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Jo Anne Crouch

USDA Agricultural Research Service, Systematic Mycology and Microbiology Laboratory, Faculty Member

Rutgers, The State University of New Jersey, Plant Biology, Graduate Adjunct Faculty

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Address: Systematic Mycology and Microbiology Lab
USDA-ARS
Room 227
10300 BALTIMORE AVENUE
BLDG 010A BARC-WEST
BELTSVILLE, MD, 20705

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Grant L . Thompson

Iowa State University

Rossana Sallenave

New Mexico State University

Pennsylvania State University

University of York

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Papers by Jo Anne Crouch

Differences among Soil-Inhabiting Microbial Communities in Poa annua Turf throughout the Growing Season

There is increasing interest in understanding plant-associated microbial communities and their im... more There is increasing interest in understanding
plant-associated microbial communities
and their impact on plant health. However,
research has been limited to major agronomic
systems and little is known about the resident
microorganisms in economically important
specialty crops, such as turfgrass. In this study,
we generated a community-wide inventory of
the archaea and bacteria that inhabit the soil
of Poa annua L. putting green turf at five time
points over a 1-yr period. Next-generation
sequencing of the nuclear ribosomal DNA 16S
revealed 1.5 ´ 105 unique operational taxonomic
units from 25 pooled soil samples. Seventeen
archaeal taxa were identified at the species
level, 53% of which were members of the
Crenarchaeota. Proteobacteria was the most
abundant bacterial phylum, comprising 36%
of the 442 taxa present. Distance analysis and
analysis of similarities revealed that the archaeal
and bacterial communities clustered according
to sample date, with samples collected during
warm months grouping separately from those
collected during cool months. Clustering was
less distinct when plotted using detrended
correspondence analysis. These data indicate
that microbial community structure varied
throughout the growing season, possibly due
to seasonal changes in temperature and/or
other environmental factors. This research
also shows that P. annua putting green turf
supports a diverse microbial community despite
management practices that include frequent
pesticide applications.

Newly emerged populations of Plasmopara halstedii infecting rudbeckia exhibit unique genotypic profiles and are distinct from sunflower-infecting strains

Phytopathology, 2016

The oomycete Plasmopara halstedii emerged at the onset of the 21st century as a destructive new p... more The oomycete Plasmopara halstedii emerged at the onset of the 21st century as a destructive new pathogen causing downy mildew disease of ornamental Rudbeckia fulgida (rudbeckia) in the U.S.A. The pathogen is also a significant global problem of sunflower (Helianthus annuus), and is widely regarded as the cause of downy mildew affecting 35 Asteraceae genera. To determine whether rudbeckia and sunflower downy mildew are caused by the same genotypes, population genetic and phylogenetic analyses were performed. A draft genome assembly of a P. halstedii isolate from sunflower was generated and used to design 15 polymorphic SSR markers. SSRs and two sequenced phylogenetic markers measured differentiation between 232 P. halstedii samples collected from 1883 to 2014. Samples clustered into two main groups, corresponding to host origin. Sunflower-derived samples separated into eight admixed sub-clusters, and rudbeckia-derived samples further separated into three sub-clusters. Pre-epidemic rudbeckia samples clustered separately from modern strains. Despite the observed genetic distinction based on host origin, P. halstedii from rudbeckia could infect sunflower, and exhibited the virulence phenotype of race 734. These data indicate that the newly emergent pathogen populations infecting commercial rudbeckia are a different species from sunflower-infecting strains, notwithstanding cross-infectivity, and genetically distinct from pre-epidemic populations infecting native rudbeckia hosts.

Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila

by Kershney Naidoo, Jo Anne Crouch, Lieschen De Vos, and Danielle Roodt

Abstract: The genomes of fungi provide an important resource to resolve issues pertaining to thei... more Abstract: The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy,
biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum
variant, Huntiella omanensis, Leptographium procerum, Sclerotinia echinophila, and Rutstroemia sydowiana
are presented in this genome announcement. These seven genomes are from a number of fungal pathogens
and economically important species. The genome sizes range from 27 Mb in the case of Ceratocystis
albifundus to 51.9 Mb for Rutstroemia sydowiana. The latter also encodes for a predicted 17 350 genes,
more than double that of Ceratocystis albifundus. These genomes will add to the growing body of knowledge
of these fungi and provide a value resource to researchers studying these fungi.

Sarcococca Blight: Use of Whole Genome Sequencing for Fungal Plant Disease Diagnosis

Plant Disease, 2016

Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effe... more Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effective mitigation strategies and appropriate regulatory responses. Most commonly, pathogen identification relies on morphology and DNA marker analysis. However, for new diseases, these approaches may not be sufficient for precise diagnosis. In this study, we used whole-genome sequencing (WGS) to identify the causal agent of a new disease affecting Sarcococca hookeriana (sarcococca). Blight symptoms were observed on sarcococca and adjacent Buxus sempervirens (boxwood) plants in Maryland during 2014. Symptoms on sarcococca were novel, and included twig dieback and dark lesions on leaves and stems. A Calonectria sp. was isolated from both hosts and used to fulfill Koch’s postulates but morphology and marker sequence data precluded species-level identification. A 51.4-Mb WGS was generated for the two isolates and identified both as Calonectria pseudonaviculata. A single-nucleotide polymorphism at a noncoding site differentiated between the two host isolates. These results indicate that the same C. pseudonaviculata genotype has the ability to induce disease on both plant species. This study marks the first application of WGS for fungal plant pathogen diagnosis and demonstrates the power of this approach to rapidly identify causal agents of new diseases.

First report of downy mildew of caused by Peronospora sp. on Agastache in the United States

Plant Disease, 2015

Polymorphic SSR Markers for Plasmopara obducens (Peronosporaceae), the Newly Emergent Downy Mildew Pathogen of Impatiens (Balsaminaceae)

Applications in Plant Sciences, 2015

Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of ... more Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana. A 202-Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2-6 alleles observed. Observed and expected heterozygosity ranged from 0.000-0.892 and 0.023-0.746, respectively. Just 17 markers were sufficient to identify all multilocus genotypes. These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.

Species Identification and Variation in the North American Cranberry Fruit Rot Complex

Acta Horticulturae, 2009

Many different species of pathogenic fungi cause cranberry fruit rot. The contribution of any giv... more Many different species of pathogenic fungi cause cranberry fruit rot. The contribution of any given species can he quite variable depending on a host of cultural and environmental factors. Control of fruit rot can be problematic in the Northeast and in other growing regions since losses due to fruit rot can be episodic. One possible cause for inadequate control is that pathogenic fungi typically have differential sensitivity to fungicides. Thus, variation in the species or populations of the fungi present can affect the success and quality of control. Our primary objective in this project was to determine the variation within five species of cranberry fruit rot pathogens (Phylloslictu vaccinii, Coleoplwma empefri, C'o//etotrichzirn aculatU!fl, ('olletotrichuin gloeosporioides, and Phyxulospora vaccinil) across geographic regions INJ, MA, Wi and British Columbia (BC)I using morphologic and molecular characters. Our secondary objective was to reexamine the taxonomy of these pathogens at the molecular level, particularly those that are cranberry-or Vacciniwn species-specific. Our results suggest that morphologically, within-species variation was low. We did however collect atypical non-pigmented C. acutatuin from BC and Physalosporu i'accinii isolates from all regions varied from (lark gray to pure white oil juice agar medium. Molecular analysis of ribosomal ITS sequences showed a low level of variability for most pathogen species, with the exception of the morphologically distinct isolates. Phylogenetic analysis showed that the aty pical, non-chromogenic C'. acutatwn formed a distinct, but closely related dade, to the normal pink-pigmented isolates. In contrast, the pure white isolates of Physalospora i'accinii possessed an ITS sequence distinct from those of the gray strains, suggesting they may represent a different species.

Downy mildew on Coleus (Plectranthus scutellarioides) caused by Peronospora belbahrii sensu lato in Tennessee

Plant Disease, 2015

Genetic Diversity of Switchgrass Populations Grown in New Jersey

Genetic Diversity of Switchgrass Populations in the Northeast

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass ( Poa annua )

PeerJ, 2015

The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) tur... more The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.

Fungi Can Be Friends or Foes

Fungi are a large and diverse group of organisms. Some fungi, like mushrooms, are edible and cons... more Fungi are a large and diverse group of organisms. Some fungi, like mushrooms, are edible and considered crops. Others, however, can cause serious diseases of crop and forest plants, and those diseases can have negative effects on local and international economies as well as on the supply of food and other materials that agriculture provides. The Agricultural Research Service maintains a unique resource—the U.S. National Fungus Collections—for helpful and detailed information about fungi. Accurate knowledge of fungi is critical for controlling the diseases they cause. North America’s Largest Fungarium In 1869, the Smithsonian Institution transferred its fungal collection to the U.S. Department of Agriculture. It later became the Mycological Collections and finally the U.S. National Fungus Collections. “The collection had fewer than 3,000 specimens in 1885. It has grown to more than 1 million collected specimens and is the largest fungarium in North America today,” says Amy Rossman, r...

Simple Synteny: An accessible tool for genome comparison

Understanding the co-localization of genetic loci amongst species is a frequent task of many biol... more Understanding the co-localization of genetic loci amongst species is a frequent task of many biologists. While there are a number of programs currently available for generating syntenic maps, many are inaccessible to biologists who lack the required computer or scripting skills needed for proper installation or data preprocessing. We present here Simple Synteny, a free and open-source image generator for use in syntenic analysis. Simple Synteny provides an easy interface for comparing multiple genomes by only requiring the user to submit FASTA files for the genomes and genes of interest. The program employs gene color coordination across genomes, indicator arrows for changes in gene direction and automatic contig and gene resizing to produce publication-quality images which are clear and simple to interpret. Directions for using the tool and example analyses are provided. The server can be reached at: http://www.simplesynteny.com

Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae)

Applications in plant sciences, 2014

Colletotrichum-ng.2372

A Multiplex Real-Time PCR Assay for the Detection of Puccinia horiana and P. chrysanthemi on Chrysanthemum

Plant Disease, 2015

Influence of Host and Geographic Locale on the Distribution of Colletotrichum cereale Lineages

PLoS ONE, 2014

Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus ha... more Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera turfgrass. Colletotrichum cereale exists as two lineages, designated clades A and B, but little is known about the distribution of these clades in natural environments, or what role these subdivisions may play in the trajectory of disease outbreaks. In this study, our objective was to determine the frequency of C. cereale clades A and B. To rapidly discriminate between the two C. cereale clades, a real-time PCR assay was developed based on the Apn2 gene. A collection of 700 C. cereale pathogens and endophytes from twenty Pooideae grass genera were genotyped. 87% of the collection was identifed as part of clade A, 11.7% as part of clade B, and 1.3% was a mixture. Colletotrichum cereale from turfgrass hosts in North America were most commonly members of clade A (78%). The overabundance of clade A in turfgrass isolates was directly attributable to the dominance of this lineage from southern sampling sites, irrespective of host. In contrast, 111 C. cereale turfgrass isolates collected from northern sampling sites were evenly distributed between clades A and B. Only 28% of C. cereale from A. stolonifera at northern sampling sites were part of clade A. These data show that environmental factors such as geographic location and host identity likely played a role in the distribution of the major C. cereale clades in North American turfgrass.

Anthracnose of Centipedegrass Turf

Applied Turfgrass Science, 2012

IMA Genome-F 3: Draft genomes of <I>Amanita</I> <I>jacksonii</I>,<I>Ceratocystis albifundus</I>, <I>Fusarium circinatum</I>, <I>Huntiella omanensis</I>, <I>Leptographium procerum</I>, <I>Rutstroemia sydowiana</I>, and <I>Sclerotinia echinophila</I>

IMA Fungus, 2014

First Report of Impatiens Downy Mildew Outbreaks Caused by Plasmopara obducens Throughout the Hawai'ian Islands

Plant Disease, 2014

Differences among Soil-Inhabiting Microbial Communities in Poa annua Turf throughout the Growing Season

There is increasing interest in understanding plant-associated microbial communities and their im... more There is increasing interest in understanding
plant-associated microbial communities
and their impact on plant health. However,
research has been limited to major agronomic
systems and little is known about the resident
microorganisms in economically important
specialty crops, such as turfgrass. In this study,
we generated a community-wide inventory of
the archaea and bacteria that inhabit the soil
of Poa annua L. putting green turf at five time
points over a 1-yr period. Next-generation
sequencing of the nuclear ribosomal DNA 16S
revealed 1.5 ´ 105 unique operational taxonomic
units from 25 pooled soil samples. Seventeen
archaeal taxa were identified at the species
level, 53% of which were members of the
Crenarchaeota. Proteobacteria was the most
abundant bacterial phylum, comprising 36%
of the 442 taxa present. Distance analysis and
analysis of similarities revealed that the archaeal
and bacterial communities clustered according
to sample date, with samples collected during
warm months grouping separately from those
collected during cool months. Clustering was
less distinct when plotted using detrended
correspondence analysis. These data indicate
that microbial community structure varied
throughout the growing season, possibly due
to seasonal changes in temperature and/or
other environmental factors. This research
also shows that P. annua putting green turf
supports a diverse microbial community despite
management practices that include frequent
pesticide applications.

Newly emerged populations of Plasmopara halstedii infecting rudbeckia exhibit unique genotypic profiles and are distinct from sunflower-infecting strains

Phytopathology, 2016

The oomycete Plasmopara halstedii emerged at the onset of the 21st century as a destructive new p... more The oomycete Plasmopara halstedii emerged at the onset of the 21st century as a destructive new pathogen causing downy mildew disease of ornamental Rudbeckia fulgida (rudbeckia) in the U.S.A. The pathogen is also a significant global problem of sunflower (Helianthus annuus), and is widely regarded as the cause of downy mildew affecting 35 Asteraceae genera. To determine whether rudbeckia and sunflower downy mildew are caused by the same genotypes, population genetic and phylogenetic analyses were performed. A draft genome assembly of a P. halstedii isolate from sunflower was generated and used to design 15 polymorphic SSR markers. SSRs and two sequenced phylogenetic markers measured differentiation between 232 P. halstedii samples collected from 1883 to 2014. Samples clustered into two main groups, corresponding to host origin. Sunflower-derived samples separated into eight admixed sub-clusters, and rudbeckia-derived samples further separated into three sub-clusters. Pre-epidemic rudbeckia samples clustered separately from modern strains. Despite the observed genetic distinction based on host origin, P. halstedii from rudbeckia could infect sunflower, and exhibited the virulence phenotype of race 734. These data indicate that the newly emergent pathogen populations infecting commercial rudbeckia are a different species from sunflower-infecting strains, notwithstanding cross-infectivity, and genetically distinct from pre-epidemic populations infecting native rudbeckia hosts.

Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila

by Kershney Naidoo, Jo Anne Crouch, Lieschen De Vos, and Danielle Roodt

Abstract: The genomes of fungi provide an important resource to resolve issues pertaining to thei... more Abstract: The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy,
biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum
variant, Huntiella omanensis, Leptographium procerum, Sclerotinia echinophila, and Rutstroemia sydowiana
are presented in this genome announcement. These seven genomes are from a number of fungal pathogens
and economically important species. The genome sizes range from 27 Mb in the case of Ceratocystis
albifundus to 51.9 Mb for Rutstroemia sydowiana. The latter also encodes for a predicted 17 350 genes,
more than double that of Ceratocystis albifundus. These genomes will add to the growing body of knowledge
of these fungi and provide a value resource to researchers studying these fungi.

Sarcococca Blight: Use of Whole Genome Sequencing for Fungal Plant Disease Diagnosis

Plant Disease, 2016

Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effe... more Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effective mitigation strategies and appropriate regulatory responses. Most commonly, pathogen identification relies on morphology and DNA marker analysis. However, for new diseases, these approaches may not be sufficient for precise diagnosis. In this study, we used whole-genome sequencing (WGS) to identify the causal agent of a new disease affecting Sarcococca hookeriana (sarcococca). Blight symptoms were observed on sarcococca and adjacent Buxus sempervirens (boxwood) plants in Maryland during 2014. Symptoms on sarcococca were novel, and included twig dieback and dark lesions on leaves and stems. A Calonectria sp. was isolated from both hosts and used to fulfill Koch’s postulates but morphology and marker sequence data precluded species-level identification. A 51.4-Mb WGS was generated for the two isolates and identified both as Calonectria pseudonaviculata. A single-nucleotide polymorphism at a noncoding site differentiated between the two host isolates. These results indicate that the same C. pseudonaviculata genotype has the ability to induce disease on both plant species. This study marks the first application of WGS for fungal plant pathogen diagnosis and demonstrates the power of this approach to rapidly identify causal agents of new diseases.

First report of downy mildew of caused by Peronospora sp. on Agastache in the United States

Plant Disease, 2015

Polymorphic SSR Markers for Plasmopara obducens (Peronosporaceae), the Newly Emergent Downy Mildew Pathogen of Impatiens (Balsaminaceae)

Applications in Plant Sciences, 2015

Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of ... more Simple sequence repeat (SSR) markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana. A 202-Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identify 13,483 SSR motifs. Primers were synthesized for 62 marker candidates, of which 37 generated reliable PCR products. Testing of the 37 markers using 96 P. obducens samples showed 96% of the markers were polymorphic, with 2-6 alleles observed. Observed and expected heterozygosity ranged from 0.000-0.892 and 0.023-0.746, respectively. Just 17 markers were sufficient to identify all multilocus genotypes. These are the first SSR markers available for this pathogen, and one of the first molecular resources. These markers will be useful in assessing variation in pathogen populations and determining the factors contributing to the emergence of destructive impatiens downy mildew disease.

Species Identification and Variation in the North American Cranberry Fruit Rot Complex

Acta Horticulturae, 2009

Many different species of pathogenic fungi cause cranberry fruit rot. The contribution of any giv... more Many different species of pathogenic fungi cause cranberry fruit rot. The contribution of any given species can he quite variable depending on a host of cultural and environmental factors. Control of fruit rot can be problematic in the Northeast and in other growing regions since losses due to fruit rot can be episodic. One possible cause for inadequate control is that pathogenic fungi typically have differential sensitivity to fungicides. Thus, variation in the species or populations of the fungi present can affect the success and quality of control. Our primary objective in this project was to determine the variation within five species of cranberry fruit rot pathogens (Phylloslictu vaccinii, Coleoplwma empefri, C'o//etotrichzirn aculatU!fl, ('olletotrichuin gloeosporioides, and Phyxulospora vaccinil) across geographic regions INJ, MA, Wi and British Columbia (BC)I using morphologic and molecular characters. Our secondary objective was to reexamine the taxonomy of these pathogens at the molecular level, particularly those that are cranberry-or Vacciniwn species-specific. Our results suggest that morphologically, within-species variation was low. We did however collect atypical non-pigmented C. acutatuin from BC and Physalosporu i'accinii isolates from all regions varied from (lark gray to pure white oil juice agar medium. Molecular analysis of ribosomal ITS sequences showed a low level of variability for most pathogen species, with the exception of the morphologically distinct isolates. Phylogenetic analysis showed that the aty pical, non-chromogenic C'. acutatwn formed a distinct, but closely related dade, to the normal pink-pigmented isolates. In contrast, the pure white isolates of Physalospora i'accinii possessed an ITS sequence distinct from those of the gray strains, suggesting they may represent a different species.

Downy mildew on Coleus (Plectranthus scutellarioides) caused by Peronospora belbahrii sensu lato in Tennessee

Plant Disease, 2015

Genetic Diversity of Switchgrass Populations Grown in New Jersey

Genetic Diversity of Switchgrass Populations in the Northeast

Development of a greenhouse-based inoculation protocol for the fungus Colletotrichum cereale pathogenic to annual bluegrass ( Poa annua )

PeerJ, 2015

The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) tur... more The fungus Colletotrichum cereale incites anthracnose disease on Poa annua (annual bluegrass) turfgrass. Anthracnose disease is geographically widespread throughout the world and highly destructive to cool-season turfgrasses, with infections by C. cereale resulting in extensive turf loss. Comprehensive research aimed at controlling turfgrass anthracnose has been performed in the field, but knowledge of the causal organism and its basic biology is still needed. In particular, the lack of a reliable greenhouse-based inoculation protocol performed under controlled environmental conditions is an obstacle to the study of C. cereale and anthracnose disease. Our objective was to develop a consistent and reproducible inoculation protocol for the two major genetic lineages of C. cereale. By adapting previously successful field-based protocols and combining with components of existing inoculation procedures, the method we developed consistently produced C. cereale infection on two susceptible P. annua biotypes. Approximately 7 to 10 days post-inoculation, plants exhibited chlorosis and thinning consistent with anthracnose disease symptomology. Morphological inspection of inoculated plants revealed visual signs of the fungus (appressoria and acervuli), although acervuli were not always present. After stringent surface sterilization of inoculated host tissue, C. cereale was consistently re-isolated from symptomatic tissue. Real-time PCR detection analysis based on the Apn2 marker confirmed the presence of the pathogen in host tissue, with both lineages of C. cereale detected from all inoculated plants. When a humidifier was not used, no infection developed for any biotypes or fungal isolates tested. The inoculation protocol described here marks significant progress for in planta studies of C. cereale, and will enable scientifically reproducible investigations of the biology, infectivity and lifestyle of this important grass pathogen.

Fungi Can Be Friends or Foes

Fungi are a large and diverse group of organisms. Some fungi, like mushrooms, are edible and cons... more Fungi are a large and diverse group of organisms. Some fungi, like mushrooms, are edible and considered crops. Others, however, can cause serious diseases of crop and forest plants, and those diseases can have negative effects on local and international economies as well as on the supply of food and other materials that agriculture provides. The Agricultural Research Service maintains a unique resource—the U.S. National Fungus Collections—for helpful and detailed information about fungi. Accurate knowledge of fungi is critical for controlling the diseases they cause. North America’s Largest Fungarium In 1869, the Smithsonian Institution transferred its fungal collection to the U.S. Department of Agriculture. It later became the Mycological Collections and finally the U.S. National Fungus Collections. “The collection had fewer than 3,000 specimens in 1885. It has grown to more than 1 million collected specimens and is the largest fungarium in North America today,” says Amy Rossman, r...

Simple Synteny: An accessible tool for genome comparison

Understanding the co-localization of genetic loci amongst species is a frequent task of many biol... more Understanding the co-localization of genetic loci amongst species is a frequent task of many biologists. While there are a number of programs currently available for generating syntenic maps, many are inaccessible to biologists who lack the required computer or scripting skills needed for proper installation or data preprocessing. We present here Simple Synteny, a free and open-source image generator for use in syntenic analysis. Simple Synteny provides an easy interface for comparing multiple genomes by only requiring the user to submit FASTA files for the genomes and genes of interest. The program employs gene color coordination across genomes, indicator arrows for changes in gene direction and automatic contig and gene resizing to produce publication-quality images which are clear and simple to interpret. Directions for using the tool and example analyses are provided. The server can be reached at: http://www.simplesynteny.com

Development of polymorphic genic-SSR markers by cDNA library sequencing in boxwood, Buxus spp. (Buxaceae)

Applications in plant sciences, 2014

Colletotrichum-ng.2372

A Multiplex Real-Time PCR Assay for the Detection of Puccinia horiana and P. chrysanthemi on Chrysanthemum

Plant Disease, 2015

Influence of Host and Geographic Locale on the Distribution of Colletotrichum cereale Lineages

PLoS ONE, 2014

Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus ha... more Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera turfgrass. Colletotrichum cereale exists as two lineages, designated clades A and B, but little is known about the distribution of these clades in natural environments, or what role these subdivisions may play in the trajectory of disease outbreaks. In this study, our objective was to determine the frequency of C. cereale clades A and B. To rapidly discriminate between the two C. cereale clades, a real-time PCR assay was developed based on the Apn2 gene. A collection of 700 C. cereale pathogens and endophytes from twenty Pooideae grass genera were genotyped. 87% of the collection was identifed as part of clade A, 11.7% as part of clade B, and 1.3% was a mixture. Colletotrichum cereale from turfgrass hosts in North America were most commonly members of clade A (78%). The overabundance of clade A in turfgrass isolates was directly attributable to the dominance of this lineage from southern sampling sites, irrespective of host. In contrast, 111 C. cereale turfgrass isolates collected from northern sampling sites were evenly distributed between clades A and B. Only 28% of C. cereale from A. stolonifera at northern sampling sites were part of clade A. These data show that environmental factors such as geographic location and host identity likely played a role in the distribution of the major C. cereale clades in North American turfgrass.

Anthracnose of Centipedegrass Turf

Applied Turfgrass Science, 2012

IMA Genome-F 3: Draft genomes of <I>Amanita</I> <I>jacksonii</I>,<I>Ceratocystis albifundus</I>, <I>Fusarium circinatum</I>, <I>Huntiella omanensis</I>, <I>Leptographium procerum</I>, <I>Rutstroemia sydowiana</I>, and <I>Sclerotinia echinophila</I>

IMA Fungus, 2014

First Report of Impatiens Downy Mildew Outbreaks Caused by Plasmopara obducens Throughout the Hawai'ian Islands

Plant Disease, 2014

First Report of Boxwood Blight Caused by Calonectria pseudonaviculata in Delaware, Maryland, New Jersey and New York

by Martha Malapi-Wight, Julie Hebert, and Jo Anne Crouch

Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

by Martha Malapi-Wight and Jo Anne Crouch

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium... more The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium
lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented
in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically
important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to
44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to
resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our
understanding of the lifestyles through comparative studies with closely related organisms.

Draft Genome Sequence of Dactylonectria macrodidyma, a Plant Pathogenic Fungus in the Nectriaceae

by Martha Malapi-Wight and Jo Anne Crouch

Dactylonectria macrodidyma is part of the Nectriaceae, a family containing important plant pathog... more Dactylonectria macrodidyma is part of the Nectriaceae, a family containing important plant pathogens. This species possesses the ability to induce disease on grapevine, avocado, and olive. Here, we report the first draft genome of D. macrodidyma isolate JAC15-245. The assembled genome was 58 Mbp and contained an estimated 16,454 genes.