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Oh SY, Cho HJ, Eimes JA, Han SK, Kim CS, Lim YW. Guild Patterns of Basidiomycetes Community Associated With Quercus mongolica in Mt. Jeombong, Republic of Korea. MYCOBIOLOGY 2018; 46:13-23. [PMID: 29998029 PMCID: PMC6037075 DOI: 10.1080/12298093.2018.1454009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/27/2018] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
Depending on the mode of nutrition exploitation, major fungal guilds are distinguished as ectomycorrhizal and saprotrophic fungi. It is generally known that diverse environmental factors influence fungal communities; however, it is unclear how fungal communities respond differently to environment factors depend on fungal guilds. In this study, we investigated basidiomycetes communities associated with Quercus mongolica using 454 pyrosequencing. We attempted to detect guild pattern (ectomycorrhizal or saprotrophic fungal communities) by comparing the influence of geography and source (root and surrounding soil). A total of 515 mOTUs were detected from root (321) and soil (394) of Q. mongolica at three sites of Mt. Jeombong in Inje County. We found that patterns of diversity and community structure were different depending on the guilds. In terms of alpha diversity, only ectomycorrhizal fungi showed significant differences between sources. In terms of community structure, however, geography significantly influenced the ectomycorrhizal community, while source appeared to have a greater influence on the saprotrophic community. Therefore, a guild-based view will help to elucidates novel features of the relationship between environmental factors and fungal communities.
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Affiliation(s)
- Seung-Yoon Oh
- School of Biological Sciences and Institution of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Hae Jin Cho
- School of Biological Sciences and Institution of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - John A. Eimes
- University College, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sang-Kuk Han
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institution of Microbiology, Seoul National University, Seoul, Republic of Korea
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Cryptic diversity, pathogenicity, and evolutionary species boundaries in Cercospora populations associated with Cercospora leaf spot of Beta vulgaris. Fungal Biol 2018; 122:264-282. [PMID: 29551200 DOI: 10.1016/j.funbio.2018.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/18/2018] [Accepted: 01/31/2018] [Indexed: 12/16/2022]
Abstract
The taxonomy and evolutionary species boundaries in a global collection of Cercospora isolates from Beta vulgaris was investigated based on sequences of six loci. Species boundaries were assessed using concatenated multi-locus phylogenies, Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Processes (PTP), and Bayes factor delimitation (BFD) framework. Cercospora beticola was confirmed as the primary cause of Cercospora leaf spot (CLS) on B. vulgaris. Cercospora apii, C. cf. flagellaris, Cercospora sp. G, and C. zebrina were also identified in association with CLS on B. vulgaris. Cercospora apii and C. cf. flagellaris were pathogenic to table beet but Cercospora sp. G and C. zebrina did not cause disease. Genealogical concordance phylogenetic species recognition, GMYC and PTP methods failed to differentiate C. apii and C. beticola as separate species. On the other hand, multi-species coalescent analysis based on BFD supported separation of C. apii and C. beticola into distinct species; and provided evidence of evolutionary independent lineages within C. beticola. Extensive intra- and intergenic recombination, incomplete lineage sorting and dominance of clonal reproduction complicate evolutionary species recognition in the genus Cercospora. The results warrant morphological and phylogenetic studies to disentangle cryptic speciation within C. beticola.
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Michalecka M, Masny S, Leroy T, Puławska J. Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation. BMC Evol Biol 2018; 18:5. [PMID: 29351730 PMCID: PMC5775622 DOI: 10.1186/s12862-018-1122-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 10 orchards composed of various host cultivars. RESULTS Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. CONCLUSIONS Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.
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Affiliation(s)
- Monika Michalecka
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Sylwester Masny
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
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54
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Lee DH, Roux J, Wingfield BD, Wingfield MJ. Non-Mendelian segregation influences the infection biology and genetic structure of the African tree pathogen Ceratocystis albifundus. Fungal Biol 2017; 122:222-230. [PMID: 29551196 DOI: 10.1016/j.funbio.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/02/2017] [Accepted: 12/12/2017] [Indexed: 02/04/2023]
Abstract
The African fungal tree pathogen, Ceratocystis albifundus, undergoes uni-directional mating type switching, giving rise to either self-fertile or self-sterile progeny. Self-sterile isolates lack the MAT1-2-1 gene and have reduced fitness such as slower growth and reduced pathogenicity, relative to self-fertile isolates. While it has been hypothesized that there is a 1:1 ratio of self-fertile to self-sterile ascospore progeny in relatives of C. albifundus, some studies have reported a significant bias in this ratio. This could be due to the fact that either fewer self-sterile ascospores are produced or that self-sterile ascospores have low viability. We quantified the percentage of self-sterile and self-fertile ascospores from ascospore masses in C. albifundus using real-time PCR. Primers were designed to distinguish between spores that contained the MAT1-2-1 gene and those where this gene had been deleted. A significant bias towards the self-fertile mating type was observed in all single ascospore masses taken from sexual structures produced in haploid-selfed cultures. The same result was observed from a disease outbreak situation in an intensively managed field of cultivated native trees, and this was coupled with very low population diversity in the pathogen. This was in contrast to the results obtained from ascospore masses taken from the crosses performed under laboratory conditions or ascomata on native trees in a non-disease situation, where either self-fertile or self-sterile ascospores were dominant. The results suggest that reproductive strategies play a significant role in the infection biology and genetic structure of C. albifundus populations.
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Affiliation(s)
- Dong-Hyeon Lee
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jolanda Roux
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Genetics, FABI, University of Pretoria, Pretoria, South Africa.
| | - Michael J Wingfield
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Abstract
Approximately 20% of species in the fungal kingdom are only known to reproduce by asexual means despite the many supposed advantages of sexual reproduction. However, in recent years, sexual cycles have been induced in a series of emblematic "asexual" species. We describe how these discoveries were made, building on observations of evidence for sexual potential or "cryptic sexuality" from population genetic analyses; the presence, distribution, and functionality of mating-type genes; genome analyses revealing the presence of genes linked to sexuality; the functionality of sex-related genes; and formation of sex-related developmental structures. We then describe specific studies that led to the discovery of mating and sex in certain Candida, Aspergillus, Penicillium, and Trichoderma species and discuss the implications of sex including the beneficial exploitation of the sexual cycle. We next consider whether there might be any truly asexual fungal species. We suggest that, although rare, imperfect fungi may genuinely be present in nature and that certain human activities, combined with the genetic flexibility that is a hallmark of the fungal kingdom, might favor the evolution of asexuality under certain conditions. Finally, we argue that fungal species should not be thought of as simply asexual or sexual, but rather as being composed of isolates on a continuum of sexual fertility.
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Abstract
Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.
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57
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Romero Luna MP, Aime MC, Chilvers MI, Wise KA. Genetic Diversity of Stenocarpella maydis in the Major Corn Production Areas of the United States. PLANT DISEASE 2017; 101:2020-2026. [PMID: 30677369 DOI: 10.1094/pdis-02-17-0292-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The fungus Stenocarpella maydis (Berk.) B. Sutton, causal agent of Diplodia ear rot, is a prevalent corn (Zea mays L.) pathogen in the United States. Although S. maydis reduces grain quality, causes yield loss, and can produce mycotoxins in some countries, few studies have examined its biology and genetic diversity. We analyzed the genetic diversity of 174 S. maydis isolates sampled across the major corn production areas in the United States using nine different microsatellites. In all, 55 unique multilocus genotypes (MLG) were observed out of the 174 S. maydis isolates tested. After conducting a Bayesian clustering analysis by STRUCTURE, it was observed that the most probable number of genetic groups was two; however, no separation by their geographical location was identified. According to the minimum spanning network, the S. maydis population is linked across geographic regions of the United States but also contains private genotypes. Temporal diversity in the inoculum source was also observed at one location across 4 years. The haploid stage of S. maydis was confirmed and both mating type genes were amplified among selected isolates with unique MLG. We theorize that, although S. maydis is primarily an asexual fungus, sporadic cryptic recombination may occur, which could contribute to the genetic diversity observed in this study.
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Affiliation(s)
- Martha P Romero Luna
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824
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58
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Farrer RA, Fisher MC. Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. ADVANCES IN GENETICS 2017; 100:73-140. [PMID: 29153405 DOI: 10.1016/bs.adgen.2017.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.
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59
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Yang J, Maharachchikumbura SSN, Liu JK, Hyde KD, Gareth Jones E, Al-Sadi AM, Liu ZY. Pseudostanjehughesia aquitropica gen. et sp. nov. and Sporidesmium sensu lato species from freshwater habitats. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1339-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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60
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Turissini DA, Gomez OM, Teixeira MM, McEwen JG, Matute DR. Species boundaries in the human pathogen Paracoccidioides. Fungal Genet Biol 2017; 106:9-25. [PMID: 28602831 PMCID: PMC8335726 DOI: 10.1016/j.fgb.2017.05.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/12/2017] [Accepted: 05/31/2017] [Indexed: 12/29/2022]
Abstract
The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.
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Affiliation(s)
- David A Turissini
- Biology Department, University of North Carolina, Chapel Hill, NC, USA
| | - Oscar M Gomez
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; Biology Institute, Universidad de Antioquia, Medellín, Colombia
| | - Marcus M Teixeira
- Northern Arizona Center for Valley Fever Research, Flagstaff, AZ, USA
| | - Juan G McEwen
- Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC, USA.
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Mating-type genes of the anamorphic fungus Ulocladium botrytis affect both asexual sporulation and sexual reproduction. Sci Rep 2017; 7:7932. [PMID: 28801599 PMCID: PMC5554195 DOI: 10.1038/s41598-017-08471-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 11/23/2022] Open
Abstract
Ulocladium was thought to be a strictly asexual genus of filamentous fungi. However, Ulocladium strains were shown to possess both MAT1-1-1 and MAT1-2-1 genes as observed in homothallic filamentous Ascomycetes. Here, we demonstrate that the U. botrytis MAT genes play essential roles for controlling asexual traits (conidial size and number). Using reciprocal genetic transformation, we demonstrate that MAT genes from the related heterothallic species Cochliobolus heterostrophus can also influence U. botrytis colony growth, conidial number and size, and have a strong effect on the range of the number of septa/conidium. Moreover, U. botrytis MAT genes can also affect similar aspects of asexual reproduction when expressed in C. heterostrophus. Heterologous complementation using C. heterostrophus MAT genes shows that they have lost the ability to regulate sexual reproduction in U. botrytis, under the conditions we employed, while the reciprocal heterologous complementation demonstrates that U. botrytis MAT genes have the ability to partially induce sexual reproduction in C. heterostrophus. Thus, the genetic backgrounds of C. heterostrophus and U. botrytis play significant roles in determining the function of MAT genes on sexual reproduction in these two fungi species. These data further support the role of MAT genes in controlling asexual growth in filamentous Ascomycetes but also confirm that heterothallic and homothallic Dothideomycete fungi can be interconverted by the exchange of MAT genes.
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62
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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63
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Abstract
The Fusarium oxysporum species complex (FOSC) comprises a multitude of strains that cause vascular wilt diseases of economically important crops throughout the world. Although sexual reproduction is unknown in the FOSC, horizontal gene transfer may contribute to the observed diversity in pathogenic strains. Development of disease in a susceptible crop requires F. oxysporum to advance through a series of transitions, beginning with spore germination and culminating with establishment of a systemic infection. In principle, each transition presents an opportunity to influence the risk of disease. This includes modifications of the microbial community in soil, which can affect the ability of pathogen propagules to survive, germinate, and infect plant roots. In addition, many host attributes, including the composition of root exudates, the structure of the root cortex, and the capacity to recognize and respond quickly to invasive growth of a pathogen, can impede development of F. oxysporum.
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Affiliation(s)
- Thomas R Gordon
- Department of Plant Pathology, University of California, Davis, California 95616;
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64
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Mostert D, Molina AB, Daniells J, Fourie G, Hermanto C, Chao CP, Fabregar E, Sinohin VG, Masdek N, Thangavelu R, Li C, Yi G, Mostert L, Viljoen A. The distribution and host range of the banana Fusarium wilt fungus, Fusarium oxysporum f. sp. cubense, in Asia. PLoS One 2017; 12:e0181630. [PMID: 28719631 PMCID: PMC5515439 DOI: 10.1371/journal.pone.0181630] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 07/04/2017] [Indexed: 11/24/2022] Open
Abstract
Fusarium oxysporum formae specialis cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, which is considered to be the most destructive disease of bananas. The fungus is believed to have evolved with its host in the Indo-Malayan region, and from there it was spread to other banana-growing areas with infected planting material. The diversity and distribution of Foc in Asia was investigated. A total of 594 F. oxysporum isolates collected in ten Asian countries were identified by vegetative compatibility groups (VCGs) analysis. To simplify the identification process, the isolates were first divided into DNA lineages using PCR-RFLP analysis. Six lineages and 14 VCGs, representing three Foc races, were identified in this study. The VCG complex 0124/5 was most common in the Indian subcontinent, Vietnam and Cambodia; whereas the VCG complex 01213/16 dominated in the rest of Asia. Sixty-nine F. oxysporum isolates in this study did not match any of the known VCG tester strains. In this study, Foc VCG diversity in Bangladesh, Cambodia and Sri Lanka was determined for the first time and VCGs 01221 and 01222 were first reported from Cambodia and Vietnam. New associations of Foc VCGs and banana cultivars were recorded in all the countries where the fungus was collected. Information obtained in this study could help Asian countries to develop and implement regulatory measures to prevent the incursion of Foc into areas where it does not yet occur. It could also facilitate the deployment of disease resistant banana varieties in infested areas.
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Affiliation(s)
- Diane Mostert
- Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa
| | - Agustin B. Molina
- Bioversity International–Asia Pacific, IRRI campus, Los Banos, Philippines
| | - Jeff Daniells
- Department of Agriculture and Fisheries, South Johnstone, Queensland, Australia
| | - Gerda Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Catur Hermanto
- Indonesian Agency for Agriculture Research and Development, Jakarta, Indonesia
| | | | - Emily Fabregar
- Lapanday Foods Corporation, Barrio Pampanga, Lanang, Davao City, Philippines
| | - Vida G. Sinohin
- Bioversity International–Asia Pacific, IRRI campus, Los Banos, Philippines
| | - Nik Masdek
- Malaysian Agricultural Research and Development Institute, Selangor, Malaysia
| | - Raman Thangavelu
- ICAR-National Research Center for Banana, Tiruchirappalli, Tamil Nadu, India
| | - Chunyu Li
- Guangdong Academy of Agricultural Sciences, Institution of Fruit Tree Research, Guangzhou, Guangdong Province, China
| | - Ganyun Yi
- Guangdong Academy of Agricultural Sciences, Institution of Fruit Tree Research, Guangzhou, Guangdong Province, China
| | - Lizel Mostert
- Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa
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65
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Hagen F, Lumbsch HT, Arsic Arsenijevic V, Badali H, Bertout S, Billmyre RB, Bragulat MR, Cabañes FJ, Carbia M, Chakrabarti A, Chaturvedi S, Chaturvedi V, Chen M, Chowdhary A, Colom MF, Cornely OA, Crous PW, Cuétara MS, Diaz MR, Espinel-Ingroff A, Fakhim H, Falk R, Fang W, Herkert PF, Ferrer Rodríguez C, Fraser JA, Gené J, Guarro J, Idnurm A, Illnait-Zaragozi MT, Khan Z, Khayhan K, Kolecka A, Kurtzman CP, Lagrou K, Liao W, Linares C, Meis JF, Nielsen K, Nyazika TK, Pan W, Pekmezovic M, Polacheck I, Posteraro B, de Queiroz Telles F, Romeo O, Sánchez M, Sampaio A, Sanguinetti M, Sriburee P, Sugita T, Taj-Aldeen SJ, Takashima M, Taylor JW, Theelen B, Tomazin R, Verweij PE, Wahyuningsih R, Wang P, Boekhout T. Importance of Resolving Fungal Nomenclature: the Case of Multiple Pathogenic Species in the Cryptococcus Genus. mSphere 2017; 2:e00238-17. [PMID: 28875175 PMCID: PMC5577652 DOI: 10.1128/msphere.00238-17] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant differences between them, which may in turn delay future clinical advances.
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Affiliation(s)
- Ferry Hagen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | | | | | - Hamid Badali
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Sebastien Bertout
- Unité Mixte Internationale Recherches Translationnelles sur l’Infection à VIH et les Maladies Infectieuses, Laboratoire de Parasitologie et Mycologie Médicale, UFR Pharmacie, Université Montpellier, Montpellier, France
| | - R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - M. Rosa Bragulat
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - F. Javier Cabañes
- Veterinary Mycology Group, Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mauricio Carbia
- Departamento de Parasitología y Micología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Min Chen
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Anuradha Chowdhary
- Department of Medical Mycology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | | | - Oliver A. Cornely
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
- Center for Clinical Trials, University Hospital Cologne, Cologne, Germany
| | - Pedro W. Crous
- Phytopathology Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Maria S. Cuétara
- Department of Microbiology, Hospital Severo Ochoa, Madrid, Spain
| | - Mara R. Diaz
- University of Miami, NSF NIEHS Oceans and Human Health Center, Miami, Florida, USA
- Rosentiel School of Marine and Atmospheric Science, Division of Marine Biology and Fisheries, University of Miami, Miami, Florida, USA
| | | | - Hamed Fakhim
- Department of Medical Parasitology and Mycology/Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Rama Falk
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
- Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir-David, Israel
| | - Wenjie Fang
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Patricia F. Herkert
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Postgraduate Program in Microbiology, Parasitology and Pathology, Biological Sciences, Department of Basic Pathology, Federal University of Parana, Curitiba, Brazil
| | | | - James A. Fraser
- Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Josepa Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Josep Guarro
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Alexander Idnurm
- School of BioSciences, BioSciences 2, University of Melbourne, Melbourne, Australia
| | | | - Ziauddin Khan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, Thailand
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Anna Kolecka
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, USDA-ARS, Peoria, Illinois, USA
| | - Katrien Lagrou
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Wanqing Liao
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Carlos Linares
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Jacques F. Meis
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| | - Kirsten Nielsen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Tinashe K. Nyazika
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
- Malawi-Liverpool-Wellcome Trust, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Tropical Medicine, Liverpool, United Kingdom
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Second Military Medical University, Shanghai, China
- Department of Dermatology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | | | - Itzhack Polacheck
- Department of Clinical Microbiology and Infectious Diseases, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Flavio de Queiroz Telles
- Department of Communitarian Health, Hospital de Clínicas, Federal University of Parana, Curitiba, Brazil
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- IRCCS Centro Neurolesi Bonino-Pulejo, Messina, Italy
| | - Manuel Sánchez
- Medical School, Universidad Miguel Hernández, Alicante, Spain
| | - Ana Sampaio
- Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Universidade de Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, Vila Real, Portugal
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Pojana Sriburee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, Noshio, Kiyose, Tokyo, Japan
| | - Saad J. Taj-Aldeen
- Mycology Unit, Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Bart Theelen
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Rok Tomazin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Paul E. Verweij
- Centre of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Retno Wahyuningsih
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Parasitology, School of Medicine, Universitas Kristen Indonesia, Jakarta, Indonesia
| | - Ping Wang
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Teun Boekhout
- Institute of Biodiversity and Ecosystems Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Yeast Research, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
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Abstract
INTRODUCTION fungi produce substances that contain pathogen-associated molecular patterns (pamps) and damage-associated molecular patterns (damps) which bind to pattern recognition receptors, stimulating innate immune responses in humans. they also produce allergens that induce production of specific ige. Areas covered: In this review we cover both innate and adaptive immune responses to fungi. Some fungal products can activate both innate and adaptive responses and in doing so, cause an intense and complex health effects. Methods of testing for fungal allergy and evidence for clinical treatment including environmental control are also discussed. In addition, we describe controversial issues including the role of Stachybotrys and mycotoxins in adverse health effects. Expert commentary: Concerns about long-term exposure to fungi have led some patients, attorneys and fungus advocates to promote fears about a condition that has been termed toxic mold syndrome. This syndrome is associated with vague symptoms and is believed to be due to exposure to mycotoxins, though this connection has not been proven. Ultimately, more precise methods are needed to measure both fungal exposure and the resulting health effects. Once that such methods become available, much of the speculation will be replaced by knowledge.
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Affiliation(s)
- Amanda Rudert
- a Division of Allergy, Asthma & Immunology , Children's Mercy Hospitals & Clinics , Kansas City , MO , USA
| | - Jay Portnoy
- a Division of Allergy, Asthma & Immunology , Children's Mercy Hospitals & Clinics , Kansas City , MO , USA
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Bock CH, Hotchkiss MW, Young CA, Charlton ND, Chakradhar M, Stevenson KL, Wood BW. Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States. PHYTOPATHOLOGY 2017; 107:607-619. [PMID: 28414611 DOI: 10.1094/phyto-10-16-0376-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner's index = 3.49 to 4.59) and gene diversity (Nei's measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P = 0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared with that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared with that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.
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Affiliation(s)
- Clive H Bock
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Michael W Hotchkiss
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Carolyn A Young
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Nikki D Charlton
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Mattupalli Chakradhar
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Katherine L Stevenson
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Bruce W Wood
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
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Dutech C, Labbé F, Capdevielle X, Lung-Escarmant B. Genetic analysis reveals efficient sexual spore dispersal at a fine spatial scale in Armillaria ostoyae, the causal agent of root-rot disease in conifers. Fungal Biol 2017; 121:550-560. [PMID: 28606350 DOI: 10.1016/j.funbio.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 11/24/2022]
Abstract
Armillaria ostoyae (sometimes named Armillaria solidipes) is a fungal species causing root diseases in numerous coniferous forests of the northern hemisphere. The importance of sexual spores for the establishment of new disease centres remains unclear, particularly in the large maritime pine plantations of southwestern France. An analysis of the genetic diversity of a local fungal population distributed over 500 ha in this French forest showed genetic recombination between genotypes to be frequent, consistent with regular sexual reproduction within the population. The estimated spatial genetic structure displayed a significant pattern of isolation by distance, consistent with the dispersal of sexual spores mostly at the spatial scale studied. Using these genetic data, we inferred an effective density of reproductive individuals of 0.1-0.3 individuals/ha, and a second moment of parent-progeny dispersal distance of 130-800 m, compatible with the main models of fungal spore dispersal. These results contrast with those obtained for studies of A. ostoyae over larger spatial scales, suggesting that inferences about mean spore dispersal may be best performed at fine spatial scales (i.e. a few kilometres) for most fungal species.
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Affiliation(s)
- Cyril Dutech
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France.
| | - Frédéric Labbé
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France
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Regulation of conidiation in Botrytis cinerea involves the light-responsive transcriptional regulators BcLTF3 and BcREG1. Curr Genet 2017; 63:931-949. [PMID: 28382431 DOI: 10.1007/s00294-017-0692-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 01/25/2023]
Abstract
Botrytis cinerea is a plant pathogenic fungus with a broad host range. Due to its rapid growth and reproduction by asexual spores (conidia), which increases the inoculum pressure, the fungus is a serious problem in different fields of agriculture. The formation of the conidia is promoted by light, whereas the formation of sclerotia as survival structures occurs in its absence. Based on this observation, putative transcription factors (TFs) whose expression is induced upon light exposure have been considered as candidates for activating conidiation and/or repressing sclerotial development. Previous studies reported on the identification of six light-responsive TFs (LTFs), and two of them have been confirmed as crucial developmental regulators: BcLTF2 is the positive regulator of conidiation, whose expression is negatively regulated by BcLTF1. Here, the functional characterization of the four remaining LTFs is reported. BcLTF3 has a dual function, as it represses conidiophore development by repressing bcltf2 in light and darkness, and is moreover essential for conidiogenesis. In bcltf3 deletion mutants conidium initials grow out to hyphae, which develop secondary conidiophores. In contrast, no obvious functions could be assigned to BcLTF4, BcLTF5 and BcLTF6 in these experiments. BcREG1, previously reported to be required for virulence and conidiogenesis, has been re-identified as light-responsive transcriptional regulator. Studies with bcreg1 overexpression strains indicated that BcREG1 differentially affects conidiation by acting as a repressor of BcLTF2-induced conidiation in the light and as an activator of a BcLTF2-independent conidiation program in the dark.
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71
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Rodriguez-Algaba J, Sørensen CK, Labouriau R, Justesen AF, Hovmøller MS. Genetic diversity within and among aecia of the wheat rust fungus Puccinia striiformis on the alternate host Berberis vulgaris. Fungal Biol 2017; 121:541-549. [PMID: 28606349 DOI: 10.1016/j.funbio.2017.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/10/2017] [Indexed: 10/19/2022]
Abstract
An isolate of the fungus Puccinia striiformis, causing yellow (stripe) rust on cereals and grasses, was selfed on the alternate (sexual) host, Berberis vulgaris. This enabled us to investigate genetic variability of progeny isolates within and among aecia. Nine aecial clusters each consisting of an aecium (single aecial cup) and nine clusters containing multiple aecial cups were selected from 18 B. vulgaris leaves. Aeciospores from each cluster were inoculated on susceptible wheat seedlings and 64 progeny isolates were recovered. Molecular genotyping using 37 simple sequence repeat markers confirmed the parental origin of all progeny isolates. Thirteen molecular markers, which were heterozygous in the parental isolate, were used to analyse genetic diversity within and among aecial cups. The 64 progeny isolates resulted in 22 unique recombinant multilocus genotypes and none of them were resampled in different aecial clusters. Isolates derived from a single cup were always of the same genotype whereas isolates originating from clusters containing up to nine aecial cups revealed one to three genotypes per cluster. These results implied that each aecium was the result of a successful fertilization in a corresponding pycnium and that an aecium consisted of genetically identical aeciospores probably multiplied via repetitive mitotic divisions. Furthermore, the results suggested that aecia within a cluster were the result of independent fertilization events often involving genetically different pycniospores. The application of molecular markers represented a major advance in comparison to previous studies depending on phenotypic responses on host plants. The study allowed significant conclusions about fundamental aspects of the biology and genetics of an important cereal rust fungus.
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Affiliation(s)
- Julian Rodriguez-Algaba
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark.
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Rodrigo Labouriau
- Department of Mathematics, Faculty of Science and Technology, Aarhus University, Ny Munkegade 118, 8000 Aarhus, Denmark
| | - Annemarie F Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Moussa TAA, Al-Zahrani HS, Kadasa NMS, Ahmed SA, de Hoog GS, Al-Hatmi AMS. Two new species of the Fusarium fujikuroi species complex isolated from the natural environment. Antonie van Leeuwenhoek 2017; 110:819-832. [PMID: 28303400 PMCID: PMC5427105 DOI: 10.1007/s10482-017-0855-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 03/07/2017] [Indexed: 11/04/2022]
Abstract
Two new species in the Fusarium fujikuroi species complex (FFSC) are introduced. One of these, represented by strain CBS 454.97 was isolated from plant debris (Striga hermonthica) in the Sudan, while the second, represented by strains CBS 119850 and CBS 483.94, which originated from soil in Australia. Molecular analyses were performed including TEF1 spanning 576 bp region, 860 bp region of rPB2, and 500 bp BT2 region. Phylogenetic trees based on these regions showed that the two species are clearly distinct from all known taxa in the F. fujikuroi species complex. Based on phenotypic, physiological characters and molecular data, we introduce Fusarium sudanense and Fusarium terricola as novel species in the complex.
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Affiliation(s)
- Tarek A A Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Hassan S Al-Zahrani
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Naif M S Kadasa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Sarah A Ahmed
- Westerdijk Fungal Biodiversity Institute, PO Box 85167, 3508 AD, Utrecht, The Netherlands.,Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - G Sybren de Hoog
- Biological Sciences Department, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia.,Westerdijk Fungal Biodiversity Institute, PO Box 85167, 3508 AD, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Abdullah M S Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, PO Box 85167, 3508 AD, Utrecht, The Netherlands. .,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands. .,Directorate General of Health Services, Ministry of Health, Ibri Hospital, Ibri, Oman.
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73
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Steenkamp ET, Wingfield BD, Desjardins AE, Marasas WF, Wingfield MJ. Cryptic speciation inFusarium subglutinans. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833158] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Anne E. Desjardins
- Mycotoxin Research Unit, National Center for Agricultural Utilization of Research, USDA, Agricultural Research Services, 1815 N University Street, Preoria, Illinois 61604
| | - Walter F.O. Marasas
- PROMEC, Medical Research Council, P.O. Box 19070, Tygerberg 7505, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
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74
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Aoki T, O'Donnell K, Homma Y, Lattanzi AR. Sudden-death syndrome of soybean is caused by two morphologically and phylogenetically distinct species within theFusarium solanispecies complex—F. virguliformein North America andF. tucumaniaein South America. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Takayuki Aoki
- National Institute of Agrobiological Sciences, Genetic Diversity Department, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Kerry O'Donnell
- Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604-3999
| | - Yoshihisa Homma
- Japan International Research Center for Agricultural Sciences, Biological Resources Division, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8686 Japan
| | - Alfredo R. Lattanzi
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria (INTA-EEA) Marcos Juárez, Casilla de Correo 21, 2580 Marcos Juárez, Córdoba, Argentina
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75
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LoBuglio KF, Taylor JW. Recombination and genetic differentiation in the mycorrhizal fungusCenococcum geophilumFr. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833171] [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)
| | - John W. Taylor
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102
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76
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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
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77
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Ceresini PC, Shew HD, Vilgalys RJ, Rosewich UL, Cubeta MA. Genetic structure of populations ofRhizoctonia solaniAG-3 on potato in eastern North Carolina. Mycologia 2017. [DOI: 10.1080/15572536.2003.11833210] [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
| | - U. Liane Rosewich
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, Saint Paul, Minnesota 55108
| | - Marc A. Cubeta
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695
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78
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Guerber JC, Liu B, Correll JC, Johnston PR. Characterization of diversity inColletotrichum acutatumsensu latoby sequence analysis of two gene introns, mtDNA and intron RFLPs, and mating compatibility. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833047] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - James C. Correll
- Department of Plant Pathology, University of Arkansas, 217 Plant Sciences, Fayetteville, Arkansas 72701
| | - Peter R. Johnston
- Herbarium PDD, Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, New Zealand
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Farr DF, Elliott M, Rossman AY, Edmonds RL. Fusicoccum arbutisp. nov. causing cankers on Pacific madrone in western North America with notes onFusicoccum dimidiatum,the correct name forScytalidium dimidiatumandNattrassia mangiferae. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832803] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- David F. Farr
- Systematic Botany & Mycology Laboratory, USDA Agricultural Research Service, Room 304, B011a, 10300 Baltimore Ave., Beltsville, Maryland 20705
| | - Marianne Elliott
- College of Forest Resources, University of Washington, Seattle, Washington 98195
| | - Amy Y. Rossman
- Systematic Botany & Mycology Laboratory, USDA Agricultural Research Service, Room 304, B011a, 10300 Baltimore Ave., Beltsville, Maryland 20705
| | - Robert L. Edmonds
- College of Forest Resources, University of Washington, Seattle, Washington 98195
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80
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Kraemer SA, Boynton PJ. Evidence for microbial local adaptation in nature. Mol Ecol 2017; 26:1860-1876. [DOI: 10.1111/mec.13958] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Susanne A. Kraemer
- Ashworth Laboratories; University of Edinburgh; King's Buildings EH9 3FL Edinburgh UK
| | - Primrose J. Boynton
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Str. 2 24306 Plön Germany
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81
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Winton LM, Hansen EM, Stone JK. Population structure suggests reproductively isolated lineages ofPhaeocryptopus gaeumannii. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Jeffrey K. Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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Blackwell M, Hibbett DS, Taylor JW, Spatafora JW. Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 2017. [DOI: 10.1080/15572536.2006.11832613] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - David S. Hibbett
- Department of Biology, Clark University, Worcester, Massachusetts 01610
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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83
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Duan X, Tellier A, Wan A, Leconte M, de Vallavieille-Pope C, Enjalbert J. Puccinia striiformisf.sp.triticipresents high diversity and recombination in the over-summering zone of Gansu, China. Mycologia 2017; 102:44-53. [DOI: 10.3852/08-098] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- X. Duan
- State Key Laboratory of Biology for Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - A. Tellier
- Section of Evolutionary Biology, LMU BioCenter, 2 Grosshaderner Straße 82152 Planegg-Martinsried, Germany
| | - A. Wan
- Department of Plant Pathology, Washington State University, PO Box 646430, Pullman, Washington 99164-6430
| | - M. Leconte
- INRA, UMR BIOGER CPP, F-78850 Thiverval-Grignon, France
| | | | - J. Enjalbert
- INRA, UMR 0320/UMR 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France
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84
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Priyamvada H, Akila M, Singh RK, Ravikrishna R, Verma RS, Philip L, Marathe RR, Sahu LK, Sudheer KP, Gunthe SS. Terrestrial Macrofungal Diversity from the Tropical Dry Evergreen Biome of Southern India and Its Potential Role in Aerobiology. PLoS One 2017; 12:e0169333. [PMID: 28072853 PMCID: PMC5224982 DOI: 10.1371/journal.pone.0169333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/15/2016] [Indexed: 11/25/2022] Open
Abstract
Macrofungi have long been investigated for various scientific purposes including their food and medicinal characteristics. Their role in aerobiology as a fraction of the primary biological aerosol particles (PBAPs), however, has been poorly studied. In this study, we present a source of macrofungi with two different but interdependent objectives: (i) to characterize the macrofungi from a tropical dry evergreen biome in southern India using advanced molecular techniques to enrich the database from this region, and (ii) to assess whether identified species of macrofungi are a potential source of atmospheric PBAPs. From the DNA analysis, we report the diversity of the terrestrial macrofungi from a tropical dry evergreen biome robustly supported by the statistical analyses for diversity conclusions. A total of 113 macrofungal species belonging to 54 genera and 23 families were recorded, with Basidiomycota and Ascomycota constituting 96% and 4% of the species, respectively. The highest species richness was found in the family Agaricaceae (25.3%) followed by Polyporaceae (15.3%) and Marasmiaceae (10.8%). The difference in the distribution of commonly observed macrofungal families over this location was compared with other locations in India (Karnataka, Kerala, Maharashtra, and West Bengal) using two statistical tests. The distributions of the terrestrial macrofungi were distinctly different in each ecosystem. We further attempted to demonstrate the potential role of terrestrial macrofungi as a source of PBAPs in ambient air. In our opinion, the findings from this ecosystem of India will enhance our understanding of the distribution, diversity, ecology, and biological prospects of terrestrial macrofungi as well as their potential to contribute to airborne fungal aerosols.
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Affiliation(s)
- Hema Priyamvada
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
- * E-mail: (HP); (SSG)
| | - M. Akila
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Raj Kamal Singh
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
| | - R. Ravikrishna
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India
| | - R. S. Verma
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Ligy Philip
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
| | - R. R. Marathe
- Department of Management Studies, Indian Institute of Technology Madras, Chennai, India
| | - L. K. Sahu
- Physical Research Laboratory, Navarangpura, Ahmedabad, India
| | - K. P. Sudheer
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
| | - S. S. Gunthe
- EWRE Division, Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, India
- * E-mail: (HP); (SSG)
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85
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Pereira DADS, Ceresini PC, Castroagudín VL, Ramos-Molina LM, Chavarro-Mesa E, Negrisoli MM, Campos SN, Pegolo MES, Takada HM. Population Genetic Structure of Rhizoctonia oryzae-sativae from Rice in Latin America and Its Adaptive Potential to Emerge as a Pathogen on Urochloa Pastures. PHYTOPATHOLOGY 2017; 107:121-131. [PMID: 27571310 DOI: 10.1094/phyto-05-16-0219-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fungus Rhizoctonia oryzae-sativae is an important pathogen that causes the aggregated sheath spot disease on rice. In this study, we investigated the genetic structure of rice-adapted populations of R. oryzae-sativae sampled from traditional rice-cropping areas from the Paraíba Valley, São Paulo, Brazil, and from Meta, in the Colombian Llanos, in South America. We used five microsatellite loci to measure population differentiation and infer the pathogen's reproductive system. Gene flow was detected among the three populations of R. oryzae-sativae from lowland rice in Brazil and Colombia. In contrast, a lack of gene flow was observed between the lowland and the upland rice populations of the pathogen. Evidence of sexual reproduction including low clonality, Hardy-Weinberg equilibrium within loci and gametic equilibrium between loci, indicated the predominance of a mixed reproductive system in all populations. In addition, we assessed the adaptive potential of the Brazilian populations of R. oryzae-sativae to emerge as a pathogen to Urochloa spp. (signalgrass) based on greenhouse aggressiveness assays. The Brazilian populations of R. oryzae-sativae were probably only incipiently adapted as a pathogen to Urochloa spp. Comparison between RST and QST showed the predominance of diversifying selection in the divergence between the two populations of R. oryzae-sativae from Brazil.
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Affiliation(s)
- Danilo A Dos Santos Pereira
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Paulo C Ceresini
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Vanina L Castroagudín
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Lina M Ramos-Molina
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Edisson Chavarro-Mesa
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Matheus Mereb Negrisoli
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Samara Nunes Campos
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Mauro E S Pegolo
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
| | - Hélio Minoru Takada
- First, second, third, sixth, seventh and eighth authors, UNESP University of São Paulo State, Campus de Ilha Solteira, SP, Brazil; fourth and fifth authors, UNESP Campus de Jaboticabal, SP, Brazil; eighth author, APTA/IAC, Agronomic Institute of Campinas, Vale do Paraíba Regional Center, Pindamonhangaba, SP, Brazil
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86
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Yamada K, Sonoda R, Ishikawa K. Population Genetic Structure of QoI-Resistant Pestalotiopsis longiseta Isolates Causing Tea Gray Blight. PLANT DISEASE 2016; 100:1686-1691. [PMID: 30686227 DOI: 10.1094/pdis-09-15-1114-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Resistance to the quinone outside inhibitor (QoI) fungicides in the tea gray blight-causing fungus Pestalotiopsis longiseta is a serious problem in Japanese tea cultivation. We conducted a population genetic analysis of QoI-resistant P. longiseta isolates on the Makinohara Plateau, Shizuoka Prefecture, Japan's largest tea-growing area, to elucidate the disease's epidemiology and the spread of QoI resistance. Inter simple sequence repeat (ISSR) analysis of 1,083 isolates from 395 fields collected from 2009 to 2012 detected 42 ISSR types, designated as PL01 to PL42. A total of 18, seven, and 38 ISSR types were detected in highly resistant, moderately resistant, and sensitive isolates, respectively. No distinct phylogenetic relationship corresponding to QoI sensitivity or sampling location was observed. No annual changes in the population genetic structure of highly resistant isolates were observed during the study period. A different ISSR type was predominant among QoI-resistant isolates in each region. Analysis of molecular variance revealed significant genetic differentiation in populations of highly resistant isolates among regions (FCT = 0.213) and farmers (FCT = 0.071). Consequently, we speculate that QoI-resistant P. longiseta strains occurred in a number of clonal lineages and spread by both natural and artificial transmission, such as rain splash and plucking machines, throughout each region on the Makinohara Plateau.
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Affiliation(s)
- Kengo Yamada
- NARO Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Shizuoka 428-8501, Japan
| | - Ryoichi Sonoda
- National Institute for Agro-Environmental Sciences, Tsukuba, Ibaraki 305-8604, Japan
| | - Koichi Ishikawa
- NARO Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization (NARO), Shimada, Shizuoka 428-8501, Japan
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87
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Testa AC, Oliver RP, Hane JK. OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes. Genome Biol Evol 2016; 8:2044-64. [PMID: 27289099 PMCID: PMC4943192 DOI: 10.1093/gbe/evw121] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/03/2022] Open
Abstract
We present a novel method to measure the local GC-content bias in genomes and a survey of published fungal species. The method, enacted as "OcculterCut" (https://sourceforge.net/projects/occultercut, last accessed April 30, 2016), identified species containing distinct AT-rich regions. In most fungal taxa, AT-rich regions are a signature of repeat-induced point mutation (RIP), which targets repetitive DNA and decreases GC-content though the conversion of cytosine to thymine bases. RIP has in turn been identified as a driver of fungal genome evolution, as RIP mutations can also occur in single-copy genes neighboring repeat-rich regions. Over time RIP perpetuates "two speeds" of gene evolution in the GC-equilibrated and AT-rich regions of fungal genomes. In this study, genomes showing evidence of this process are found to be common, particularly among the Pezizomycotina. Further analysis highlighted differences in amino acid composition and putative functions of genes from these regions, supporting the hypothesis that these regions play an important role in fungal evolution. OcculterCut can also be used to identify genes undergoing RIP-assisted diversifying selection, such as small, secreted effector proteins that mediate host-microbe disease interactions.
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Affiliation(s)
- Alison C Testa
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - Richard P Oliver
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - James K Hane
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Perth, Australia Curtin Institute for Computation, Curtin University, Perth, Australia
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88
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Cummings NJ, Ambrose A, Braithwaite M, Bissett J, Roslan HA, Abdullah J, Stewart A, Agbayani FV, Steyaert J, Hill RA. Diversity of root-endophytic Trichoderma from Malaysian Borneo. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1192-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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89
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90
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The genetic landscape of Ceratocystis albifundus populations in South Africa reveals a recent fungal introduction event. Fungal Biol 2016; 120:690-700. [PMID: 27109366 DOI: 10.1016/j.funbio.2016.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/27/2022]
Abstract
Geographical range expansion or host shifts is amongst the various evolutionary forces that underlie numerous emerging diseases caused by fungal pathogens. In this regard, Ceratocystis albifundus, the causal agent of a serious wilt disease of Acacia mearnsii trees in Africa, was recently identified killing cultivated Protea cynaroides in the Western Cape (WC) Province of South Africa. Protea cynaroides is an important native plant in the area and a key component of the Cape Floristic Region. The appearance of this new disease outbreak, together with isolates of C. albifundus from natural ecosystems as well as plantations of nonnative trees, provided an opportunity to consider questions relating to the possible origin and movement of the pathogen in South Africa. Ten microsatellite markers were used to determine the genetic diversity, population structure, and possible gene flow in a collection of 193 C. albifundus isolates. All populations, other than those from the WC, showed high levels of genetic diversity. An intermediate level of gene flow was found amongst populations of the pathogen. The results suggest that a limited number of individuals have recently been introduced into the WC, resulting in a novel disease problem in the area.
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91
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Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, de Vallavieille-Pope C, Enjalbert J. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Mol Ecol Resour 2016; 16:845-61. [DOI: 10.1111/1755-0998.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sajid Ali
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; the University of Agriculture, Peshawar; 25000 Peshawar Pakistan
| | - Samuel Soubeyrand
- UR546 Biostatistics and Spatial Processes; INRA; 84914 Avignon France
| | - Pierre Gladieux
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR385 Biologie et Génétique des Interactions Plante-Parasite; CIRAD; INRA; F-34398 Montpellier France
| | - Tatiana Giraud
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - Marc Leconte
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Angélique Gautier
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Mamadou Mboup
- DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center; 24, rue du Moulin 68740 Nambsheim France
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; No. 2 Yuanmingyuan West Road Beijing 100193 China
| | | | - Jérôme Enjalbert
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- GQE - Le Moulon; INRA; Univ. Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; F-91190 Gif-sur-Yvette France
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92
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Nirmaladevi D, Venkataramana M, Srivastava RK, Uppalapati SR, Gupta VK, Yli-Mattila T, Clement Tsui KM, Srinivas C, Niranjana SR, Chandra NS. Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici. Sci Rep 2016; 6:21367. [PMID: 26883288 PMCID: PMC4756691 DOI: 10.1038/srep21367] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022] Open
Abstract
The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin.
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Affiliation(s)
- D. Nirmaladevi
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - M. Venkataramana
- DRDO-BU-CLS, Barathiar University Campus, Coimbatore, Tamil Nadu, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. R. Uppalapati
- Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | - Vijai Kumar Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - T. Yli-Mattila
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - K. M. Clement Tsui
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - C. Srinivas
- Department of Microbiology and Biotechnology, Jnanabarathi Campus, Bangalore University, Bangalore, Karnataka, India
| | - S. R. Niranjana
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
| | - Nayaka S. Chandra
- DOS in Biotechnology, University of Mysore, Manasagangothri, Mysore, Karnataka, India
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93
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Vogt G. Stochastic developmental variation, an epigenetic source of phenotypic diversity with far-reaching biological consequences. J Biosci 2015; 40:159-204. [PMID: 25740150 DOI: 10.1007/s12038-015-9506-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article reviews the production of different phenotypes from the same genotype in the same environment by stochastic cellular events, nonlinear mechanisms during patterning and morphogenesis, and probabilistic self-reinforcing circuitries in the adult life. These aspects of phenotypic variation are summarized under the term 'stochastic developmental variation' (SDV) in the following. In the past, SDV has been viewed primarily as a nuisance, impairing laboratory experiments, pharmaceutical testing, and true-to-type breeding. This article also emphasizes the positive biological effects of SDV and discusses implications for genotype-to-phenotype mapping, biological individuation, ecology, evolution, and applied biology. There is strong evidence from experiments with genetically identical organisms performed in narrowly standardized laboratory set-ups that SDV is a source of phenotypic variation in its own right aside from genetic variation and environmental variation. It is obviously mediated by molecular and higher-order epigenetic mechanisms. Comparison of SDV in animals, plants, fungi, protists, bacteria, archaeans, and viruses suggests that it is a ubiquitous and phylogenetically old phenomenon. In animals, it is usually smallest for morphometric traits and highest for life history traits and behaviour. SDV is thought to contribute to phenotypic diversity in all populations but is particularly relevant for asexually reproducing and genetically impoverished populations, where it generates individuality despite genetic uniformity. In each generation, SDV produces a range of phenotypes around a well-adapted target phenotype, which is interpreted as a bet-hedging strategy to cope with the unpredictability of dynamic environments. At least some manifestations of SDV are heritable, adaptable, selectable, and evolvable, and therefore, SDV may be seen as a hitherto overlooked evolution factor. SDV is also relevant for husbandry, agriculture, and medicine because most pathogens are asexuals that exploit this third source of phenotypic variation to modify infectivity and resistance to antibiotics. Since SDV affects all types of organisms and almost all aspects of life, it urgently requires more intense research and a better integration into biological thinking.
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany,
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94
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Levetin E, Horner WE, Scott JA. Taxonomy of Allergenic Fungi. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2015; 4:375-385.e1. [PMID: 26725152 DOI: 10.1016/j.jaip.2015.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/16/2015] [Indexed: 12/11/2022]
Abstract
The Kingdom Fungi contains diverse eukaryotic organisms including yeasts, molds, mushrooms, bracket fungi, plant rusts, smuts, and puffballs. Fungi have a complex metabolism that differs from animals and plants. They secrete enzymes into their surroundings and absorb the breakdown products of enzyme action. Some of these enzymes are well-known allergens. The phylogenetic relationships among fungi were unclear until recently because classification was based on the sexual state morphology. Fungi lacking an obvious sexual stage were assigned to the artificial, now-obsolete category, "Deuteromycetes" or "Fungi Imperfecti." During the last 20 years, DNA sequencing has resolved 8 fungal phyla, 3 of which contain most genera associated with important aeroallergens: Zygomycota, Ascomycota, and Basidiomycota. Advances in fungal classification have required name changes for some familiar taxa. Because of regulatory constraints, many fungal allergen extracts retain obsolete names. A major benefit from this reorganization is that specific immunoglobulin E (IgE) levels in individuals sensitized to fungi appear to closely match fungal phylogenetic relationships. This close relationship between molecular fungal systematics and IgE sensitization provides an opportunity to systematically look at cross-reactivity and permits representatives from each taxon to serve as a proxy for IgE to the group.
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Affiliation(s)
- Estelle Levetin
- Faculty of Biological Science, University of Tulsa, Tulsa, Okla.
| | | | - James A Scott
- Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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95
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Population genetic analysis reveals cryptic sex in the phytopathogenic fungus Alternaria alternata. Sci Rep 2015; 5:18250. [PMID: 26666175 PMCID: PMC4678894 DOI: 10.1038/srep18250] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 11/16/2015] [Indexed: 11/08/2022] Open
Abstract
Reproductive mode can impact population genetic dynamics and evolutionary landscape of plant pathogens as well as on disease epidemiology and management. In this study, we monitored the spatial dynamics and mating type idiomorphs in ~700 Alternaria alternata isolates sampled from the main potato production areas in China to infer the mating system of potato early blight. Consistent with the expectation of asexual species, identical genotypes were recovered from different locations separated by hundreds of kilometers of geographic distance and spanned across many years. However, high genotype diversity, equal MAT1-1 and MAT1-2 frequencies within and among populations, no genetic differentiation and phylogenetic association between two mating types, combined with random association amongst neutral markers in some field populations, suggested that sexual reproduction may also play an important role in the epidemics and evolution of the pathogen in at least half of the populations assayed despite the fact that no teleomorphs have been observed yet naturally or artificially. Our results indicated that A. alternata may adopt an epidemic mode of reproduction by combining many cycles of asexual propagation with fewer cycles of sexual reproduction, facilitating its adaptation to changing environments and making the disease management on potato fields even more difficult.
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97
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Abstract
Banana (Musa spp.) is one of the world's most important fruits. In 2011, 145 million metric tons, worth an estimated $44 billion, were produced in over 130 countries. Fusarium wilt (also known as Panama disease) is one of the most destructive diseases of this crop. It devastated the 'Gros Michel'-based export trades before the mid-1900s, and threatens the Cavendish cultivars that were used to replace it; in total, the latter cultivars are now responsible for approximately 45% of all production. An overview of the disease and its causal agent, Fusarium oxysporum f. sp. cubense, is presented below. Despite a substantial positive literature on biological, chemical, or cultural measures, management is largely restricted to excluding F. oxysporum f. sp. cubense from noninfested areas and using resistant cultivars where the pathogen has established. Resistance to Fusarium wilt is poor in several breeding targets, including important dessert and cooking cultivars. Better resistance to this and other diseases is needed. The history and impact of Fusarium wilt is summarized with an emphasis on tropical race 4 (TR4), a 'Cavendish'-killing variant of the pathogen that has spread dramatically in the Eastern Hemisphere.
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Affiliation(s)
- Randy C Ploetz
- University of Florida, Tropical Research & Education Center, 18905 SW 280th Street, Homestead 33031-3314
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98
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Rocha CML, Vellicce GR, García MG, Pardo EM, Racedo J, Perera MF, de Lucía A, Gilli J, Bogado N, Bonnecarrère V, German S, Marcelino F, Ledesma F, Reznikov S, Ploper LD, Welin B, Castagnaro AP. Use of AFLP markers to estimate molecular diversity of Phakopsora pachyrhizi. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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99
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Jimu L, Chen S, Wingfield MJ, Mwenje E, Roux J. Three genetic groups of the Eucalyptus stem canker pathogen Teratosphaeria zuluensis introduced into Africa from an unknown source. Antonie van Leeuwenhoek 2015; 109:21-33. [PMID: 26499489 DOI: 10.1007/s10482-015-0606-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
Abstract
The Eucalyptus stem canker pathogen Teratosphaeria zuluensis was discovered in South Africa in 1988 and it has subsequently been found in several other African countries as well as globally. In this study, the population structure, genetic diversity and evolutionary history of T. z uluensis were analysed using microsatellite markers to gain an enhanced understanding of its movement in Africa. Isolates were collected from several sites in Malawi, Mozambique, Uganda and Zambia. Data obtained were compared with those previously published for a South African population. The data obtained from 334 isolates, amplified across eight microsatellite loci, were used for assignment, differentiation and genetic diversity tests. STRUCTURE analyses, θ st and genetic distances revealed the existence of two clusters, one dominated by isolates from South Africa and the other by isolates from the Zambezi basin including Malawi, Mozambique and Zambia. High levels of admixture were found within and among populations, dominated by the Mulanje population in Malawi. Moderate to low genetic diversity of the populations supports the previously held view that the pathogen was introduced into Africa. The clonal nature of the Ugandan population suggests a very recent introduction, most likely from southern Africa.
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Affiliation(s)
- Luke Jimu
- Department of Plant Production and Soil Science, Forest Science Postgraduate Programme, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
| | - ShuaiFei Chen
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eddie Mwenje
- Bindura University of Science Education (BUSE), P. Bag 1020, Bindura, Zimbabwe
| | - Jolanda Roux
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
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100
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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.
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