1
|
Golan J, Wang YW, Adams CA, Cross H, Elmore H, Gardes M, Gonçalves SC, Hess J, Richard F, Wolfe B, Pringle A. Death caps (Amanita phalloides) frequently establish from sexual spores, but individuals can grow large and live for more than a decade in invaded forests. THE NEW PHYTOLOGIST 2024; 242:1753-1770. [PMID: 38146206 DOI: 10.1111/nph.19483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/18/2023] [Indexed: 12/27/2023]
Abstract
Global change is reshaping Earth's biodiversity, but the changing distributions of nonpathogenic fungi remain largely undocumented, as do mechanisms enabling invasions. The ectomycorrhizal Amanita phalloides is native to Europe and invasive in North America. Using population genetics and genomics, we sought to describe the life history traits of this successfully invading symbiotic fungus. To test whether death caps spread underground using hyphae, or aboveground using sexual spores, we mapped and genotyped mushrooms from European and US sites. Larger genetic individuals (genets) would suggest spread mediated by vegetative growth, while many small genets would suggest dispersal mediated by spores. To test whether genets are ephemeral or persistent, we also sampled from populations over time. At nearly every site and across all time points, mushrooms resolve into small genets. Individuals frequently establish from sexual spores. But at one Californian site, a single individual measuring nearly 10 m across dominated. At two Californian sites, the same genetic individuals were discovered in 2004, 2014, and 2015, suggesting single individuals (both large and small) can reproduce repeatedly over relatively long timescales. A flexible life history strategy combining both mycelial growth and spore dispersal appears to underpin the invasion of this deadly perennial ectomycorrhizal fungus.
Collapse
Affiliation(s)
- Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yen-Wen Wang
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Catharine A Adams
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, 94720, USA
| | - Hugh Cross
- National Ecological Observatory Network-Battelle, 1685 38th, Suite 100, Boulder, CO, 80301, USA
| | - Holly Elmore
- Rethink Priorities, 530 Divisadero St. PMB #796, San Francisco, CA, 94117, USA
| | - Monique Gardes
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174 UPS-CNRS-IRD, Université Toulouse 3 Paul Sabatier, 118 Route de Narbonne, Toulouse Cedex, F-31062, France
| | - Susana C Gonçalves
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, 3000-456, Portugal
| | | | - Franck Richard
- CEFE, Université de Montpellier - CNRS - EPHE - IRD, 1919 route de Mende, F-34293, Montpellier Cedex 5, France
| | - Benjamin Wolfe
- Department of Biology, Tufts University, Medford, MA, 02155, USA
| | - Anne Pringle
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
2
|
Silva RA, Ferro CG, Lehner MDS, Paula TJ, Mizubuti ESG. The Population of Sclerotinia sclerotiorum in Brazil Is Structured by Mycelial Compatibility Groups. PLANT DISEASE 2021; 105:3376-3384. [PMID: 33934631 DOI: 10.1094/pdis-01-21-0110-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil, and 68.5% of the isolates were assigned to either MCG 1 or MCG 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was because of differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). By contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs; lineages originating from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time, and affect many hosts, but there is evidence of some degree of outcrossing, which may lead to a more genetically variable population in the future.
Collapse
Affiliation(s)
- Rhaphael A Silva
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Camila G Ferro
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Miller da S Lehner
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Trazilbo J Paula
- Empresa de Pesquisa Agropecuária de Minas Gerais, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Eduardo S G Mizubuti
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| |
Collapse
|
3
|
|
4
|
Kedves O, Shahab D, Champramary S, Chen L, Indic B, Bóka B, Nagy VD, Vágvölgyi C, Kredics L, Sipos G. Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere. Pathogens 2021; 10:pathogens10010076. [PMID: 33467216 PMCID: PMC7830283 DOI: 10.3390/pathogens10010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/11/2022] Open
Abstract
Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.
Collapse
Affiliation(s)
- Orsolya Kedves
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Danish Shahab
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Simang Champramary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
| | - Liqiong Chen
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Boris Indic
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
| | - Bettina Bóka
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Viktor Dávid Nagy
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Közép fasor 52, H-6726 Szeged, Hungary; (O.K.); (D.S.); (S.C.); (L.C.); (B.B.); (V.D.N.); (C.V.)
- Correspondence: (L.K.); (G.S.); Tel.: +36-62-544516 (L.K.); +36-99-518769 (G.S.)
| | - György Sipos
- Functional Genomics and Bioinformatics Group, Research Center for Forestry and Wood Industry, University of Sopron, Bajcsy-Zsilinszky str. 4., H-9400 Sopron, Hungary;
- Correspondence: (L.K.); (G.S.); Tel.: +36-62-544516 (L.K.); +36-99-518769 (G.S.)
| |
Collapse
|
5
|
Rasmussen DA, Grünwald NJ. Phylogeographic Approaches to Characterize the Emergence of Plant Pathogens. PHYTOPATHOLOGY 2021; 111:68-77. [PMID: 33021879 DOI: 10.1094/phyto-07-20-0319-fi] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. This approach has been instrumental in understanding the emergence, spread, and evolution of a range of plant pathogens. In particular, phylogeography can address questions about where a pathogen originated, whether it is native or introduced, and when and how often introductions occurred. We review the theory, methods, and approaches underpinning phylogeographic inference and highlight applications providing novel insights into the emergence and spread of select pathogens. We hope that this review will be useful in assessing the power, pitfalls, and opportunities presented by various phylogeographic approaches.
Collapse
Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
| | - Niklaus J Grünwald
- Horticultural Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR
| |
Collapse
|
6
|
Cheng Q, Frost KE, Dung JKS. Population Genetic Structure of Claviceps purpurea in Cool-Season Grass Seed Crops of Oregon. PHYTOPATHOLOGY 2020; 110:1773-1780. [PMID: 32573347 DOI: 10.1094/phyto-01-20-0005-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ergot, caused by Claviceps purpurea, is a primary disease concern in irrigated cool-season grass seed production systems of Oregon. In order to better understand the genetic diversity, population structure, and the epidemiology of C. purpurea in grasses grown for seed, 226 isolates were obtained using a hierarchical sampling strategy from two fields each of Kentucky bluegrass (n = 102) and perennial ryegrass (n = 124) and characterized using 12 microsatellite markers. A total of 194 unique multilocus genotypes (MLGs) were identified in this study. There were moderate levels of genotypic diversity (H = 3.43 to 4.23) and gene diversity (Hexp = 0.45 to 0.57) within fields. After clone correction, analysis of molecular variance revealed that 66% of the genetic variation occurred between the two C. purpurea isolates collected from the same seed head of individual plants, indicating that many of the seed heads bearing multiple sclerotia were infected by ascospores rather than conidia. However, the majority of the clonal isolates obtained in this study were collected from the same seed head (i.e., the two isolates were identical MLGs), indicating a role of conidia (honeydew) in secondary infections within seed heads. Genetic differentiation was observed between populations from different hosts (22%) but was confounded by geography. The standardized index of association ranged from 0.007 to 0.122 among the four populations, suggesting potential outcrossing and differences in the relative contribution of ascospores and conidia to ergot among the fields. The results from this study provide insights into the epidemiology of ergot in cool-season grass seed crops of Oregon.
Collapse
Affiliation(s)
- Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR
| | - Kenneth E Frost
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR
| | - Jeremiah K S Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR
| |
Collapse
|
7
|
Castroagudín VL, Weiland JE, Baysal-Gurel F, Cubeta MA, Daughtrey ML, Gauthier NW, LaMondia J, Luster DG, Hand FP, Shishkoff N, Williams-Woodward J, Yang X, LeBlanc N, Crouch JA. One Clonal Lineage of Calonectria pseudonaviculata Is Primarily Responsible for the Boxwood Blight Epidemic in the United States. PHYTOPATHOLOGY 2020; 110:1845-1853. [PMID: 32584205 DOI: 10.1094/phyto-04-20-0130-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae 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 C. pseudonaviculata populations prior to 2014 had a clonal structure, and only the MAT1-2 idiomorph was observed. In this study, we examined C. pseudonaviculata 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 MAT1 idiomorph typing. All isolates presented C. pseudonaviculata-specific alleles, indicating that C. henricotiae is still absent in the U.S. states sampled. The presence of only the MAT1-2 idiomorph and gametic linkage disequilibrium suggests the prevalence of asexual reproduction. The contemporary C. pseudonaviculata 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. C. pseudonaviculata 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.
Collapse
Affiliation(s)
- Vanina L Castroagudín
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
| | - Jerry E Weiland
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, OR 97339
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110
| | - Marc A Cubeta
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606
| | - Margery L Daughtrey
- School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
| | | | - James LaMondia
- Connecticut Agricultural Experiment Station, Valley Laboratory, Windsor, CT 06095
| | - Douglas G Luster
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | | | - Nina Shishkoff
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | | | - Xiao Yang
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | - Nicholas LeBlanc
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606
| | - Jo Anne Crouch
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
| |
Collapse
|
8
|
Mahalingam T, Chen W, Rajapakse CS, Somachandra KP, Attanayake RN. Genetic Diversity and Recombination in the Plant Pathogen Sclerotinia sclerotiorum Detected in Sri Lanka. Pathogens 2020; 9:E306. [PMID: 32331222 PMCID: PMC7238271 DOI: 10.3390/pathogens9040306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 01/20/2023] Open
Abstract
Sclerotinia sclerotiorum is an important fungal pathogen on many economically important crops including cabbage worldwide. Even though population structure and genetic diversity of S. sclerotiorum is well studied in temperate climatic conditions, only a few studies have been conducted in tropical countries. It is also not clear whether the populations are clonal or recombining in the tropics. In filling this information gap, 47 isolates of S. sclerotiorum were collected from commercial cabbage (Brassica oleracea L.) fields in Nuwara Eliya district of Sri Lanka, where the disease has been previously reported. All the isolates were subjected to genetic diversity study using mycelial compatibility grouping and microsatellite markers. Fourteen mycelial compatibility groups (MCGs) and 23 multilocus haplotypes (MLHs) were recorded. Mean expected heterozygosity of the population was 0.56. MLHs were weakly correlated with MCGs. Population genetic structure analysis and principal coordinates identified three genetic clusters. Genetic recombination was inferred within each genetic cluster when isolates were subjected to clone correction. There was evidence of multiple infections on single plant as detected by the presence of more than one MCG on each cabbage plant. However, multiple infections did not increase the disease severity in detached leaf assay. We found high genetic diversity and recombination of S. sclerotiorum population in a tropical country, Sri Lanka. Importance of detecting genetic structure when inferring recombination was also highlighted.
Collapse
Affiliation(s)
- Thirega Mahalingam
- Department of Plant and Molecular Biology, University of Kelaniya, Kelaniya 11600, Sri Lanka;
| | - Weidong Chen
- United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Grain Legume Genetics and Physiology Research Unit, Washington State University, Pullman, WA 99164, USA;
| | | | | | | |
Collapse
|
9
|
Gold KM, Townsend PA, Larson ER, Herrmann I, Gevens AJ. Contact Reflectance Spectroscopy for Rapid, Accurate, and Nondestructive Phytophthora infestans Clonal Lineage Discrimination. PHYTOPATHOLOGY 2020; 110:851-862. [PMID: 31880984 DOI: 10.1094/phyto-08-19-0294-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Populations of Phytophthora infestans, the oomycete causal agent of potato late blight in the United States, are predominantly asexual, and isolates are characterized by clonal lineage or asexual descendants of a single genotype. Current tools for clonal lineage identification are time consuming and require laboratory equipment. We previously found that foliar spectroscopy can be used for high-accuracy pre- and postsymptomatic detection of P. infestans infections caused by clonal lineages US-08 and US-23. In this work, we found subtle but distinct differences in spectral responses of potato foliage infected by these clonal lineages in both growth-chamber time-course experiments (12- to 24-h intervals over 5 days) and naturally infected samples from commercial production fields. In both settings, we measured continuous visible to shortwave infrared reflectance (400 to 2,500 nm) on leaves using a portable spectrometer with contact probe. We consistently discriminated between infections caused by the two clonal lineages across all stages of disease progression using partial least squares (PLS) discriminant analysis, with total accuracies ranging from 88 to 98%. Three-class random forest differentiation between control, US-08, and US-23 yielded total discrimination accuracy ranging from 68 to 76%. Differences were greatest during presymptomatic infection stages and progressed toward uniformity as symptoms advanced. Using PLS-regression trait models, we found that total phenolics, sugar, and leaf mass per area were different between lineages. Shortwave infrared wavelengths (>1,100 nm) were important for clonal lineage differentiation. This work provides a foundation for future use of hyperspectral sensing as a nondestructive tool for pathovar differentiation.
Collapse
Affiliation(s)
- Kaitlin M Gold
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A
| | - Philip A Townsend
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A
| | - Eric R Larson
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A
| | - Ittai Herrmann
- The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Amanda J Gevens
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, U.S.A
| |
Collapse
|
10
|
Petkar A, Harris-Shultz K, Wang H, Brewer MT, Sumabat L, Ji P. Genetic and phenotypic diversity of Fusarium oxysporum f. sp. niveum populations from watermelon in the southeastern United States. PLoS One 2019; 14:e0219821. [PMID: 31318912 PMCID: PMC6638948 DOI: 10.1371/journal.pone.0219821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 07/03/2019] [Indexed: 12/03/2022] Open
Abstract
Fusarium wilt of watermelon, caused by Fusarium oxysporum f. sp. niveum (FON), occurs worldwide and is responsible for substantial yield losses in watermelon-producing areas of the southeastern United States. Management of this disease largely relies on the use of integrated pest management (i.e., fungicides, resistant cultivars, crop rotation, etc.). Knowledge about race structure and genetic diversity of FON in the southeastern US is limited. To determine genetic diversity of the pathogen, FON isolates were collected from symptomatic watermelon plants in commercial fields in Georgia and Florida, USA, and identified based on morphological characteristics and PCR analysis using FON-specific primers. Discriminant analysis of principal components (DAPC) of 99 isolates genotyped with 15 simple sequence repeat (SSR) markers grouped the isolates in eight distinct clusters with two prominent clusters (clusters 1 and 8). Cluster 1 consisted of a total of 14 isolates, out of which 85.7% of the isolates were collected in Florida. However, most of the isolates (92.4%) in cluster 8 were collected in Georgia. Both DAPC and pairwise population differentiation analysis (ФPT) revealed that the genetic groups were closely associated with geographical locations of pathogen collection. Three races of FON (races 0, 2 and 3) were identified in the phenotypic analysis; with race 3 identified for the first time in Georgia. Overall, 5.1%, 38.9% and 55.9% of the isolates were identified as race 0, race 2 and race 3, respectively. The majority of the isolates in cluster 1 and cluster 8 belonged to either race 2 (35.6%) or race 3 (45.8%). Additionally, no relationship between genetic cluster assignment and races of the isolates was observed. The information obtained on genotypic and phenotypic diversity of FON in the southeastern US will help in development of effective disease management programs to combat Fusarium wilt.
Collapse
Affiliation(s)
- Aparna Petkar
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, Georgia, United States of America
| | - Karen Harris-Shultz
- United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Crop Genetics and Breeding Research Unit, Tifton, Georgia, United States of America
| | - Hongliang Wang
- United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Crop Genetics and Breeding Research Unit, Tifton, Georgia, United States of America
| | - Marin Talbot Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Leilani Sumabat
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Pingsheng Ji
- Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, Georgia, United States of America
- * E-mail:
| |
Collapse
|
11
|
Affiliation(s)
- Rimvydas Vasiliauskas
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07 Uppsala, Sweden
| |
Collapse
|
12
|
Kim MS, Klopfenstein NB, McDonald GI, Arumuganathan K, Vidaver AK. Characterization of North American Armillaria species by nuclear DNA content and RFLP analysis. Mycologia 2019. [DOI: 10.1080/00275514.2000.12061232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Mee-Sook Kim
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| | - Ned B. Klopfenstein
- USDA Forest Service, RMRS, Forestry Sciences Laboratory, 1221 S. Main, Moscow, Idaho 83843-4298
| | - Geral I. McDonald
- USDA Forest Service, RMRS, Forestry Sciences Laboratory, 1221 S. Main, Moscow, Idaho 83843-4298
| | | | - Anne K. Vidaver
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska 68583-0722
| |
Collapse
|
13
|
Affiliation(s)
- James J. Worrall
- College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210
| |
Collapse
|
14
|
Xu L, Li G, Jiang D, Chen W. Sclerotinia sclerotiorum: An Evaluation of Virulence Theories. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:311-338. [PMID: 29958073 DOI: 10.1146/annurev-phyto-080417-050052] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oxalic acid production in Sclerotinia sclerotiorum has long been associated with virulence. Research involving UV-induced, genetically undefined mutants that concomitantly lost oxalate accumulation, sclerotial formation, and pathogenicity supported the conclusion that oxalate is an essential pathogenicity determinant of S. sclerotiorum. However, recent investigations showed that genetically defined mutants that lost oxalic acid production but accumulated fumaric acid could cause disease on many plants and substantiated the conclusion that acidic pH, not oxalic acid per se, is the necessary condition for disease development. Critical evaluation of available evidence showed that the UV-induced mutants harbored previously unrecognized confounding genetic defects in saprophytic growth and pH responsiveness, warranting reevaluation of the conclusions about virulence based on the UV-induced mutants. Furthermore, analyses of the evidence suggested a hypothesis for the existence of an unrecognized regulator responsive to acidic pH. Identifying the unknown pH regulator would offer a new avenue for investigating pH sensing/regulation in S. sclerotiorum and novel targets for intervention in disease control strategies.
Collapse
Affiliation(s)
- Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Weidong Chen
- Grain Legume Genetics and Physiology Research Unit, US Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, Washington 99164, USA
- Departments of Plant Pathology and Molecular Plant Sciences Program, Washington State University, Pullman, Washington 99164, USA;
| |
Collapse
|
15
|
Epps MJ, Arnold AE. Quantifying beetle-macrofungal associations in a temperate biodiversity hot spot. Mycologia 2018; 110:269-285. [DOI: 10.1080/00275514.2018.1430439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mary Jane Epps
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
| | - A. Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
| |
Collapse
|
16
|
Willbur JF, Ding S, Marks ME, Lucas H, Grau CR, Groves CL, Kabbage M, Smith DL. Comprehensive Sclerotinia Stem Rot Screening of Soybean Germplasm Requires Multiple Isolates of Sclerotinia sclerotiorum. PLANT DISEASE 2017; 101:344-353. [PMID: 30681926 DOI: 10.1094/pdis-07-16-1055-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sclerotinia sclerotiorum population variability directly affects Sclerotinia stem rot (SSR) resistance breeding programs. In the north-central United States, however, soybean germplasm selection has often involved only a single isolate. Forty-four S. sclerotiorum isolates from Illinois, Michigan, Minnesota, Nebraska, Wisconsin, Poland, and across 11 different host species were evaluated for variation in isolate in vitro growth, in vitro oxalate production, and in planta aggressiveness on the susceptible soybean 'Williams 82'. Significant differences (P < 0.0001) were detected in isolate in planta aggressiveness, in vitro growth, and in vitro oxalate production. Furthermore, diverse isolate characteristics were observed within all hosts and locations of collection. Aggressiveness was not correlated to colony growth and was only weakly correlated (r = 0.26, P < 0.0001) to isolate oxalate production. In addition, the host or location of collection did not explain isolate aggressiveness. Isolate oxalic acid production, however, may be partially explained by the host (P < 0.05) and location (P < 0.01) of collection. Using a representative subset of nine S. sclerotiorum isolates and soybean genotypes exhibiting susceptible or resistant responses (determined using a single isolate), a significant interaction (P = 0.04) was detected between isolates and genotypes when SSR severity was evaluated. Our findings suggest that screening of S. sclerotiorum-resistant soybean germplasm should be performed with multiple isolates to account for the overall diversity of S. sclerotiorum isolates found throughout the soybean-growing regions of the United States.
Collapse
Affiliation(s)
- J F Willbur
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - S Ding
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - M E Marks
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - H Lucas
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - C R Grau
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - C L Groves
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - M Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| | - D L Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison 53706
| |
Collapse
|
17
|
Ceresini PC, Shew HD, Vilgalys RJ, Cubeta MA. Genetic diversity ofRhizoctonia solaniAG-3 from potato and tobacco in North Carolina. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Paulo C. Ceresini
- Departamento de Biologia, Faculdade de Engenharia, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), 15385-000, Ilha Solteira, São Paulo, Brazil
| | - H. David Shew
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
| | - Rytas J. Vilgalys
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Marc A. Cubeta
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
18
|
McAlpin C, Horn B, Wicklow D. DNA fingerprinting analysis of vegetative compatibility groups inAspergillus caelatus. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- C.E. McAlpin
- National Center for Agricultural Utilization Research, USDA, ARS, Peoria, Illinois 61604
| | - B.W. Horn
- National Peanut Laboratory, USDA, ARS, Dawson, Georgia 31742
| | - D.T. Wicklow
- National Center for Agricultural Utilization Research, USDA, ARS, Peoria, Illinois 61604
| |
Collapse
|
19
|
Affiliation(s)
| | | | - Jan Stenlid
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, S-750 07 Uppsala, Sweden
| |
Collapse
|
20
|
Yang D, Zhang J, Wu M, Chen W, Li G, Yang L. Characterization of the Mycelial Compatibility Groups and Mating Type Alleles in Populations of Sclerotinia minor in Central China. PLANT DISEASE 2016; 100:2313-2318. [PMID: 30682912 DOI: 10.1094/pdis-12-15-1453-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ninety-five single-sclerotium isolates were obtained from lettuce and weeds in three counties in central China. They were identified belonging to Sclerotinia minor based on colony morphology and the S. minor-specific DNA marker. Mycelial compatibility groups (MCGs) and the mating type (MAT) alleles in these isolates were determined using the methods of paired cultures and specific PCR, respectively, and the MCG data were used to calculate Shannon's H index (H) and Simpson index (S), thereby evaluating diversity of S. minor. Eight MCGs (MCG1 to MCG8) and two MAT alleles (Inv+, Inv-) were identified in these isolates. Low diversity was detected for the total 95 isolates (H = 1.748, S = 0.786). Isolates of different MCGs or with different MAT alleles did not significantly differ (P > 0.05) in mycelial growth rate on potato dextrose agar (PDA, 20°C) or lesion diameter on lettuce leaves (20°C), but slightly differed in the number of sclerotia produced on PDA (20°C). Furthermore, this study reported five new host plants of S. minor in China, including Capsella bursa-pastoris, Oenanthe javanica, Fragaria gracilis, Ranunculus ternatus, and Salvia plebeia, and identified three hypovirulent isolates. These results broaden our understanding about the population biology of S. minor.
Collapse
Affiliation(s)
- Dan Yang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weidong Chen
- United States Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Yang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
21
|
Fry WE. Phytophthora infestans: New Tools (and Old Ones) Lead to New Understanding and Precision Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:529-47. [PMID: 27359366 DOI: 10.1146/annurev-phyto-080615-095951] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
New tools have revealed that migrations of Phytophthora infestans have been a dominant feature of the population biology of this pathogen for the past 50 years, and maybe for the past 170 years. We now have accurate information on the composition of many P. infestans populations. However, migration followed by selection can lead and has led to dramatically rapid changes in populations over large regions. Except for the highlands of central Mexico, many populations of P. infestans have probably been in flux over the past several decades. There is some evidence that this pathogen has different characteristics in the field than it does in the lab, and early field phenotypic analyses of hypotheses concerning fitness and pathogenicity would be beneficial. The newly available capacity to acquire and process vast amounts of weather and weather forecast data in combination with advancements in molecular diagnostics enables much greater precision in late blight management to produce recommendations that are site, host, and pathogen specific.
Collapse
Affiliation(s)
- William E Fry
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850;
| |
Collapse
|
22
|
Jaimes YY, Gonzalez C, Rojas J, Cornejo OE, Mideros MF, Restrepo S, Cilas C, Furtado EL. Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia. PLANT DISEASE 2016; 100:1548-1558. [PMID: 30686241 DOI: 10.1094/pdis-12-15-1498-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Frosty pod rot (FPR) disease on cocoa, caused by Moniliophthora roreri, is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple-sequence repeats (SSR) markers. In total, 117 different multilocus genotypes were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association (IA and řd) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoing sporadic recombination or partial recombination through parasexuality. A Bayesian clustering analysis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geographical differentiation among isolates. Similar results were obtained by a discriminant analysis of principal components, a principal coordinate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did contribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.
Collapse
Affiliation(s)
- Yeirme Y Jaimes
- Corpoica, Research Center La Suiza, Rionegro-Santander, Colombia; CAPES PEC-PG Fellow; and Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
| | | | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Maria F Mideros
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Christian Cilas
- CIRAD, UR Bioagresseurs, Campus de Baillarguet, TA A-106/D, 34398 Montpellier Cedex 5, France
| | - E L Furtado
- CNPq Fellow, Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
| |
Collapse
|
23
|
Tok FM, Derviş S, Arslan M. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD) and simple sequence repeat (SSR) analyses. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1208059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Fatih Mehmet Tok
- Faculty of Agriculture, Department of Plant Protection, Mustafa Kemal University, Hatay, Turkey
| | - Sibel Derviş
- Faculty of Agriculture, Department of Plant Protection, Mustafa Kemal University, Hatay, Turkey
| | - Mehmet Arslan
- Faculty of Agriculture, Department of Agricultural Biotechnology, Erciyes University, Kayseri, Turkey
| |
Collapse
|
24
|
Abstract
Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305-E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.
Collapse
|
25
|
Kamvar ZN, Brooks JC, Grünwald NJ. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front Genet 2015; 6:208. [PMID: 26113860 PMCID: PMC4462096 DOI: 10.3389/fgene.2015.00208] [Citation(s) in RCA: 415] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies.
Collapse
Affiliation(s)
- Zhian N. Kamvar
- Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Jonah C. Brooks
- College of Electrical Engineering and Computer Science, Oregon State UniversityCorvallis, OR, USA
| | - Niklaus J. Grünwald
- Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Horticultural Crops Research Laboratory, USDA Agricultural Research ServiceCorvallis, OR, USA
| |
Collapse
|
26
|
Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE. Exploring origins, invasion history and genetic diversity ofImperata cylindrica(L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Mol Ecol 2015; 24:2177-93. [DOI: 10.1111/mec.13167] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/31/2022]
Affiliation(s)
- A. Millie Burrell
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
| | - Alan E. Pepper
- Department of Biology; Texas A&M University; College Station TX 77843-3258 USA
| | - George Hodnett
- Department of Soil and Crop Sciences; Texas A&M University; College Station TX 77843-2474 USA
| | - John A. Goolsby
- Cattle Fever Tick Research Laboratory; USDA-ARS; Moore Air Base Building 6419 Edinburg TX 78541 USA
| | - William A. Overholt
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Alexis E. Racelis
- Department of Biology; University of Texas Pan American; 1201 West University Drive Edinburg TX 78539 USA
| | - Rodrigo Diaz
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Patricia E. Klein
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
| |
Collapse
|
27
|
Gramaje D, León M, Santana M, Crous PW, Armengol J. Multilocus ISSR markers reveal two major genetic groups in Spanish and South African populations of the grapevine fungal pathogen Cadophora luteo-olivacea. PLoS One 2014; 9:e110417. [PMID: 25310345 PMCID: PMC4195744 DOI: 10.1371/journal.pone.0110417] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
Cadophora luteo-olivacea is a lesser-known fungal trunk pathogen of grapevine which has been recently isolated from vines showing decline symptoms in grape growing regions worldwide. In this study, 80 C. luteo-olivacea isolates (65 from Spain and 15 from South Africa) were studied. Inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 55 polymorphic loci from four ISSR primers selected from an initial screen of 13 ISSR primers. The ISSR markers revealed 40 multilocus genotypes (MLGs) in the global population. Minimum spanning network analysis showed that the MLGs from South Africa clustered around the most frequent genotype, while the genotypes from Spain were distributed all across the network. Principal component analysis and dendrograms based on genetic distance and bootstrapping identified two highly differentiated genetic clusters in the Spanish and South African C. luteo-olivacea populations, with no intermediate genotypes between these clusters. Movement within the Spanish provinces may have occurred repeatedly given the frequent retrieval of the same genotype in distant locations. The results obtained in this study provide new insights into the population genetic structure of C. luteo-olivacea in Spain and highlights the need to produce healthy and quality planting material in grapevine nurseries to avoid the spread of this fungus throughout different grape growing regions.
Collapse
Affiliation(s)
- David Gramaje
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, Valencia, Spain
| | - Maela León
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, Valencia, Spain
| | - Marcela Santana
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, Valencia, Spain
| | - Pedro W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, Valencia, Spain
| |
Collapse
|
28
|
Attanayake RN, Tennekoon V, Johnson DA, Porter LD, del Río-Mendoza L, Jiang D, Chen W. Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay. Heredity (Edinb) 2014; 113:353-63. [PMID: 24781807 DOI: 10.1038/hdy.2014.37] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 11/09/2022] Open
Abstract
The occurrence and frequency of outcrossing in homothallic fungal species in nature is an unresolved question. Here we report detection of frequent outcrossing in the homothallic fungus Sclerotinia sclerotiorum. In using multilocus linkage disequilibrium (LD) to infer recombination among microsatellite alleles, high mutation rates confound the estimates of recombination. To distinguish high mutation rates from recombination to infer outcrossing, 8 population samples comprising 268 S. sclerotiorum isolates from widely distributed agricultural fields were genotyped for 12 microsatellite markers, resulting in multiple polymorphic markers on three chromosomes. Each isolate was homokaryotic for the 12 loci. Pairwise LD was estimated using three methods: Fisher's exact test, index of association (IA) and Hedrick's D'. For most of the populations, pairwise LD decayed with increasing physical distance between loci in two of the three chromosomes. Therefore, the observed recombination of alleles cannot be simply attributed to mutation alone. Different recombination rates in various DNA regions (recombination hot/cold spots) and different evolutionary histories of the populations could explain the observed differences in rates of LD decay among the chromosomes and among populations. The majority of the isolates exhibited mycelial incompatibility, minimizing the possibility of heterokaryon formation and mitotic recombination. Thus, the observed high intrachromosomal recombination is due to meiotic recombination, suggesting frequent outcrossing in these populations, supporting the view that homothallism favors universal compatibility of gametes instead of traditionally believed haploid selfing in S. sclerotiorum. Frequent outcrossing facilitates emergence and spread of new traits such as fungicide resistance, increasing difficulties in managing Sclerotinia diseases.
Collapse
Affiliation(s)
- R N Attanayake
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - V Tennekoon
- Department of Economics, University of Oklahoma, Norman, OK, USA
| | - D A Johnson
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - L D Porter
- USDA-ARS, Vegetable and Forage Crops Research Unit, Prosser, WA, USA
| | - L del Río-Mendoza
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - D Jiang
- Department of Plant Protection, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - W Chen
- 1] Department of Plant Pathology, Washington State University, Pullman, WA, USA [2] USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, USA
| |
Collapse
|
29
|
Kamvar ZN, Tabima JF, Grünwald NJ. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2014; 2:e281. [PMID: 24688859 PMCID: PMC3961149 DOI: 10.7717/peerj.281] [Citation(s) in RCA: 1402] [Impact Index Per Article: 140.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/30/2014] [Indexed: 12/29/2022] Open
Abstract
Many microbial, fungal, or oomcyete populations violate assumptions for population genetic analysis because these populations are clonal, admixed, partially clonal, and/or sexual. Furthermore, few tools exist that are specifically designed for analyzing data from clonal populations, making analysis difficult and haphazard. We developed the R package poppr providing unique tools for analysis of data from admixed, clonal, mixed, and/or sexual populations. Currently, poppr can be used for dominant/codominant and haploid/diploid genetic data. Data can be imported from several formats including GenAlEx formatted text files and can be analyzed on a user-defined hierarchy that includes unlimited levels of subpopulation structure and clone censoring. New functions include calculation of Bruvo’s distance for microsatellites, batch-analysis of the index of association with several indices of genotypic diversity, and graphing including dendrograms with bootstrap support and minimum spanning networks. While functions for genotypic diversity and clone censoring are specific for clonal populations, several functions found in poppr are also valuable to analysis of any populations. A manual with documentation and examples is provided. Poppr is open source and major releases are available on CRAN: http://cran.r-project.org/package=poppr. More supporting documentation and tutorials can be found under ‘resources’ at: http://grunwaldlab.cgrb.oregonstate.edu/.
Collapse
Affiliation(s)
- Zhian N Kamvar
- Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , USA
| | - Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , USA ; Horticultural Crops Research Laboratory, USDA-ARS , Corvallis, OR , USA
| |
Collapse
|
30
|
Herrera CM, Pozo MI, Bazaga P. Nonrandom genotype distribution among floral hosts contributes to local and regional genetic diversity in the nectar-living yeastMetschnikowia reukaufii. FEMS Microbiol Ecol 2013; 87:568-75. [DOI: 10.1111/1574-6941.12245] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/03/2013] [Accepted: 11/04/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - María I. Pozo
- Estación Biológica de Doñana; CSIC; Sevilla Spain
- Laboratory of Plant Ecology; University of Leuven; Heverlee Belgium
| | - Pilar Bazaga
- Estación Biológica de Doñana; CSIC; Sevilla Spain
| |
Collapse
|
31
|
Attanayake RN, Carter PA, Jiang D, Del Río-Mendoza L, Chen W. Sclerotinia sclerotiorum populations infecting canola from China and the United States are genetically and phenotypically distinct. PHYTOPATHOLOGY 2013; 103:750-761. [PMID: 23464902 DOI: 10.1094/phyto-07-12-0159-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity was assessed with sensitivity to three fungicides, production of oxalate and sclerotia, growth rate, and virulence on two canola cultivars. No shared MCGs or multilocus haplotypes were detected between the two populations, and populations differed significantly (P < 0.001). Recombination was detected in both populations but was greater in the Chinese population. A polymerase chain reaction detection assay showed that ~60% of the isolates were inversion-plus at the mating type locus. The two populations differed significantly (P < 0.05) for all of the phenotypic traits except for sensitivity to fungicide fluazinam and virulence. Isolates in the Chinese population were unique in several aspects. Despite the phenotypic differentiation, heritabilities of the phenotypic traits were similar for both populations. Significant correlations were found among five phenotypic traits. Cross resistance to benomyl and iprodione was detected. Virulence was not significantly correlated with any other phenotypic trait and had the least heritability. However, both populations were equally virulent on either a susceptible or a moderately resistant canola cultivars.
Collapse
Affiliation(s)
- Renuka N Attanayake
- Department of Plant Pahtology, Washington State University, Pullman, 99164, USA
| | | | | | | | | |
Collapse
|
32
|
McKay AH, Förster H, Adaskaveg JE. Distinguishing Galactomyces citri-aurantii from G. geotrichum and characterizing population structure of the two postharvest sour rot pathogens of fruit crops in California. PHYTOPATHOLOGY 2012; 102:528-538. [PMID: 22494250 DOI: 10.1094/phyto-05-11-0156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A growth assay in lemon juice and polymerase chain reaction amplifications using newly designed species-specific primers from endopolygalacturonase and β-tubulin genes rapidly differentiated isolates of the morphologically similar fruit sour rot pathogens Galactomyces citriaurantii and G. geotrichum. Isolates of both species were collected from agricultural soils and decaying fruit at locations within and outside California, including worldwide locations, and were used in population genetic studies based on amplified fragment length polymorphic (AFLP) DNA markers. For all four geographically defined subpopulations (three counties of California and locations outside California) among 97 isolates of G. citri-aurantii and for the two subpopulations (origin within or outside California) among 35 isolates of G. geotrichum, the proportion of polymorphic loci and haplotypic diversity was high. In total, 82 unique haplotypes were identified for G. citri-aurantii for the four subpopulations and, of these, 80 haplotypes were unique among subpopulations. For G. geotrichum, 25 unique haplotypes were identified among the two subpopulations and no haplotype was shared. Indices of genetic differences (F(ST)) between subpopulations within each species were all low (e.g., 0.038 for G. geotrichum and 0.085 to 0.226 for G. citriaurantii), indicating a low level of genetic differentiation. Following clone correction, mating type segregation ratios for G. citri-aurantii did not significantly (P > 0.1) deviate from a 1:1 ratio for all four subpopulations or the entire population. Tests of the index of association (I(A)) and parsimony tree-length permutation tests (PTLPT) supported a random mating structure for clone-corrected data for the Kern, Tulare, and Ventura County subpopulations and the null hypothesis of random mating could not be rejected. Additionally, PTLPT also supported random mating for the "outside of California" population. For G. geotrichum, random mating was only tested using I(A) and PTLPT and the null hypothesis of random mating was not rejected (P > 0.05) using clone-corrected data. Further evidence that sexual recombination likely occurs in both species of Galactomyces was the lack of grouping consistency in the unweighted pair-group method with arithmetic mean clustering of AFLP data. A high confidence based on bootstrap values was obtained for only a few of the nodes in each of the two trees. A mixed reproduction system with an out-crossing sexual mating system and a prolific asexual phase is proposed for both species.
Collapse
Affiliation(s)
- A H McKay
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
| | | | | |
Collapse
|
33
|
Billiard S, López-Villavicencio M, Hood ME, Giraud T. Sex, outcrossing and mating types: unsolved questions in fungi and beyond. J Evol Biol 2012; 25:1020-38. [PMID: 22515640 DOI: 10.1111/j.1420-9101.2012.02495.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Variability in the way organisms reproduce raises numerous, and still unsolved, questions in evolutionary biology. In this study, we emphasize that fungi deserve a much greater emphasis in efforts to address these questions because of their multiple advantages as model eukaryotes. A tremendous diversity of reproductive modes and mating systems can be found in fungi, with many evolutionary transitions among closely related species. In addition, fungi show some peculiarities in their mating systems that have received little attention so far, despite the potential for providing insights into important evolutionary questions. In particular, selfing can occur at the haploid stage in addition to the diploid stage in many fungi, which is generally not possible in animals and plants but has a dramatic influence upon the structure of genetic systems. Fungi also present several advantages that make them tractable models for studies in experimental evolution. Here, we briefly review the unsolved questions and extant hypotheses about the evolution and maintenance of asexual vs. sexual reproduction and of selfing vs. outcrossing, focusing on fungal life cycles. We then propose how fungi can be used to address these long-standing questions and advance our understanding of sexual reproduction and mating systems across all eukaryotes.
Collapse
Affiliation(s)
- S Billiard
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, Villeneuve d'Ascq Cedex, France.
| | | | | | | |
Collapse
|
34
|
HERRERA CM, POZO MI, BAZAGA P. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast. Mol Ecol 2011; 20:4395-407. [DOI: 10.1111/j.1365-294x.2011.05217.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Csöndes I, Cseh A, Taller J, Poczai P. Genetic diversity and effect of temperature and pH on the growth of Macrophomina phaseolina isolates from sunflower fields in Hungary. Mol Biol Rep 2011; 39:3259-69. [PMID: 21695429 DOI: 10.1007/s11033-011-1094-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
Abstract
The effects of temperature and pH on the growth of 45 Hungarian Macrophomina phaseolina isolates from different locations and hosts were compared on the basis of their genetic diversity. One Spanish and two Serbian isolates were also included in the experiment. The most favourable temperature regimes for the development of the isolates ranged between 25 and 35 °C. The optimal pH for the pathogen varied between 4.0 and 6.0, but growth was observed on potato dextrose agar even at pH values of 3.0, 7.0 and 8.0. RAPD analysis with 13 different primer pairs generated 148 unambiguous bands. RFLP analysis involving 8 different restriction endonucleases was performed on a 1550 bp fragment of the rDNA region containing internal transcribed spacers (ITS1, ITS2), the 5.8S rDNA and part of the 25S rDNA. The greatest genetic distance values were obtained for three isolates, two from Hungary and one from Spain, which had similar values, but were quite distinct from all the others. A strong positive correlation was observed between the genetic distances and the growth parameters measured at various temperatures, and between the geographical data and the growth data sets at different pH values, but the correlation was less strong in the latter case. While Hungarian M. phaseolina populations are thought to reproduce clonally, the present results indicate the coexistence of different haplotypes in this area, and besides the geographical dominance of a given haplotype it was found that a closer genetic relationship might exist between spatially distinct haplotypes.
Collapse
Affiliation(s)
- Izabella Csöndes
- Department of Botany and Plant Production, Faculty of Animal Science, University of Kaposvár, PO Box 16, 7400 Kaposvár, Hungary.
| | | | | | | |
Collapse
|
36
|
Grünwald NJ, Goss EM. Evolution and population genetics of exotic and re-emerging pathogens: novel tools and approaches. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:249-267. [PMID: 21370974 DOI: 10.1146/annurev-phyto-072910-095246] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species, allowing for the unprecedented reconstruction of the demographic history of pathogens. Specifically, recent advances in the application of coalescent, maximum likelihood (ML), and Bayesian methods to population genetic data combined with increasing availability of affordable sequencing and parallel computing have created the opportunity to apply these methods to a broad range of questions regarding the evolution of emerging pathogens. These approaches are particularly powerful when used to test multiple competing hypotheses. We provide several examples illustrating how coalescent analysis provides critical insights into understanding migration pathways as well as processes of divergence, speciation, and recombination.
Collapse
Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA.
| | | |
Collapse
|
37
|
Dunn AR, Milgroom MG, Meitz JC, McLeod A, Fry WE, McGrath MT, Dillard HR, Smart CD. Population Structure and Resistance to Mefenoxam of Phytophthora capsici in New York State. PLANT DISEASE 2010; 94:1461-1468. [PMID: 30743368 DOI: 10.1094/pdis-03-10-0221] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 2006, 2007, and 2008, we sampled 257 isolates of Phytophthora capsici from vegetables at 22 sites in four regions of New York, to determine variation in mefenoxam resistance and population genetic structure. Isolates were assayed for mefenoxam resistance and genotyped for mating type and five microsatellite loci. We found mefenoxam-resistant isolates at a high frequency in the Capital District and Long Island, but none were found in western New York or central New York. Both A1 and A2 mating types were found at 12 of the 22 sites, and we detected 126 distinct multilocus genotypes, only nine of which were found at more than one site. Significant differentiation (FST) was found in more than 98% of the pairwise comparisons between sites; approximately 24 and 16% of the variation in the population was attributed to differences among regions and sites, respectively. These results indicate that P. capsici in New York is highly diverse, but gene flow among regions and fields is restricted. Therefore, each field needs to be considered an independent population, and efforts to prevent movement of inoculum among fields need to be further emphasized to prevent the spread of this pathogen.
Collapse
Affiliation(s)
- A R Dunn
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - M G Milgroom
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - J C Meitz
- Department of Plant Pathology, University of Stellenbosch, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - A McLeod
- Department of Plant Pathology, University of Stellenbosch, Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - W E Fry
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853
| | - M T McGrath
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Riverhead, NY 11901
| | - H R Dillard
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - C D Smart
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| |
Collapse
|
38
|
Hosoya T, Hirose D, Fujisaki M, Tokumasu S, Kakishima M, Osono T, Kubono T. Internal transcribed spacer haplotype diversity and their geographical distribution in Dasyscyphella longistipitata (Hyaloscyphaceae, Helotiales) occurring on Fagus crenata cupules in Japan. MYCOSCIENCE 2010. [DOI: 10.1007/s10267-009-0020-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
39
|
Saleh AA, Ahmed HU, Todd TC, Travers SE, Zeller KA, Leslie JF, Garrett KA. Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean and sorghum. Mol Ecol 2010; 19:79-91. [PMID: 19943894 DOI: 10.1111/j.1365-294x.2009.04433.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Agricultural and wild ecosystems may interact through shared pathogens such as Macrophomina phaseolina, a generalist clonal fungus with more than 284 plant hosts that is likely to become more important under climate change scenarios of increased heat and drought stress. To evaluate the degree of subdivision in populations of M. phaseolina in Kansas agriculture and wildlands, we compared 143 isolates from maize fields adjacent to tallgrass prairie, nearby sorghum fields, widely dispersed soybean fields and isolates from eight plant species in tallgrass prairie. Isolate growth phenotypes were evaluated on a medium containing chlorate. Genetic characteristics were analysed based on amplified fragment length polymorphisms and the sequence of the rDNA-internal transcribed spacer (ITS) region. The average genetic similarity was 58% among isolates in the tallgrass prairie, 71% in the maize fields, 75% in the sorghum fields and 80% in the dispersed soybean fields. The isolates were divided into four clusters: one containing most of the isolates from maize and soybean, two others containing isolates from wild plants and sorghum, and a fourth containing a single isolate recovered from Solidago canadensis in the tallgrass prairie. Most of the sorghum isolates had the dense phenotype on media containing chlorate, while those from other hosts had either feathery or restricted phenotypes. These results suggest that the tallgrass prairie supports a more diverse population of M. phaseolina per area than do any of the crop species. Subpopulations show incomplete specialization by host. These results also suggest that inoculum produced in agriculture may influence tallgrass prairie communities, and conversely that different pathogen subpopulations in tallgrass prairie can interact there to generate 'hybrids' with novel genetic profiles and pathogenic capabilities.
Collapse
Affiliation(s)
- A A Saleh
- Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506-5502, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
Lourenço V, Moya A, González-Candelas F, Carbone I, Maffia LA, Mizubuti ESG. Molecular diversity and evolutionary processes of Alternaria solani in Brazil inferred using genealogical and coalescent approaches. PHYTOPATHOLOGY 2009; 99:765-774. [PMID: 19453237 DOI: 10.1094/phyto-99-6-0765] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.
Collapse
Affiliation(s)
- Valdir Lourenço
- Departamento de Fitopatologia, Universidade Federal de Viçosa, 36570-000 Viçosa, MG, Brazil
| | | | | | | | | | | |
Collapse
|
41
|
Bernardes de Assis J, Peyer P, Rush MC, Zala M, McDonald BA, Ceresini PC. Divergence between sympatric rice- and soybean-infecting populations of Rhizoctonia solani anastomosis group-1 IA. PHYTOPATHOLOGY 2008; 98:1326-33. [PMID: 19000008 DOI: 10.1094/phyto-98-12-1326] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rhizoctonia solani anastomosis group (AG)-1 IA causes soybean foliar blighting (aerial blight) and rice sheath blight diseases. Although taxonomically related within the AG-1 complex, sister populations of R. solani AG-1 IA infecting Poaceae (rice) and Fabaceae (soybean) are genetically distinct based on internal transcribed spacer rDNA. However, there is currently no information available regarding the extent of genetic differentiation and host specialization between rice- and soybean-infecting populations of R. solani AG-1 IA. We used 10 microsatellite loci to compare sympatric R. solani AG-1 IA populations infecting rice and soybeans in Louisiana and one allopatric rice-infecting population from Texas. None of the 154 multilocus genotypes found among the 223 isolates were shared among the three populations. Partitioning of genetic diversity showed significant differentiation among sympatric populations from different host species (Phi(ST) = 0.39 to 0.41). Historical migration patterns between sympatric rice- and soybean-infecting populations from Louisiana were asymmetrical. Rice- and soybean-derived isolates of R. solani AG-1 IA were able to infect both rice and soybean, but were significantly more aggressive on their host of origin, consistent with host specialization. The soybean-infecting population from Louisiana was more clonal than the sympatric rice-infecting population. Most of the loci in the soybean-infecting populations were out of Hardy-Weinberg equilibrium (HWE), but the sympatric rice-infecting population from Louisiana was mainly in HWE. All populations presented evidence for a mixed reproductive system.
Collapse
|
42
|
Jo YK, Chang SW, Boehm M, Jung G. Rapid development of fungicide resistance by Sclerotinia homoeocarpa on turfgrass. PHYTOPATHOLOGY 2008; 98:1297-1304. [PMID: 19000004 DOI: 10.1094/phyto-98-12-1297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Dollar spot, caused by Sclerotinia homoeocarpa, is the most prevalent and economically important turfgrass disease in North America. Increasing levels of fungicide resistance, coupled with tightening environmental scrutiny of existing fungicides, has left fewer options for managing dollar spot. More knowledge about S. homoeocarpa populations is needed to improve dollar spot management strategies, especially with respect to minimizing the development of fungicide resistance. Population diversity of S. homoeocarpa was examined using inter-simple sequence repeat markers and vegetative compatibility assays. Two subgroups were found in S. homoeocarpa field populations on both fairway and putting green turfgrass at a research field in Wisconsin. These subgroups were genetically different, vegetatively incompatible, and had different fungicide sensitivities. The frequency of the two genetic subgroups differed significantly between the fairway and putting green, but was uniform within the fairway or within the green. Population dynamics of S. homoeocarpa in response to two systemic fungicides (thiophanate-methyl and propiconazole) were assessed based on in vitro fungicide sensitivity. Dynamics of S. homoeocarpa populations depended on the presence of fungicide-resistant isolates in the initial populations before fungicide applications and changed rapidly after fungicide applications. Shifting of the population toward propiconazole resistance was gradual, whereas thiophanate-methyl resistance developed rapidly in the population. In conclusion, field populations of S. homoeocarpa containing genetically distinct, vegetatively incompatible groups were different on turfgrass that was managed differently, and they were changed rapidly after exposure to fungicides.
Collapse
Affiliation(s)
- Young-Ki Jo
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | | | | | | |
Collapse
|
43
|
Chapter 6 Population biology of forest decomposer basidiomycetes. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0275-0287(08)80008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
44
|
Rosendahl S. Communities, populations and individuals of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2008; 178:253-266. [PMID: 18248587 DOI: 10.1111/j.1469-8137.2008.02378.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Arbuscular mycorrhizal fungi in the phylum Glomeromycota are found globally in most vegetation types, where they form a mutualistic symbiosis with plant roots. Despite their wide distribution, only relatively few species are described. The taxonomy is based on morphological characters of the asexual resting spores, but molecular approaches to community ecology have revealed a considerable unknown diversity from colonized roots. Although the lack of genetic recombination is not unique in the fungal kingdom, arbuscular mycorrhizal fungi are probably ancient asexuals. The long asexual evolution of the fungi has resulted in considerable genetic diversity within morphologically recognizable species, and challenges our concepts of individuals and populations. This review critically examines the concepts of species, communities, populations and individuals of arbuscular mycorrhizal fungi.
Collapse
Affiliation(s)
- Søren Rosendahl
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, DK 1353 Copenhagen K, Denmark
| |
Collapse
|
45
|
Arnaud-Haond S, Duarte CM, Alberto F, Serrão EA. Standardizing methods to address clonality in population studies. Mol Ecol 2007; 16:5115-39. [PMID: 17944846 DOI: 10.1111/j.1365-294x.2007.03535.x] [Citation(s) in RCA: 326] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although clonal species are dominant in many habitats, from unicellular organisms to plants and animals, ecological and particularly evolutionary studies on clonal species have been strongly limited by the difficulty in assessing the number, size and longevity of genetic individuals within a population. The development of molecular markers has allowed progress in this area, and although allozymes remain of limited use due to their typically low level of polymorphism, more polymorphic markers have been discovered during the last decades, supplying powerful tools to overcome the problem of clonality assessment. However, population genetics studies on clonal organisms lack a standardized framework to assess clonality, and to adapt conventional data analyses to account for the potential bias due to the possible replication of the same individuals in the sampling. Moreover, existing studies used a variety of indices to describe clonal diversity and structure such that comparison among studies is difficult at best. We emphasize the need for standardizing studies on clonal organisms, and particularly on clonal plants, in order to clarify the way clonality is taken into account in sampling designs and data analysis, and to allow further comparison of results reported in distinct studies. In order to provide a first step towards a standardized framework to address clonality in population studies, we review, on the basis of a thorough revision of the literature on population structure of clonal plants and of a complementary revision on other clonal organisms, the indices and statistics used so far to estimate genotypic or clonal diversity and to describe clonal structure in plants. We examine their advantages and weaknesses as well as various conceptual issues associated with statistical analyses of population genetics data on clonal organisms. We do so by testing them on results from simulations, as well as on two empirical data sets of microsatellites of the seagrasses Posidonia oceanica and Cymodocea nodosa. Finally, we also propose a selection of new indices and methods to estimate clonal diversity and describe clonal structure in a way that should facilitate comparison between future studies on clonal plants, most of which may be of interest for clonal organisms in general.
Collapse
Affiliation(s)
- S Arnaud-Haond
- CCMAR - CIMAR Laboratório Associado, Univ. Algarve, Gambelas, 8005-139, Faro, Portugal.
| | | | | | | |
Collapse
|
46
|
Ceresini PC, Shew HD, James TY, Vilgalys RJ, Cubeta MA. Phylogeography of the Solanaceae-infecting Basidiomycota fungus Rhizoctonia solani AG-3 based on sequence analysis of two nuclear DNA loci. BMC Evol Biol 2007; 7:163. [PMID: 17854492 PMCID: PMC2048936 DOI: 10.1186/1471-2148-7-163] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 09/13/2007] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) is an important pathogen of cultivated plants in the family Solanaceae. Isolates of R. solani AG-3 are taxonomically related based on the composition of cellular fatty acids, phylogenetic analysis of nuclear ribosomal DNA (rDNA) and beta-tubulin gene sequences, and somatic hyphal interactions. Despite the close genetic relationship among isolates of R. solani AG-3, field populations from potato and tobacco exhibit comparative differences in their disease biology, dispersal ecology, host specialization, genetic diversity and population structure. However, little information is available on how field populations of R. solani AG-3 on potato and tobacco are shaped by population genetic processes. In this study, two field populations of R. solani AG-3 from potato in North Carolina (NC) and the Northern USA; and two field populations from tobacco in NC and Southern Brazil were examined using sequence analysis of two cloned regions of nuclear DNA (pP42F and pP89). RESULTS Populations of R. solani AG-3 from potato were genetically diverse with a high frequency of heterozygosity, while limited or no genetic diversity was observed within the highly homozygous tobacco populations from NC and Brazil. Except for one isolate (TBR24), all NC and Brazilian isolates from tobacco shared the same alleles. No alleles were shared between potato and tobacco populations of R. solani AG-3, indicating no gene flow between them. To infer historical events that influenced current geographical patterns observed for populations of R. solani AG-3 from potato, we performed an analysis of molecular variance (AMOVA) and a nested clade analysis (NCA). Population differentiation was detected for locus pP89 (Phi ST = 0.257, significant at P < 0.05) but not for locus pP42F (Phi ST = 0.034, not significant). Results based on NCA of the pP89 locus suggest that historical restricted gene flow is a plausible explanation for the geographical association of clades. Coalescent-based simulations of genealogical relationships between populations of R. solani AG-3 from potato and tobacco were used to estimate the amount and directionality of historical migration patterns in time, and the ages of mutations of populations. Low rates of historical movement of genes were observed between the potato and tobacco populations of R. solani AG-3. CONCLUSION The two sisters populations of the basidiomycete fungus R. solani AG-3 from potato and tobacco represent two genetically distinct and historically divergent lineages that have probably evolved within the range of their particular related Solanaceae hosts as sympatric species.
Collapse
Affiliation(s)
- Paulo C Ceresini
- ETH Zurich – Swiss Federal Institute of Technology, IBZ, Universitaetstrasse 2, LFW B28, 8092 Zurich, Switzerland/Universidade Estadual Paulista – UNESP, Departamento de Fitossanidade, Engenharia Rural e Solos, 15385-000, Ilha Solteira, São Paulo, Brazil
| | - H David Shew
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Timothy Y James
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Marc A Cubeta
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
47
|
Gonthier P, Nicolotti G, Linzer R, Guglielmo F, Garbelotto M. Invasion of European pine stands by a North American forest pathogen and its hybridization with a native interfertile taxon. Mol Ecol 2007; 16:1389-400. [PMID: 17391264 DOI: 10.1111/j.1365-294x.2007.03250.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It was recently reported that North American (NA) individuals of the forest pathogen Heterobasidion annosum were found in a single pine stand near Rome, in association with the movement of US troops during World War II. Here, we report on some aspects of the invasion biology of this pathogen in Italian coastal pinewoods, and on its interaction with native (EU) Heterobasidion populations. Spores of Heterobasidion were sampled using woody traps in pine stands along 280 km of coast around Rome. DNA of single-spore colonies was characterized by two sets of nuclear and one set of mitochondrial taxon-specific polymerase chain reaction primers. NA spores were found not only in a single site, but in many locations over a wide geographic area. Invasion occurred at an estimated rate of 1.3 km/year through invasion corridors provided by single trees, and not necessarily by sizable patches of forests. Within the 100-km long range of expansion, the NA taxon was dominant in all pure pine stands. Because abundance of the EU taxon is low and identical among stands within and outside the area invaded by NA individuals, we infer that the exotic population has invaded habitats mostly unoccupied by the native species. Discrepancy between a mitochondrial and a nuclear marker occurred in 3.8% of spores from one site, a mixed oak-pine forest where both taxa were equally represented. Combined phylogenetic analyses on nuclear and mitochondrial loci confirmed these isolates were recombinant. The finding of hybrids indicates that genetic interaction between NA and EU Heterobasidion taxa is occurring as a result of their current sympatry.
Collapse
Affiliation(s)
- P Gonthier
- Department of Exploitation, University of Torino, Via L. da Vinci 44, I-10095 Grugliasco, Italy
| | | | | | | | | |
Collapse
|
48
|
Taheri P, Gnanamanickam S, Höfte M. Characterization, Genetic Structure, and Pathogenicity of Rhizoctonia spp. Associated with Rice Sheath Diseases in India. PHYTOPATHOLOGY 2007; 97:373-83. [PMID: 18943659 DOI: 10.1094/phyto-97-3-0373] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
ABSTRACT Isolates of Rhizoctonia spp. were obtained from rice in India during 2000-2003. Characterization by conventional techniques and polymerase chain reaction showed that from 110 isolates, 99 were R. solani and 11 were R. oryzae-sativae. Of 99 isolates identified as R. solani, 96 were AG1-IA, 1 was AG1-IB, and 2 were AG1-IC. Amplified fragment length polymorphism (AFLP) analyzes were used to determine genetic relationships in Rhizoctonia pathogen populations collected from different geographic regions. Cluster analysis based on the AFLP data separated isolates belonging to the three different intraspecific groups of R. solani AG1 and differentiated R. solani from R. oryzae-sativae. Analysis of molecular variance (AMOVA) revealed that geographic region was the dominant factor determining population structure of R. solani AG1-1A; host cultivar had no significant effect. Pathogenicity tests on Oryza sativa cv. Zenith revealed that isolates of R. solani AG1-1A and AG1-1B were more virulent than R. solani AG1-IC and R. oryzae-sativae isolates.
Collapse
|
49
|
van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BPHJ. Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiol Rev 2007; 31:239-77. [PMID: 17326816 DOI: 10.1111/j.1574-6976.2007.00065.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It is common knowledge that pathogenic viruses can change hosts, with avian influenza, the HIV, and the causal agent of variant Creutzfeldt-Jacob encephalitis as well-known examples. Less well known, however, is that host jumps also occur with more complex pathogenic microorganisms such as bacteria and fungi. In extreme cases, these host jumps even cross kingdom of life barriers. A number of requirements need to be met to enable a microorganism to cross such kingdom barriers. Potential cross-kingdom pathogenic microorganisms must be able to come into close and frequent contact with potential hosts, and must be able to overcome or evade host defences. Reproduction on, in, or near the new host will ensure the transmission or release of successful genotypes. An unexpectedly high number of cross-kingdom host shifts of bacterial and fungal pathogens are described in the literature. Interestingly, the molecular mechanisms underlying these shifts show commonalities. The evolution of pathogenicity towards novel hosts may be based on traits that were originally developed to ensure survival in the microorganism's original habitat, including former hosts.
Collapse
Affiliation(s)
- Peter van Baarlen
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|
50
|
Bendel M, Kienast F, Rigling D. Genetic population structure of three Armillaria species at the landscape scale: a case study from Swiss Pinus mugo forests. ACTA ACUST UNITED AC 2006; 110:705-12. [PMID: 16616839 DOI: 10.1016/j.mycres.2006.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 02/11/2006] [Indexed: 10/24/2022]
Abstract
Armillaria species are plant pathogens that cause Armillaria root rot and are known to cause mortality of mountain pines (Pinus mugo) in the Swiss National Park in the Central Alps. The identity of isolates and the spatially explicit population structure of the Armillaria species were investigated in a 3.3km(2) study area in the Swiss National Park. In total, 242 Armillaria isolates, 205 from wood samples and 37 from epiphytic rhizomorphs, were collected. Species were identified using haploid-diploid pairings and genets were determined using intraspecific somatic incompatibility tests. The population structure differed markedly among the Armillaria species. A. cepistipes and A. borealis mainly occurred as genets of small spatial extent (mean 0.2ha, and 0.6ha), whereas A. ostoyae formed significantly larger genets (mean 6.8ha). The largest A. ostoyae genet extended over approx. 37ha. Several disease centres associated with Heterobasidion annosum were found to be embedded within large Armillaria genets. The extension of large A. ostoyae genets suggests that forests that occupy the study area have developed in the presence of these Armillaria genets. The finding of large Armillaria genets supports the assumption that large genets occur in areas with cold climate and little precipitation.
Collapse
Affiliation(s)
- Muriel Bendel
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
| | | | | |
Collapse
|