org/10.1007/s00572-014-0616-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512280PMC
August 2015

Feasibility of flotation concentration of fungal spores as a method to identify toxigenic mushrooms.

Vet Med (Auckl) 2015 16;6:1-9. Epub 2014 Dec 16.

Department of Molecular and Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA,

Purpose: Mushroom poisoning is a recurring and challenging problem in veterinary medicine. Diagnosis of mushroom exposure in animals is hampered by the lack of rapid diagnostic tests. Our study evaluated the feasibility of using flotation concentration and microscopic evaluation of spores for mushroom identification. Evaluation of this method in living animals exposed to toxigenic mushrooms is limited by ethical constraints; therefore, we relied upon the use of an in vitro model that mimics the oral and gastric phases of digestion.

Methods: In our study, mycologist-identified toxigenic (poisonous) and nontoxigenic fresh mushrooms were collected in North Carolina, USA. In phase 1, quantitative spore recovery rates were determined following magnesium sulfate, modified Sheather's sugar solution, and zinc sulfate flotation (n=16 fungal species). In phase 2, mushrooms (n=40 fungal species) were macerated and digested for up to 2 hours in a salivary and gastric juice simulant. The partially digested material was acid neutralized, filtered, and spores concentrated using zinc sulfate flotation followed by microscopic evaluation of spore morphology.

Results: Mean spore recovery rates for the three flotation fluids ranged from 32.5% to 41.0% (=0.82). Mean (± standard error of the mean) spp. spore recovery rates were 38.1%±3.4%, 36.9%±8.6%, and 74.5%±1.6% (=0.0012) for the magnesium sulfate, Sheather's sugar, and zinc sulfate solutions, respectively. Zinc sulfate flotation following in vitro acid digestion (phase 2) yielded spore numbers adequate for microscopic visualization in 97.5% of trials. The most common spore shapes observed were globose, spiked, elliptical, smooth and reticulate.

Conclusion: Flotation can concentrate mushroom spores; however, false negative results can occur. Spore morphology could not be used to differentiate species of mushroom-forming fungi since the spore shape and surface characteristics seen in the present study were often observed with multiple species of mushroom-forming fungi.
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http://dx.doi.org/10.2147/VMRR.S67794DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067785PMC
December 2014

Suppression subtractive hybridization and comparative expression of a pore-forming toxin and glycosyl hydrolase genes in Rhizoctonia solani during potato sprout infection.

Mol Genet Genomics 2015 Jun 4;290(3):877-900. Epub 2014 Dec 4.

Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, 21,111 Lakeshore Rd., Ste. Anne de Bellevue, Montreal, QC, H9X 3V9, Canada.

Rhizoctonia solani is a plant pathogenic fungus that causes black scurf on tubers and stem and stolon canker on underground parts of potato plant. Early in the season, the fungus attacks germinating sprouts underground before they emerge from the soil. Damage at this stage results in delayed emergence of weakened plants with poor and uneven stands. The mechanism underlying this phenomenon has been investigated in this study by coupling a cDNA-suppression subtractive hybridization (SSH) library to differential screening to identify transcripts of R. solani that are down-regulated during infection of potato sprouts. We report on the identification of 33 unique genes with functions related to carbohydrate binding, vitamin synthesis, pathogenicity, translation, ATP and nucleic acid binding and other categories. RACE-PCR was used to clone and characterize the first full-length cDNA clones, RSENDO1 and RSGLYC1 that encode for an eukaryotic delta-endotoxin CytB protein and an intracellular glycosyl hydrolase, respectively. Quantitative real-time PCR revealed the down-regulation of RSENDO1 during infection of potato sprouts and the up-regulation of RSGLYC1 when the fungus was grown on a cellulose-based nutrient medium. In contrast, additional experiments have highlighted the down-regulation of RSENDO1 when R. solani was co-cultured with the mycoparasite Stachybotrys elegans and the bacterial antagonist Bacillus subtilis B26. These results advance our understanding of R. solani-potato interaction in subterranean parts of the plant. Such approaches could be considered in building an efficient integrated potato disease management program.
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http://dx.doi.org/10.1007/s00438-014-0962-xDOI Listing
June 2015

Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP.

Genome Announc 2014 Oct 30;2(5). Epub 2014 Oct 30.

J. Craig Venter Institute, Rockville, Maryland, USA.

The soil fungus Rhizoctonia solani is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence of R. solani strain Rhs1AP. A comprehensive understanding of the heterokaryotic genome complexity and organization of R. solani may provide insight into the plant disease ecology and adaptive behavior of the fungus.
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http://dx.doi.org/10.1128/genomeA.01072-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214984PMC
October 2014

Population Structure of the Blueberry Pathogen Monilinia vaccinii-corymbosi in the United States.

Phytopathology 2015 Apr;105(4):533-41

Department of Plant Pathology, North Carolina State University, Campus Box 7567, Raleigh 27695-001.

The fungus Monilinia vaccinii-corymbosi causes disease of blueberry (Vaccinium section Cyanococcus) shoots, flowers, and fruit. The objective of our research was to examine the population biology and genetics of M. vaccinii-corymbosi in the United States. A total of 480 samples of M. vaccinii-corymbosi were collected from 18 blueberry fields in 10 states; one field in Georgia, Massachusetts, Maine, Michigan, Mississippi, New Jersey, New York, Oregon, and Washington and nine fields in North Carolina. Analysis with 10 microsatellite markers revealed 247 unique multilocus haplotypes (MLHs), with 244 MLHs detected within 11 fields in the Northeast, Northwest, Midwest, and Southeast and three MLHs detected within seven fields in the Southeast United States. Genetic similarity and low genetic diversity of M. vaccinii-corymbosi isolates from the seven fields in the Southeast United States suggested the presence of an expansive, self-fertile population. Tests for linkage disequilibrium within 10 fields that contained ≥12 MLHs supported random mating in six fields and possible inbreeding and/or self-fertilization in four fields. Analysis of molecular variance, discriminate analysis of principal components, and Bayesian cluster analysis provided evidence for population structure and restricted gene flow among fields. This research represents the first comprehensive investigation of the genetic diversity and structure of field populations of M. vaccinii-corymbosi.
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http://dx.doi.org/10.1094/PHYTO-03-14-0074-RDOI Listing
April 2015

Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3.

FEMS Microbiol Lett 2014 Mar 17;352(2):165-73. Epub 2014 Feb 17.

The J. Craig Venter Institute, Rockville, MD, USA.

The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.
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http://dx.doi.org/10.1111/1574-6968.12387DOI Listing
March 2014

Phylogenetic and phenotypic characterization of Fomes fasciatus and Fomes fomentarius in the United States.

Mycologia 2013 Nov-Dec;105(6):1524-34. Epub 2013 Aug 8.

North Carolina State University, Department of Plant Pathology, Raleigh, North Carolina 27695-7616.

The wood-decay fungi Fomes fasciatus and F. fomentarius share many morphological characters that historically have made species delimitation challenging. We examined morphological, molecular and physiological characters of basidiomata and pure cultures of F. fasciatus and F. fomentarius sampled from multiple plant hosts and geographic regions in the United States to determine whether they support separation of the two species. We find that mean basidiospore size is significantly larger in F. fomentarius and represents the most informative morphological character for delineating the species. Basidiomata and pore-surface shape provided additional resolution of the species, but these characters often overlap and are more variable than basidiospore size. Phylogenetic analyses of ITS and RPB2 sequences suggest that F. fasciatus and F. fomentarius represent distinct evolutionary lineages. The two species share less than 88% maximum identity for the ITS region. Limited intraspecific sequence variation at each locus also was observed. In vitro experiments of hyphal-growth response to a wide range of temperatures support differences in physiology between the two species.
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http://dx.doi.org/10.3852/12-336DOI Listing
January 2014

The population genetic structure of Rhizoctonia solani AG-3PT from potato in the Colombian Andes.

Phytopathology 2013 Aug;103(8):862-9

Universidad Nacional de Colombia, Bogota, Colombia.

The soilborne fungus Rhizoctonia solani anastomosis group 3 (AG-3PT) is a globally important potato pathogen. However, little is known about the population genetic processes affecting field populations of R. solani AG-3PT, especially in the South American Colombian Andes, which is near the center of diversity of the two most common groups of cultivated potato, Solanum tuberosum and S. phureja. We analyzed the genetic structure of 15 populations of R. solani AG-3PT infecting potato in Colombia using 11 simple-sequence repeat (SSR) markers. In total, 288 different multilocus genotypes were identified among 349 fungal isolates. Clonal fractions within field populations were 7 to 33%. RST statistics indicated a very low level of population differentiation overall, consistent with high contemporary gene flow, though moderate differentiation was found for the most distant southern populations. Genotype flow was also detected, with the most common genotype found widely distributed among field populations. All populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction, but two populations displayed evidence of inbreeding.
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http://dx.doi.org/10.1094/PHYTO-11-12-0278-RDOI Listing
August 2013

Structural analysis of the Rhizoctonia solani agglutinin reveals a domain-swapping dimeric assembly.

FEBS J 2013 Apr 7;280(8):1750-63. Epub 2013 Mar 7.

Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.

Unlabelled: Rhizoctonia solani agglutinin (RSA) is a 15.5-kDa lectin accumulated in the mycelium and sclerotia of the soil born plant pathogenic fungus R. solani. Although it is considered to serve as a storage protein and is implicated in fungal insecticidal activity, its physiological role remains unclear as a result of a lack of any structure/function relationship information. Glycan arrays showed that RSA displays high selectivity towards terminal nonreducing N-acetylgalactosamine residues. We determined the amino acid sequence of RSA and also determined the crystal structures of the free form and the RSA-N-acetylgalactosamine complex at 1.6 and 2.2 Å resolution, respectively. RSA is a homodimer comprised of two monomers adopting the β-trefoil fold. Each monomer accommodates two different carbohydrate-binding sites in an asymmetric way. Despite RSA topology similarities with R-type lectins, the two-monomer assembly involves an N-terminal swap, thus creating a dimer association novel to R-type lectins. Structural characterization of the two carbohydrate-binding sites offers insights on the structural determinants of the RSA carbohydrate specificity.

Database: Structural data have been deposited in the Protein Data Bank database under accession numbers 4G9M and 4G9N.

Structured Digital Abstract: RSA and RSA bind by x-ray crystallography (View interaction).
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http://dx.doi.org/10.1111/febs.12190DOI Listing
April 2013

Modulation of the phenylacetic acid metabolic complex by quinic acid alters the disease-causing activity of Rhizoctonia solani on tomato.

Phytochemistry 2013 May 1;89:47-52. Epub 2013 Feb 1.

Department of Plant Pathology, North Carolina State University, P.O. Campus Box 7251, Raleigh, NC 27695, USA.

The metabolic control of plant growth regulator production by the plant pathogenic fungus Rhizoctonia solani Kühn (teleomorph=Thanatephorus cucumeris (A.B. Frank) Donk) and consequences associated with the parasitic and saprobic activity of the fungus were investigated. Fourteen genetically distinct isolates of the fungus belonging to anastomosis groups (AG) AG-3, AG-4, and AG-1-IA were grown on Vogel's minimal medium N with and without the addition of a 25 mM quinic acid (QA) source of carbon. The effect of QA on fungal biomass was determined by measuring the dry wt of mycelia produced under each growth condition. QA stimulated growth of 13 of 14 isolates of R. solani examined. The production of phenylacetic acid (PAA) and the chemically related derivatives 2-hydroxy-PAA, 3-hydroxy-PAA, 4-hydroxy-PAA, and 3-methoxy-PAA on the two different media was compared by gas chromatography coupled with mass spectrometry (GC-MS). The presence of QA in the growth medium of R. solani altered the PAA production profile, limiting the conversion of PAA to derivative forms. The effect of QA on the ability of R. solani to cause disease was examined by inoculating tomato (Solanum lycopersicum L.) plants with 11 isolates of R. solani AG-3 grown on media with and without the addition of 25 mM QA. Mean percent survival of tomato plants inoculated with R. solani was significantly higher when the fungal inoculum was generated on growth medium containing QA. The results of this study support the hypotheses that utilization of QA by R. solani leads to reduced production of the plant growth regulators belonging to the PAA metabolic complex which can suppress plant disease development.
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http://dx.doi.org/10.1016/j.phytochem.2012.09.018DOI Listing
May 2013

Permanent genetic resources added to molecular ecology resources database 1 April 2012 - 31 May 2012.

Mol Ecol Resour 2012 Sep 1;12(5):972-4. Epub 2012 Aug 1.

Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.

This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii-corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross-tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri.
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http://dx.doi.org/10.1111/j.1755-0998.2012.03173.xDOI Listing
September 2012

Elucidating the role of the phenylacetic acid metabolic complex in the pathogenic activity of Rhizoctonia solani anastomosis group 3.

Mycologia 2012 Jul-Aug;104(4):793-803. Epub 2012 Mar 31.

Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.

The soil fungus Rhizoctonia solani produces phytotoxic phenylacetic acid (PAA) and hydroxy (OH-) and methoxy (MeO-) derivatives of PAA. However, limited information is available on the specific role that these compounds play in the development of Rhizoctonia disease symptoms and concentration(s) required to induce a host response. Reports that PAA inhibits the growth of R. solani conflict with the established ability of the fungus to produce and metabolize PAA. Experiments were conducted to clarify the role of the PAA metabolic complex in Rhizoctonia disease. In this study the concentration of PAA and derivatives required to induce tomato root necrosis and stem canker, in the absence of the fungus, and the concentration that inhibits mycelial growth of R. solani were determined. The effect of exogenous PAA and derivatives of PAA on tomato seedling growth also was investigated. Growth of tomato seedlings in medium containing 0.1-7.5 mM PAA and derivatives induced necrosis of up to 85% of root system. Canker development resulted from injection of tomato seedling stems with 7.5 mM PAA, 3-OH-PAA, or 3-MeO-PAA. PAA in the growth medium reduced R. solani biomass, with 50% reduction observed at 7.5 mM. PAA, and derivatives were quantified from the culture medium of 14 isolates of R. solani belonging to three distinct anastomosis groups by GC-MS. The quantities ranged from below the limit of detection to 678 nM, below the concentrations experimentally determined to be phytotoxic. Correlation analyses revealed that isolates of R. solani that produced high PAA and derivatives in vitro also caused high mortality on tomato seedlings. The results of this investigation add to the body of evidence that the PAA metabolic complex is involved in Rhizoctonia disease development but do not indicate that production of these compounds is the primary or the only determinant of pathogenicity.
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http://dx.doi.org/10.3852/11-084DOI Listing
September 2012

Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani.

J Biotechnol 2012 Apr 1;158(3):144-50. Epub 2012 Feb 1.

Department of Plant Pathology, NC State University, Raleigh, NC 27695, United States.

The aneuploid and heterokaryotic nuclear condition of the soil fungus Rhizoctonia solani have provided challenges in obtaining a complete genome sequence. To better aid in the assembly and annotation process, a protoplast and single nucleotide polymorphism (SNP)-based method was developed to identify regenerated protoplasts with a reduced nuclear genome. Protocol optimization experiments showed that enzymatic digestion of mycelium from a 24 h culture of R. solani increased the proportion of protoplasts with a diameter of ≤7.5 μm and 1-4 nuclei. To determine whether strains regenerated from protoplasts with a reduced number of nuclei were genetically different from the parental strain, triallelic SNPs identified from variance records of the genomic DNA sequence reads of R. solani were used in PCR-based genotyping assays. Results from 16 of the 24 SNP-based PCR assays provided evidence that one of the three alleles was missing in the 11 regenerated protoplast strains, suggesting that these strains represent a reduced genomic complement of the parental strain. The protoplast and triallelic SNP-based method used in this study may be useful in strain development and analysis of other basidiomycete fungi with complex nuclear genomes.
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http://dx.doi.org/10.1016/j.jbiotec.2012.01.024DOI Listing
April 2012

Vascular Streak Dieback of cacao in Southeast Asia and Melanesia: in planta detection of the pathogen and a new taxonomy.

Fungal Biol 2012 Jan 23;116(1):11-23. Epub 2011 Jul 23.

United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA.

Vascular Streak Dieback (VSD) disease of cacao (Theobroma cacao) in Southeast Asia and Melanesia is caused by a basidiomycete (Ceratobasidiales) fungus Oncobasidium theobromae (syn. =Thanatephorus theobromae). The most characteristic symptoms of the disease are green-spotted leaf chlorosis or, commonly since about 2004, necrotic blotches, followed by senescence of leaves beginning on the second or third flush behind the shoot apex, and blackening of infected xylem in the vascular traces at the leaf scars resulting from the abscission of infected leaves. Eventually the shoot apex is killed and infected branches die. In susceptible cacao the fungus may grow through the xylem down into the main stem and kill a mature cacao tree. Infections in the stem of young plants prior to the formation of the first 3-4 lateral branches usually kill the plant. Basidiospores released from corticioid basidiomata developed on leaf scars or along cracks in the main vein of infected leaves infect young leaves. The pathogen commonly infects cacao but there are rare reports from avocado. As both crops are introduced to the region, the pathogen is suspected to occur asymptomatically in native vegetation. The pathogen is readily isolated but cultures cannot be maintained. In this study, DNA was extracted from pure cultures of O. theobromae obtained from infected cacao plants sampled from Indonesia. The internal transcribed spacer region (ITS), consisting of ITS1, 5.8S ribosomal RNA and ITS2, and a portion of nuclear large subunit (LSU) were sequenced. Phylogenetic analysis of ITS sequences placed O. theobromae sister to Ceratobasidium anastomosis groups AG-A, AG-Bo, and AG-K with high posterior probability. Therefore the new combination Ceratobasidium theobromae is proposed. A PCR-based protocol was developed to detect and identify C. theobromae in plant tissue of cacao enabling early detection of the pathogen in plants. A second species of Ceratobasidium, Ceratobasidium ramicola, identified through ITS sequence analysis, was isolated from VSD-affected cacao plants in Java, and is widespread in diseased cacao collected from Indonesia.
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http://dx.doi.org/10.1016/j.funbio.2011.07.009DOI Listing
January 2012

Characterization of a Basidiomycete fungus from stored sugar beet roots.

Mycologia 2012 Jan-Feb;104(1):70-8. Epub 2011 Nov 8.

Department of Bioresource Sciences, Akita Prefectural University, Akita, Japan.

Eighteen isolates from sugar beet roots associated with an unknown etiology were characterized based on observations of morphological characters, hyphal growth at 4-28 C, production of phenol oxidases and sequence analysis of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA (rDNA). The isolates did not produce asexual or sexual spores, had binucleate hyphal cells with clamp connections, grew 4-22 C with estimated optimal growth at 14.5 C and formed a dark brown pigment on potato dextrose or malt extract agar amended with 0.5% tannic acid. Color changes observed when solutions of gum guiac, guiacol and syringaldzine were applied directly to mycelium grown on these media indicated that all isolates produced phenol oxidases. Sequences of ITS and LSU regions on the rDNA gene from 15 isolates were 99.2-100% identical, and analysis of sequence data with maximum likelihood and maximum parsimony suggest that the isolates from sugar beet roots are phylogenetically related to Athelia bombacina, Granulobasidium vellereum and Cyphella digitalis. High statistical support for both loci under different criteria confirmed that Athelia bombacina was consistently the closest known relative to the sugar beet isolates. Additional taxonomic investigations are needed before species can be clarified and designated for these isolates.
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http://dx.doi.org/10.3852/10-416DOI Listing
May 2012

Seasonal Prevalence of Species of Binucleate Rhizoctonia Fungi in Growing Medium, Leaf Litter, and Stems of Container-Grown Azalea.

Plant Dis 2011 Jun;95(6):705-711

Department of Plant Pathology, Center For Integrated Fungal Research, North Carolina State University.

Rhizoctonia web blight is an annual problem on container-grown azalea (Rhododendron spp.) in the southern and eastern United States but little is documented about the distribution or persistence of Rhizoctonia spp. in container-grown azalea. Sixty web-blight-damaged azalea plants ('Gumpo White') were collected in August 2005 and 2006 and arranged in a completely randomized design on an outdoor irrigation pad. A nylon mesh bag containing 30 necrotic leaves collected from web-blight-damaged 'Gumpo White' azalea plants were placed on the surface of the medium under the plant canopy in each container to simulate leaf litter. Ten plants were destructively sampled into eight zones by dividing stems into three zones (lengths of 0 to 2, 4 to 6, and 9 to 15 cm above the medium surface), bagged leaves into one leaf litter zone, and the medium into four zones (three horizontal layers: 1 to 3, 3 to 7, and 7 to 10 cm below the medium surface, with the middle layer further divided by removing the central 7.5-cm-diameter core) in December, February, and May. Only the three stem zones were sampled from 10 plants in early and late June and late July. Of 8,940 total isolations, 3,655 fungi with morphological characteristics of a Rhizoctonia sp. were recovered. Percent recovery differed from the eight zones (P < 0.0001) but did not differ between years (P = 0.3950) and sampling times (P = 0.1896). Frequency of recovery of Rhizoctonia spp. was highest from the lower stem and the leaf litter, and decreased with distance from the leaf litter. Recovery from stems over the six sample times was analyzed separately. Percent recovery differed between stem zones (P < 0.0001), sample times (P = 0.0478), and experiment years (P < 0.0001). In both years, mean recovery of Rhizoctonia spp. was higher from the lower stem and decreased with distance to the upper stem layer. From a subsample of 145 isolates, 95.1% were identified as binucleate Rhizoctonia (BNR) anastomosis groups (AGs)-A, -G, -K, -R, -S, and -U (-P), and 2.8 and 2.1% were Rhizoctonia solani AG-2 and an uncultured Laetisaria sp., respectively. Based on frequency analysis, recovery of BNR AGs differed by plant zone (P < 0.0001) but not over sample times (P = 0.4831). The six AGs of BNR are the predominant Rhizoctonia fungi occupying the habitat niches in container-grown azalea, with little change in population frequency and composition from fall to summer; thus, BNR pathogenic and nonpathogenic to azalea have established a mixed Rhizoctonia community on container-grown azalea.
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http://dx.doi.org/10.1094/PDIS-11-10-0796DOI Listing
June 2011

An In Planta Method for Assessing the Role of Basidiospores in Rhizoctonia Foliar Disease of Tomato.

Plant Dis 2010 May;94(5):515-520

Department of Plant Pathology, North Carolina State University, Mountain Horticultural Crops Research & Extension Center, Mills River 28759.

A tomato (Solanum lycopersicum) foliar blight disease of unknown etiology was observed in North Carolina (NC) during 2005 to 2006. Symptoms included necrotic lesions and blighted leaves, with signs of white mycelial growth on abaxial leaf surfaces. The morphology of isolates from symptomatic leaves was consistent with that of Rhizoctonia solani. Because the pattern of symptom expression suggested that basidiospores were the primary inoculum source, Koch's postulates were fulfilled using a method to generate basidiospores in planta. Isolates were characterized by morphology, DNA sequence analysis, hyphal anastomosis, and somatic hyphal interactions. Phylogenetic analyses and hyphal anastomosis criteria support placement of the isolates in R. solani anastomosis group 3 (AG-3). Tomato foliar blight isolates from NC form a single phylogenetic group with tomato isolates of R. solani AG-3 from Japan and are more closely related to R. solani AG-3 isolates from potato than tobacco. Isolates exhibited both compatible and incompatible hyphal interactions when paired in vitro. To our knowledge, this is the first detailed report of tomato foliar blight caused by R. solani AG-3 in North America. A comprehensive description of the technique employed for producing basidiospores is presented with potential utility for understanding foliar disease etiology in other Rhizoctonia pathosystems.
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http://dx.doi.org/10.1094/PDIS-94-5-0515DOI Listing
May 2010

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009.

Authors:
Glenn R Almany Maurício P DE Arruda Wolfgang Arthofer Z K Atallah Steven R Beissinger Michael L Berumen S M Bogdanowicz S D Brown Michael W Bruford C Burdine Jeremiah W Busch Nathan R Campbell D Carey Bryan C Carstens K H Chu Marc A Cubeta J P Cuda Zhaoxia Cui L E Datnoff J A Dávila Emily S Davis R M Davis Onno E Diekmann Eduardo Eizirik J A Fargallo Fabiano Fernandes Hideo Fukuda L R Gale Elizabeth Gallagher Yongqiang Gao Philippe Girard Anna Godhe Evonnildo C Gonçalves Licinia Gouveia Amber M Grajczyk M J Grose Zhifeng Gu Christer Halldén Karolina Härnström Amanda H Hemmingsen Gerald Holmes C H Huang Chuan-Chin Huang S P Hudman Geoffrey P Jones Loukas Kanetis Iddya Karunasagar Indrani Karunasagar Nusha Keyghobadi S J Klosterman Page E Klug J Koch Margaret M Koopman Kirsten Köppler Eriko Koshimizu Susanne Krumböck T Kubisiak J B Landis Mario L Lasta Chow-Yang Lee Qianqian Li Shou-Hsien Li Rong-Chien Lin M Liu Na Liu W C Liu Yuan Liu A Loiseau Weisha Luan K K Maruthachalam Helen M McCormick Rohan Mellick P J Monnahan Eliana Morielle-Versute Tomás E Murray Shawn R Narum Katie Neufeld P J G De Nova Peter S Ojiambo Nobuaki Okamoto Ahmad Sofiman Othman W A Overholt Renata Pardini Ian G Paterson Olivia A Patty Robert J Paxton Serge Planes Carolyn Porter Morgan S Pratchett Thomas Püttker Gordana Rasic Bilal Rasool O Rey Markus Riegler C Riehl John M K Roberts P D Roberts Elisabeth Rochel Kevin J Roe Maurizio Rossetto Daniel E Ruzzante Takashi Sakamoto V Saravanan Cladinara Roberts Sarturi Anke Schmidt Maria Paula Cruz Schneider Hannes Schuler Jeanne M Serb Ester T A Serrão Yaohua Shi Artur Silva Y W Sin Simone Sommer Christian Stauffer Carlos Augusto Strüssmann K V Subbarao Craig Syms Feng Tan Eugenio Daniel Tejedor Simon R Thorrold Robert N Trigiano María I Trucco Mirian Tieko Nunes Tsuchiya-Jerep P Vergara Mirjam S Van De Vliet Phillip A Wadl Aimin Wang Hongxia Wang R X Wang Xinwang Wang Yan Wang Andrew R Weeks Fuwen Wei William J Werner E O Wiley D A Williams Richard J Wilkins Samantha M Wisely Kimberly A With Danhua Wu Cheng-Te Yao Cynthia Yau Beng-Keok Yeap Bao-Ping Zhai Xiangjiang Zhan Guo-Yan Zhang S Y Zhang Ru Zhao Lifeng Zhu

Mol Ecol Resour 2009 Nov 29;9(6):1460-6. Epub 2009 Sep 29.

Molecular Ecology Resources Editorial Office, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.
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http://dx.doi.org/10.1111/j.1755-0998.2009.02759.xDOI Listing
November 2009

Detection of double-stranded RNA elements in the plant pathogenic fungus Rhizoctonia solani.

Methods Mol Biol 2009 ;508:171-82

Department of Plant Pathology, North Carolina State University, Raleigh, USA.

Many species of fungi have been shown to harbor double-stranded RNA (dsRNA) elements. A single fungal isolate of Rhizoctonia solani may have as many as five different dsRNA elements within them. The presence of specific dsRNA elements influence pathogenicity in host plants.
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http://dx.doi.org/10.1007/978-1-59745-062-1_14DOI Listing
April 2009

Detecting Migrants in Populations of Rhizoctonia solani Anastomosis Group 3 from Potato in North Carolina Using Multilocus Genotype Probabilities.

Phytopathology 2003 May;93(5):610-5

ABSTRACT The relative contribution of migration of Rhizoctonia solani anastomosis group 3 (AG-3) on infested potato seed tubers originating from production areas in Canada, Maine, and Wisconsin (source population) to the genetic diversity and structure of populations of R. solani AG-3 in North Carolina (NC) soil (recipient population) was examined. The frequency of alleles detected by multilocus polymerase chain reaction-restriction fragment length polymorphisms, heterozygosity at individual loci, and gametic phase disequilibrium between all pairs of loci were determined for subpopulations of R. solani AG-3 from eight sources of potato seed tubers and from five soils in NC. Analysis of molecular variation revealed little variation between seed source and NC recipient soil populations or between subpopulations within each region. Analysis of population data with a Bayesian-based statistical method previously developed for detecting migration in human populations suggested that six multilocus genotypes from the NC soil population had a statistically significant probability of being migrants from the northern source population. The one-way (unidirectional) migration of genotypes of R. solani AG-3 into NC on infested potato seed tubers from Canada, Maine, and Wisconsin provides a plausible explanation for the lack of genetic subdivision (differentiation) between populations of the pathogen in NC soils or between the northern source and the NC recipient soil populations.
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http://dx.doi.org/10.1094/PHYTO.2003.93.5.610DOI Listing
May 2003