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Kiebacher T, Szövényi P. Morphological, genetic and ecological divergence in near-cryptic bryophyte species widespread in the Holarctic: the Dicranum acutifolium complex (Dicranales) revisited in the Alps. JOURNAL OF PLANT RESEARCH 2024; 137:561-574. [PMID: 38520483 PMCID: PMC11230997 DOI: 10.1007/s10265-024-01534-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/15/2024] [Indexed: 03/25/2024]
Abstract
There is mounting evidence that reproductively isolated, but morphologically weakly differentiated species (so-called cryptic species) represent a substantial part of biological diversity, especially in bryophytes. We assessed the evolutionary history and ecological differentiation of a species pair, Dicranum brevifolium and D. septentrionale, which have overlapping ranges in the Holarctic. Despite their morphological similarity, we found similar genetic differentiation as between morphologically well-differentiated Dicranum species. Moreover, we detected gene tree discordance between plastid and nuclear markers, but neither of the two datasets resolved the two as sister species. The signal in trnL-trnF better reflects the morphological and ecological affinities and indicates a close relationship while ITS sequence data resolved the two taxa as phylogenetically distantly related. The discordance is probably unrelated to the ecological differentiation of D. septentrionale to colonise subneutral to alkaline substrates (vs. acidic in D. brevifolium), because this ability is rare in the genus and shared with D. acutifolium. This taxon is the closest relative of D. septentrionale according to the trnL-trnF data and does not share the discordance in ITS. We furthermore demonstrate that beside D. acutifolium, both D. septentrionale and D. brevifolium occur in the Alps but D. brevifolium is most likely rarer. Based on morphological analyses including factor analysis for mixed data of 45 traits we suggest treating the latter two as near-cryptic species and we recommend verifying morphological determinations molecularly.
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Affiliation(s)
- Thomas Kiebacher
- Department of Botany, Stuttgart State Museum of Natural History, Rosenstein 1, 70191, Stuttgart, Germany.
- Department of Systematic and Evolutionary Botany, University of Zurich UZH, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich UZH, Zollikerstrasse 107, 8008, Zurich, Switzerland
- Zurich-Basel Plant Science Center (PSC), ETH Zürich, Tannenstrasse 1, 8092, Zurich, Switzerland
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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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Uhlig S, Rangel-Huerta OD, Divon HH, Rolén E, Pauchon K, Sumarah MW, Vrålstad T, Renaud JB. Unraveling the Ergot Alkaloid and Indole Diterpenoid Metabolome in the Claviceps purpurea Species Complex Using LC-HRMS/MS Diagnostic Fragmentation Filtering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7137-7148. [PMID: 34148344 DOI: 10.1021/acs.jafc.1c01973] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The plant parasitic fungus Claviceps purpurea sensu lato produces sclerotia containing toxic ergot alkaloids and uncharacterized indole diterpenoids in grasses including cereals. The aim of this study was to detect as many peptide ergot alkaloids and indole diterpenoids in ergot sclerotia as possible by using a liquid chromatography-high-resolution mass spectrometry (LC-HRMS/MS) approach and applying filtering of diagnostic fragment ions for data extraction. The sample set consisted of 66 Claviceps sclerotia from four different geographic locations in southeastern Norway as well as Saskatchewan, Canada. The host plants included both wild grasses and important cereal grains such as rye. DNA sequencing showed that the sclerotia were from three Claviceps species, i.e., Claviceps purpurea sensu stricto (s.s.), Claviceps humidiphila, and Claviceps arundinis (former C. purpurea genotypes G1, G2, and G2a, respectively). All sclerotia from cereal grains were from C. purpurea s.s. Diagnostic fragment filtering was based on detecting specific product ions in MS/MS data sets that are well-conserved across the different ergot alkaloid subgroups and indole diterpenoids of the paspaline/paxilline type. The approach extracted mass spectra from 67 peptide ergot alkaloids (including C-8 epimers and lactam variants) and five indole diterpenoids. In addition, three clavines were detected by using targeted analysis. The sum of the peak areas for ergot alkaloids, which have been assigned as "major" analogues by the European Food Safety Authority (ergometrine, ergosine, ergotamine, α-ergocryptine, ergocornine, ergocristine, and their 8-S epimers), accounted for at least 50% of the extracted total ergot alkaloid metabolome. Univariate and multivariate statistical analyses showed that several of the alkaloids were specific for certain species within the C. purpurea species complex and could be used as chemotaxonomic markers for species assignment.
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Affiliation(s)
- Silvio Uhlig
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | | | - Hege H Divon
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | - Elin Rolén
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | - Kari Pauchon
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Science, Universitetstunet 3, 1430 Ås, Norway
| | - Mark W Sumarah
- London Research and Development Center, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada
| | - Trude Vrålstad
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | - Justin B Renaud
- London Research and Development Center, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3, Canada
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Dung JKS, Duringer JM, Kaur N, Scott JC, Frost KE, Walenta DL, Alderman SC, Craig AM, Hamm PB. Molecular and Alkaloid Characterization of Claviceps purpurea Sensu Lato From Grass Seed Production Areas of the U.S. Pacific Northwest. PHYTOPATHOLOGY 2021; 111:831-841. [PMID: 33141647 DOI: 10.1094/phyto-07-20-0289-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ergot, caused by Claviceps purpurea sensu lato, is an economically important seed replacement disease of Kentucky bluegrass (Poa pratensis) and perennial ryegrass (Lolium perenne) seed crops. C. purpurea sensu stricto is considered the primary Claviceps species responsible, but genetic diversity and cryptic species within C. purpurea sensu lato have previously been reported. Fifty-six C. purpurea sensu lato isolates collected from P. pratensis (n = 21) and L. perenne (n = 35) in Oregon and Washington between 2010 and 2014 were characterized via random amplified polymorphic DNA (RAPD), partial internal transcribed spacer (ITS), β-tubulin and elongation factor-1α (EF-1α) sequences, conidial size, and ergot alkaloid chemotype. Based on RAPD analysis, seven isolates from P. pratensis and 33 isolates from L. perenne collected in Oregon corresponded to C. purpurea sensu stricto, and 13 isolates collected from P. pratensis in Washington and Oregon were identified as C. humidiphila. Partial ITS, β-tubulin, and EF-1α sequences identified 10 isolates from P. pratensis as C. humidiphila, and seven isolates from P. pratensis and 33 isolates from L. perenne were identified as C. purpurea sensu stricto. Several isolates generated ambiguous RAPD bands or sequences that prevented identification. Ergot alkaloid chemotype profiling found that ergocornine and its epimer were predominant in sclerotia from P. pratensis, whereas ergotamine and its epimer were most abundant in sclerotia from L. perenne. This study confirms the presence of the C. purpurea sensu lato species complex in the U.S. Pacific Northwest and suggests that more research is needed to characterize and mitigate Claviceps spp. infection of grass seed crops in North America.
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Affiliation(s)
- Jeremiah K S Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741
| | - Jennifer M Duringer
- Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331
| | - Navneet Kaur
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR 97838
| | - Jeness C Scott
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741
| | - Kenneth E Frost
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR 97838
| | - Darrin L Walenta
- Department of Crop and Soil Science, Oregon State University Extension Service, La Grande, OR 97850
| | - Stephen C Alderman
- USDA-ARS National Forage Seed Production Research Center, Corvallis, OR 97331
| | - A Morrie Craig
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331
| | - Philip B Hamm
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR 97838
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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Liu M, Shoukouhi P, Bisson KR, Wyka SA, Broders KD, Menzies JG. Sympatric divergence of the ergot fungus, Claviceps purpurea, populations infecting agricultural and nonagricultural grasses in North America. Ecol Evol 2021; 11:273-293. [PMID: 33437429 PMCID: PMC7790621 DOI: 10.1002/ece3.7028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/02/2020] [Accepted: 11/02/2020] [Indexed: 11/08/2022] Open
Abstract
The ergot diseases of agricultural and nonagricultural grasses are caused by the infection of Claviceps spp. (Hypocreales, Ascomycota) on florets, producing dark spur-like sclerotia on spikes that are toxic to humans and animals, leading to detrimental impacts on agriculture and economy due to the downgrading of cereal grains, import-export barriers, reduced yield, and ecological concerns. At least seven phylogenetic lineages (phylogenetic species) were identified within the premolecular concept of C. purpurea s.l. (sensu lato) in agricultural areas and vicinities in Canada and the Western United States. Claviceps purpurea s.s (sensu stricto) remained as the most prevalent species with a wide host range, including cereal crops, native, invasive, and weedy grasses. The knowledge on genetic diversity and distribution of C. purpurea s.s. in North America is lacking. The objective of the present study was to shed light on genetic differentiation and evolution of the natural populations of C. purpurea s.s. Multilocus DNA sequences of samples from Canada and the Western USA were analyzed using a phylogenetic network approach, and population demographic parameters were investigated. Results showed that three distinct genetically subdivided populations exist, and the subdivision is not correlated with geographic or host differentiations. Potential intrinsic mechanisms that might play roles in leading to the cessation of gene flows among the subpopulations, that is, mating and/or vegetative incompatibility, genomic adaptation, were discussed. The neutrality of two house-keeping genes that are widely used for DNA barcoding, that is, translation elongation factor 1-α (TEF1-α) and RNA polymerase II second largest subunit (RPB2), was challenged and discussed.
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Affiliation(s)
- Miao Liu
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Parivash Shoukouhi
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Kassandra R. Bisson
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | | | | | - Jim G. Menzies
- Morden Research and Development CentreAgriculture and Agri‐Food CanadaMordenMBCanada
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Cheng Q, Frost KE, Dung JKS. Population Genetic Structure of Claviceps purpurea in Cool-Season Grass Seed Crops of Oregon. PHYTOPATHOLOGY 2020; 110:1773-1780. [PMID: 32573347 DOI: 10.1094/phyto-01-20-0005-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ergot, caused by Claviceps purpurea, is a primary disease concern in irrigated cool-season grass seed production systems of Oregon. In order to better understand the genetic diversity, population structure, and the epidemiology of C. purpurea in grasses grown for seed, 226 isolates were obtained using a hierarchical sampling strategy from two fields each of Kentucky bluegrass (n = 102) and perennial ryegrass (n = 124) and characterized using 12 microsatellite markers. A total of 194 unique multilocus genotypes (MLGs) were identified in this study. There were moderate levels of genotypic diversity (H = 3.43 to 4.23) and gene diversity (Hexp = 0.45 to 0.57) within fields. After clone correction, analysis of molecular variance revealed that 66% of the genetic variation occurred between the two C. purpurea isolates collected from the same seed head of individual plants, indicating that many of the seed heads bearing multiple sclerotia were infected by ascospores rather than conidia. However, the majority of the clonal isolates obtained in this study were collected from the same seed head (i.e., the two isolates were identical MLGs), indicating a role of conidia (honeydew) in secondary infections within seed heads. Genetic differentiation was observed between populations from different hosts (22%) but was confounded by geography. The standardized index of association ranged from 0.007 to 0.122 among the four populations, suggesting potential outcrossing and differences in the relative contribution of ascospores and conidia to ergot among the fields. The results from this study provide insights into the epidemiology of ergot in cool-season grass seed crops of Oregon.
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Affiliation(s)
- Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR
| | - Kenneth E Frost
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR
| | - Jeremiah K S Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR
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Liu M, Overy DP, Cayouette J, Shoukouhi P, Hicks C, Bisson K, Sproule A, Wyka SA, Broders K, Popovic Z, Menzies JG. Four phylogenetic species of ergot from Canada and their characteristics in morphology, alkaloid production, and pathogenicity. Mycologia 2020; 112:974-988. [PMID: 32936061 DOI: 10.1080/00275514.2020.1797372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Four ergot species (Claviceps ripicola, C. quebecensis, C. perihumidiphila, and C. occidentalis) were recognized based on analyses of DNA sequences from multiple loci, including two housekeeping genes, RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α (TEF1-α), and a single-copy ergot alkaloid synthesis gene (easE) encoding chanoclavine I synthase oxidoreductase. Morphological features, ergot alkaloid production, and pathogenicity on five common cereal crops of each species were evaluated and presented in taxonomic descriptions. A synoptic key was also provided for identification.
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Affiliation(s)
- Miao Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - David P Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Jacques Cayouette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Parivash Shoukouhi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Carmen Hicks
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Kassandra Bisson
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Stephen A Wyka
- Colorado State University , Fort Collins, Colorado 80523
| | - Kirk Broders
- Colorado State University , Fort Collins, Colorado 80523
| | - Zlatko Popovic
- Morden Research and Development Centre, Agriculture and Agri-Food Canada , 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada , 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
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Gasca-Pineda J, Velez P, Hosoya T. Phylogeography of post-Pleistocene population expansion in Dasyscyphella longistipitata (Leotiomycetes, Helotiales), an endemic fungal symbiont of Fagus crenata in Japan. MycoKeys 2020; 65:1-24. [PMID: 32218686 PMCID: PMC7086340 DOI: 10.3897/mycokeys.65.48409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/20/2020] [Indexed: 01/16/2023] Open
Abstract
During the Last Glacial Maximum (LGM), drastic environmental changes modified the topology of the Japanese Archipelago, impacting species distributions. An example is Fagus crenata, which has a present continuous distribution throughout Japan. However, by the end of the LGM it was restricted to southern refugia. Similarly, Dasyscyphella longistipitata (Leotiomycetes, Helotiales, Lachnaceae) occurs strictly on cupules of F. crenata, sharing currently an identical distribution. As the effects of the LGM remain poorly understood for saprobiotic microfungal species, herein we identified past structuring forces that shaped the current genetic diversity within D. longistipitata in relation to its host using a phylogeographic approach. We inferred present and past potential distributions through species distribution modeling, identifying environmental suitability areas in mid-southern Japan from which subsequent colonizations occurred. Our findings suggest that current high genetic diversity and lack of genetic structure within D. longistipitata are the result of recent multiple re-colonization events after the LGM.
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Affiliation(s)
- Jaime Gasca-Pineda
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090, Estado de México, Mexico Universidad Nacional Autónoma de México Estado de México Mexico
| | - Patricia Velez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico Universidad Nacional Autónoma de México Mexico City Mexico
| | - Tsuyoshi Hosoya
- National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005 Japan National Museum of Nature and Science Tsukuba Japan
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Oberti H, Dalla Rizza M, Reyno R, Murchio S, Altier N, Abreo E. Diversity of Claviceps paspali reveals unknown lineages and unique alkaloid genotypes. Mycologia 2020; 112:230-243. [PMID: 31910144 DOI: 10.1080/00275514.2019.1694827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Claviceps species affecting Paspalum spp. are a serious problem, as they infect forage grasses such as Paspalum dilatatum and P. plicatulum, producing the ergot disease. The ascomycete C. paspali is known to be the pathogen responsible for this disease in both grasses. This fungus produces alkaloids, including ergot alkaloids and indole-diterpenes, that have potent neurotropic activities in mammals. A total of 32 isolates from Uruguay were obtained from infected P. dilatatum and P. plicatulum. Isolates were phylogenetically identified using partial sequences of the genes coding for the second largest subunit of RNA polymerase subunit II (RPB2), translation elongation factor 1-α (TEF1), β-tubulin (TUB2), and the nuc rDNA 28S subunit (28S). Isolates were also genotyped by randomly amplified polymorphic DNA (RAPD) and presence of genes within the ergot alkaloid (EAS) and indole-diterpene (IDT) biosynthetic gene clusters. This study represents the first genetic characterization of several isolates of C. paspali. The results from this study provide insight into the genetic and genotypic diversity of Claviceps paspali present in P. dilatatum and suggest that isolates from P. plicatulum could be considered an ecological subspecies or specialized variant of C. paspali. Some of these isolates show hypothetical alkaloid genotypes never reported before.
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Affiliation(s)
- H Oberti
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Uruguay
| | - M Dalla Rizza
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Uruguay
| | - R Reyno
- Programa Nacional de Forraje y Pasturas, Instituto Nacional de Investigación Agropecuaria Tacuarembó, Tacuarembó, Uruguay
| | - S Murchio
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Uruguay
| | - N Altier
- Laboratorio de Bioproducción, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Uruguay
| | - E Abreo
- Laboratorio de Bioproducción, Instituto Nacional de Investigación Agropecuaria, Las Brujas, Uruguay
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Shoukouhi P, Hicks C, Menzies JG, Popovic Z, Chen W, Seifert KA, Assabgui R, Liu M. Phylogeny of Canadian ergot fungi and a detection assay by real-time polymerase chain reaction. Mycologia 2019; 111:493-505. [PMID: 30933656 DOI: 10.1080/00275514.2019.1581018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ergot disease of cereals has become increasingly important in agricultural areas of Canada since 1999. Generally, this disease is considered to be caused by Claviceps purpurea, but the taxonomy of Claviceps from these areas has not been well studied. The objectives of this study were (i) to determine the phylogenetic lineages (phylogenetic species) present in agricultural areas of Canada and (ii) to develop a molecular assay that can separate the lineages on crops from other lineages. Genetic diversity of Claviceps collected from agriculture areas in Canada were investigated using multilocus sequence typing. The loci sequenced include nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS), partial fragments of translation elongation factor 1-α (TEF1), RNA polymerase II second largest subunit (RPB2), β-tubulin (tubB), and two ergot alkaloid synthesis genes (easA, easE). Based on individual locus and concatenated alignments, phylogenetic analyses revealed seven lineages within the premolecular concept of C. purpurea, of which five corresponded with undescribed species (G2b and G4-7). Although lineages G2-7 had narrow host ranges, lineage G1 (= C. purpurea s.s.) had a broad host range that overlapped with other lineages. A molecular diagnostic quantitative polymerase chain reaction (qPCR) assay was developed and validated with 185 samples from a wide range of host plants and geographic origins, including 10 phylogenetic species in C. sect. Claviceps, 8 in C. sect. Pusillae, 1 in C. sect. Citrinae, and 1-2 species from Alternaria, Fusarium, and Penicillium. The assay can detect lineage G1 at a concentration of 7.5 pg/μL and distinguish it from other Claviceps species and lineages. This facilitates disease management by detecting the inocula from nonagriculture host plants.
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Affiliation(s)
- Parivash Shoukouhi
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
| | - Carmen Hicks
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
| | - Jim G Menzies
- b Morden Research and Development Centre , Agriculture and Agri-Food Canada , 101 Route 100, Morden , Manitoba R6M 1Y5 , Canada
| | - Zlatko Popovic
- b Morden Research and Development Centre , Agriculture and Agri-Food Canada , 101 Route 100, Morden , Manitoba R6M 1Y5 , Canada
| | - Wen Chen
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
| | - Keith A Seifert
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
| | - Rafik Assabgui
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
| | - Miao Liu
- a Biodiversity (Mycology and Microbiology), Ottawa Research and Development Centre , Agriculture and Agri-Food Canada , Ottawa , K1A 0C6 , Canada
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Dung JKS, Scott JC, Cheng Q, Alderman SC, Kaur N, Walenta DL, Frost KE, Hamm PB. Detection and Quantification of Airborne Claviceps purpurea sensu lato Ascospores from Hirst-Type Spore Traps using Real-Time Quantitative PCR. PLANT DISEASE 2018; 102:2487-2493. [PMID: 30256180 DOI: 10.1094/pdis-02-18-0310-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The U.S. Pacific Northwest states of Oregon and Washington are major producers of cool-season grass seed. Ergot, caused by fungi in the Claviceps purpurea sensu lato group, is an important seed replacement disease of grass worldwide. Microscopic methods that are currently used to quantify airborne Claviceps ascospores captured by spore traps are not currently rapid enough to allow for detecting and reporting of spore numbers in a timely manner, hindering growers from using this information to help manage ergot. We developed a SYBR Green real-time quantitative polymerase chain reaction (qPCR)-based assay for fast and efficient detection and quantification of C. purpurea sensu lato ascospores from Hirst-type spore traps. Species-specificity of the qPCR assay was confirmed against 41 C. purpurea sensu lato isolates collected from six hosts and six other Claviceps spp. Significant relationships were observed between cycle threshold (Ct) values and standard curves of serial dilutions of DNA ranging from 1 pg to 10 ng (R2 = -0.99; P = 0.0002) and DNA extracted from a conidial suspension representing 8 to 80,000 conidia (R2 = -0.99; P = 0.0004). Ct values from qPCR were significantly correlated with results from microscopic examination of spore trap samples from the field (r = -0.68; P < 0.0001) and the procedure was able to detect a single ascospore from spore trap tape samples. The qPCR procedure developed in this study provided a means for quantifying airborne Claviceps ascospores that was highly specific and useful over a wide range of spore densities, and could be performed in a matter of hours instead of days. The qPCR assay developed in this study could be part of an integrated pest management approach to help grass seed growers make risk-based fungicide application decisions for ergot management in grass grown for seed.
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Affiliation(s)
- Jeremiah K S Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Jeness C Scott
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras
| | - Stephen C Alderman
- National Forage Seed Production Research Center, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR
| | - Navneet Kaur
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Darrin L Walenta
- Union County Extension Service, Oregon State University, La Grande
| | - Kenneth E Frost
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Philip B Hamm
- Department of Botany and Plant Pathology, Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
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Wingfield BD, Liu M, Nguyen HDT, Lane FA, Morgan SW, De Vos L, Wilken PM, Duong TA, Aylward J, Coetzee MPA, Dadej K, De Beer ZW, Findlay W, Havenga M, Kolařík M, Menzies JG, Naidoo K, Pochopski O, Shoukouhi P, Santana QC, Seifert KA, Soal N, Steenkamp ET, Tatham CT, van der Nest MA, Wingfield MJ. Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructans. IMA Fungus 2018; 9:401-418. [PMID: 30622889 PMCID: PMC6317589 DOI: 10.5598/imafungus.2018.09.02.10] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 12/14/2022] Open
Abstract
This genome announcement includes draft genomes from Claviceps purpurea s.lat., including C. arundinis, C. humidiphila and C. cf. spartinae. The draft genomes of Davidsoniella eucalypti, Quambalaria eucalypti and Teratosphaeria destructans, all three important eucalyptus pathogens, are presented. The insect associate Grosmannia galeiformis is also described. The pine pathogen genome of Fusarium circinatum has been assembled into pseudomolecules, based on additional sequence data and by harnessing the known synteny within the Fusarium fujikuroi species complex. This new assembly of the F. circinatum genome provides 12 pseudomolecules that correspond to the haploid chromosome number of F. circinatum. These are comparable to other chromosomal assemblies within the FFSC and will enable more robust genomic comparisons within this species complex.
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Affiliation(s)
- Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Miao Liu
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Hai D T Nguyen
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Frances A Lane
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Seamus W Morgan
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - P Markus Wilken
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Kasia Dadej
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Z Wilhelm De Beer
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Wendy Findlay
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Minette Havenga
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Olivia Pochopski
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Parivash Shoukouhi
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Keith A Seifert
- Ottawa Research & Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave. Ottawa, Ontario K1A 0C6, Canada
| | - Nicole Soal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Catherine T Tatham
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Margriet A van der Nest
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag x20, Hatfield, Pretoria, 0028, South Africa
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Qin J, Horak E, Popa F, Rexer KH, Kost G, Li F, Yang ZL. Species diversity, distribution patterns, and substrate specificity of Strobilurus. Mycologia 2018; 110:584-604. [PMID: 29913116 DOI: 10.1080/00275514.2018.1463064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The fungal genus Strobilurus belongs to Physalacriaceae and contains approximately 11 species worldwide. Species of this genus grow and reproduce on cones of various conifers, seed pods or fruits of Magnolia and Liquidambar, and branches and wood of conifers. Previous studies focused mainly on samples from Europe and North America. And no genus-specific phylogenetic analysis has been carried out to date. The monophyly, degree of species diversity and substrate specificity, and overall distribution patterns are addressed here using morphological and molecular evidence. The authors collected samples of Strobilurus from much of its known distribution ranges and carried out morphological observations and multilocus phylogenetic analyses using five molecular markers. The results show that Strobilurus is a monophyletic group but may exclude one species, S. ohshimae. A total of 13 species was identified, with two, S. orientalis and S. pachycystidiatus, described as new from China. Several species were shown to be specific to certain substrates, whereas a few less so. Biogeographic analyses indicated that historical exchanges of species between East Asia, Europe, and North America, later vicariance events, and substrate specificity have contributed jointly to diversification of Strobilurus.
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Affiliation(s)
- Jiao Qin
- a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China.,b Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China
| | - Egon Horak
- c Schlossfeld 17, AT-6020 Innsbruck , Austria
| | - Flavius Popa
- d Department of Ecosystem Monitoring , Research and Conservation , Black Forest National Park, Kniebisstr. 67, 77740 Bad Peterstal-Griesbach , Germany
| | - Karl-Heinz Rexer
- e Systematic Botany and Mycology, FB17, Philipps University Marburg , 35032 Marburg , Germany
| | - Gerhard Kost
- e Systematic Botany and Mycology, FB17, Philipps University Marburg , 35032 Marburg , Germany
| | - Fang Li
- f School of Life Sciences , Sun Yat-sen University , Guangzhou 510275 , China
| | - Zhu L Yang
- a Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , China
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Population Genetics of Hirsutella rhossiliensis, a Dominant Parasite of Cyst Nematode Juveniles on a Continental Scale. Appl Environ Microbiol 2016; 82:6317-6325. [PMID: 27542936 DOI: 10.1128/aem.01708-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/04/2016] [Indexed: 01/17/2023] Open
Abstract
Hirsutella rhossiliensis is a parasite of juvenile nematodes, effective against a diversity of plant-parasitic nematodes. Its global distribution on various nematode hosts and its genetic variation for several geographic regions have been reported, while the global population genetic structure and factors underlying patterns of genetic variation of H. rhossiliensis are unclear. In this study, 87 H. rhossiliensis strains from five nematode species (Globodera sp., Criconemella xenoplax, Rotylenchus robustus, Heterodera schachtii, and Heterodera glycines) in Europe, the United States, and China were investigated by multilocus sequence analyses. A total of 280 variable sites (frequency, 0.6%) at eight loci and six clustering in high accordance with geographic populations or host nematode-associated populations were identified. Although H. rhossiliensis is currently recognized as an asexual fungus, recombination events were frequently detected. In addition, significant genetic isolation by geography and nematode hosts was revealed. Overall, our analyses showed that recombination, geographic isolation, and nematode host adaptation have played significant roles in the evolutionary history of H. rhossiliensis IMPORTANCE: H. rhossiliensis has great potential for use as a biocontrol agent to control nematodes in a sustainable manner as an endoparasitic fungus. Therefore, this study has important implications for the use of H. rhossiliensis as a biocontrol agent and provides interesting insights into the biology of this species.
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Obase K, Douhan GW, Matsuda Y, Smith ME. Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato. MYCORRHIZA 2016; 26:529-540. [PMID: 26968743 DOI: 10.1007/s00572-016-0690-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87-100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage.
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Affiliation(s)
- Keisuke Obase
- Microbial Ecology Laboratory, Department of Forest Microbiology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
- Department of Plant Pathology, University of Florida, 2517 Fifield Hall, Gainesville, FL, 32611-0680, USA.
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Cooperative Extension Advisor, Tulare Co., University of California, Tulare, CA, 93274, USA
| | - Yosuke Matsuda
- Laboratory of Forest Pathology and Mycology, Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, 2517 Fifield Hall, Gainesville, FL, 32611-0680, USA
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Gilmore BS, Alderman SC, Knaus BJ, Bassil NV, Martin RC, Dombrowski JE, Dung JKS. Simple sequence repeat markers that identify Claviceps species and strains. Fungal Biol Biotechnol 2016; 3:1. [PMID: 28955460 PMCID: PMC5611664 DOI: 10.1186/s40694-016-0019-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/03/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Claviceps purpurea is a pathogen that infects most members of Pooideae, a subfamily of Poaceae, and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. When the ergot body is accidently consumed by either man or animal in high enough quantities, there is extreme pain, limb loss and sometimes death. RESULTS This study was initiated to develop simple sequence repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were designed from sequence data stored at the National Center for Biotechnology Information database. The study consisted of 74 ergot isolates, from four different host species, Lolium perenne, Poa pratensis, Bromus inermis, and Secale cereale plus three additional Claviceps species, C. pusilla, C. paspali and C.fusiformis. Samples were collected from six different counties in Oregon and Washington over a 5-year period. Thirty-four SSR markers were selected, which enabled the differentiation of each isolate from one another based solely on their molecular fingerprints. Discriminant analysis of principle components was used to identify four isolate groups, CA Group 1, 2, 3, and 4, for subsequent cluster and molecular variance analyses. CA Group 1 consisting of eight isolates from the host species P. pratensis, was separated on the cluster analysis plot from the remaining three groups and this group was later identified as C. humidiphila. The other three groups were distinct from one another, but closely related. These three groups contained samples from all four of the host species. These SSRs are simple to use, reliable and allowed clear differentiation of C. humidiphila from C. purpurea. Isolates from the three separate species, C. pusilla, C. paspali and C.fusiformis, also amplified with these markers. CONCLUSIONS The SSR markers developed in this study will be helpful in defining the population structure and genetics of Claviceps strains. They will also provide valuable tools for plant breeders needing to identify resistance in crops or for researchers examining fungal movements across environments.
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Affiliation(s)
- Barbara S. Gilmore
- USDA ARS Forage Seed and Cereal Research, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Stephen C. Alderman
- USDA ARS Forage Seed and Cereal Research, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Brian J. Knaus
- USDA ARS Horticultural Crops Research Unit, 3420 NW Orchard Ave, Corvallis, OR 97331 USA
| | - Nahla V. Bassil
- USDA ARS National Clonal Germplasm Repository, 33447 Peoria Road, Corvallis, OR 97333 USA
| | - Ruth C. Martin
- USDA ARS Forage Seed and Cereal Research, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - James E. Dombrowski
- USDA ARS Forage Seed and Cereal Research, 3450 SW Campus Way, Corvallis, OR 97331 USA
| | - Jeremiah K. S. Dung
- Oregon State University, Central Oregon Agricultural Research Center, 850 NW Dogwood Lane, Madras, OR 97741 USA
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Negård M, Uhlig S, Kauserud H, Andersen T, Høiland K, Vrålstad T. Links between Genetic Groups, Indole Alkaloid Profiles and Ecology within the Grass-Parasitic Claviceps purpurea Species Complex. Toxins (Basel) 2015; 7:1431-56. [PMID: 25928134 PMCID: PMC4448156 DOI: 10.3390/toxins7051431] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 12/24/2022] Open
Abstract
The grass parasitic fungus Claviceps purpurea sensu lato produces sclerotia with toxic indole alkaloids. It constitutes several genetic groups with divergent habitat preferences that recently were delimited into separate proposed species. We aimed to 1) analyze genetic variation of C. purpurea sensu lato in Norway, 2) characterize the associated indole alkaloid profiles, and 3) explore relationships between genetics, alkaloid chemistry and ecology. Approximately 600 sclerotia from 14 different grass species were subjected to various analyses including DNA sequencing and HPLC-MS. Molecular results, supported by chemical and ecological data, revealed one new genetic group (G4) in addition to two of the three known; G1 (C. purpurea sensu stricto) and G2 (C. humidiphila). G3 (C. spartinae) was not found. G4, which was apparently con-specific with the recently described C. arundinis sp. nov, was predominantly found in very wet habitats on Molinia caerulea and infrequently in saline habitats on Leymus arenarius. Its indole-diterpene profile resembled G2, while its ergot alkaloid profile differed from G2 in high amounts of ergosedmam. In contrast to G1, indole-diterpenes were consistently present in G2 and G4. Our study supports and complements the newly proposed species delimitation of the C. purpurea complex, but challenges some species characteristics including host spectrum, habitat preferences and sclerotial floating ability.
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Affiliation(s)
- Mariell Negård
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.
| | - Silvio Uhlig
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
- Department of the Chemical and Biological Working Environment, National Institute of Occupational Health, P.O. Box 8149 Dep, 0033 Oslo, Norway.
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.
| | - Tom Andersen
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.
| | - Klaus Høiland
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.
| | - Trude Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
- Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway.
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20
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Li LF, Wang HY, Pang D, Liu Y, Liu B, Xiao HX. Phenotypic and genetic evidence for ecological speciation of Aquilegia japonica and A. oxysepala. THE NEW PHYTOLOGIST 2014; 204:1028-1040. [PMID: 25117915 DOI: 10.1111/nph.12967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Natural selection is thought to be a driving force that can cause the evolution of reproductive isolation. The genus Aquilegia is a model system to address how natural selection promotes the process of speciation. Morphological differences between A. oxysepala, A. japonica and their hybrids were quantified for two vegetative (plant height and leaf area) and three floral morphological (sepal area, corolla length and diameter) traits. We also evaluated the genetic variability of the two species and their hybrids based on two chloroplast (1225 bp), four nuclear (5811 bp) genes and 15 microsatellites. Our results revealed that differentiation of A. japonica and A. oxysepala at the ecological and morphological levels also involved divergence at the genetic level. In addition, the analysis of nucleotide variation patterns showed that the two species possessed numerous fixation sites at nuclear genes gAA4, gA7 and gAA12. Furthermore, we found that all of the phenotypic hybrids also showed a genetically admixed ancestry. These findings suggest that natural selection has indeed facilitated the formation of distinct genetic variation patterns in the two Aquilegia species and habitat adaptation has been driving the ecologically based evolution of reproductive isolation.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
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21
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Pažoutová S, Pešicová K, Chudíčková M, Šrůtka P, Kolařík M. Delimitation of cryptic species inside Claviceps purpurea. Fungal Biol 2014; 119:7-26. [PMID: 25601146 DOI: 10.1016/j.funbio.2014.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 10/07/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
Abstract
Claviceps purpurea is an ovarian parasite infecting grasses (Poaceae) including cereals and forage plants. This fungus produces toxic alkaloids and consumption of contaminated grains can cause ergotism in humans and other mammals. Recent molecular genetics studies have indicated that it included three cryptic species (G1, G2, G3). In this study, reproductive isolation amongst these groups and among material from Phragmites and Molinia was tested using gene flow statistics for five polymorphic loci, and to support these data, phylogenetic affiliations based on gene trees and a multigene phylogeny were used. The four recognized species are characterized based on morphology and host spectrum and formal taxonomic names are proposed. Claviceps purpurea sensu stricto (G1 group) represents a typical rye ergot, but infects various other grasses. Typical hosts of Claviceps humidiphila (new name for G2 species), like Phalaris arundinacea, belong to grasses preferring humid locations. Claviceps spartinae (G3) is specific to chloridoid grasses from salt barches. The material from Phragmites and Molinia can be authenticated with the species Claviceps microcephala for which the new name Claviceps arundinis is proposed here. The divergence time between species was estimated and the tools for species identification are discussed.
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Affiliation(s)
- Sylvie Pažoutová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Kamila Pešicová
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic; Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Milada Chudíčková
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Šrůtka
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague 6, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology of the ASCR, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
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Uhlig S, Egge-Jacobsen W, Vrålstad T, Miles CO. Indole-diterpenoid profiles of Claviceps paspali and Claviceps purpurea from high-resolution Fourier transform Orbitrap mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1621-1634. [PMID: 24895259 DOI: 10.1002/rcm.6938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/02/2014] [Accepted: 05/03/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE The biological activities most commonly associated with indole-diterpenoids are tremorgenicity in mammals and toxicity in insects through modulation of ion channels. The neurotoxic effects of some analogues are the cause of syndromes such as 'ryegrass staggers' and 'Paspalum staggers' in cattle and sheep. Our purpose was to obtain and interpret mass spectra of some pure Claviceps-related indole-diterpenoids (paspaline, paspalinine, paxilline, paspalitrems A and B) to facilitate identification of related compounds for which standards were not available. METHODS C. paspali-infected Paspalum dilatatum as well as C. purpurea sclerotia obtained from infected Phalaris arundinacea were extracted and the extracts separated via liquid chromatography. Low- and high-resolution mass spectra were then obtained of known and potentially unknown indole-diterpenoids. RESULTS At least 20 different indole-diterpenoids were detected in the C. paspali extract with molecular masses ranging from 405 Da (C28H40NO) to 517 Da (C32H40NO5). The C. purpurea sclerotia were shown to contain several indole-diterpenoids with molecular masses ranging from 405 Da (C28H40NO) to 419 Da (C28H38NO2). CONCLUSIONS This study demonstrates for the first time that C. purpurea may also produce indole-diterpenoids. This might explain why grazing of Phalaris spp. is occasionally connected with a tremorgenic syndrome in cattle, called 'phalaris staggers'.
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Affiliation(s)
- Silvio Uhlig
- Norwegian Veterinary Institute, P.O. Box 750 Sentrum, 0106, Oslo, Norway
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Zhang Y, Qiao M, Xu J, Cao Y, Zhang KQ, Yu ZF. Genetic diversity and recombination in natural populations of the nematode-trapping fungus Arthrobotrys oligospora from China. Ecol Evol 2013; 3:312-25. [PMID: 23467563 PMCID: PMC3586641 DOI: 10.1002/ece3.450] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/12/2012] [Accepted: 11/15/2012] [Indexed: 11/09/2022] Open
Abstract
Nematophagous fungi can trap and capture nematodes and other small invertebrates. This unique ability has made them ideal organisms from which to develop biological control agents against plant- and animal-parasitic nematodes. However, effective application of biocontrol agents in the field requires a comprehensive understanding about the ecology and population genetics of the nematophagous fungi in natural environments. Here, we genotyped 228 strains of the nematode-trapping fungus Arthrobotrys oligospora using 12 single nucleotide polymorphic markers located on eight random DNA fragments. The strains were from different ecological niches and geographical regions from China. Our analyses identified that ecological niche separations contributed significantly, whereas geographic separation contributed relatively little to the overall genetic variation in our samples of A. oligospora. Interestingly, populations from stressful environments seemed to be more variable and showed more evidence for recombination than those from benign environments at the same geographic areas. We discussed the implications of our results to the conservation and biocontrol application of A. oligospora in agriculture and forestry.
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Affiliation(s)
- Ying Zhang
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Min Qiao
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Jianping Xu
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
- Department of Biology, McMaster University1280 Main Street West, Hamilton, Ontario, Canada, L8S 4K1
| | - Yang Cao
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
| | - Ze-Fen Yu
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan UniversityKunming, Yunnan, 650091, China
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Comparison of Claviceps purpurea populations originated from experimental plots or fields of rye. Open Life Sci 2012. [DOI: 10.2478/s11535-012-0075-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
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Muñoz AG, Baxter SW, Linares M, Jiggins CD. Deep mitochondrial divergence within a Heliconius butterfly species is not explained by cryptic speciation or endosymbiotic bacteria. BMC Evol Biol 2011; 11:358. [PMID: 22151691 PMCID: PMC3287262 DOI: 10.1186/1471-2148-11-358] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 12/12/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryptic population structure can be an indicator of incipient speciation or historical processes. We investigated a previously documented deep break in the mitochondrial haplotypes of Heliconius erato chestertonii to explore the possibility of cryptic speciation, and also the possible presence of endosymbiont bacteria that might drive mitochondrial population structure. RESULTS Among a sample of 315 individuals from 16 populations of western Colombia, two principal mtDNA clades were detected with 2.15% divergence and we confirmed this structure was weakly associated with geography. The first mtDNA clade included 87% of individuals from northern populations and was the sister group of H. erato members of Andes western, while the second clade contained most individuals from southern populations (78%), which shared haplotypes with an Ecuadorian race of H. erato. In contrast, analysis using AFLP markers showed H. e. chestertonii to be a genetically homogeneous species with no association between mitochondrial divergence and AFLP structure. The lack of congruence between molecular markers suggests that cryptic speciation is not a plausible explanation for the deep mitochondrial divergence in H. e chestertonii. We also carried out the first tests for the presence of endosymbiontic bacteria in Heliconius, and identified two distinct lineages of Wolbachia within H. e. chestertonii. However, neither of the principal mitochondrial clades of H. e. chestertonii was directly associated with the patterns of infection. CONCLUSIONS We conclude that historical demographic processes are the most likely explanation for the high mitochondrial differentiation in H. e. chestertonii, perhaps due to gene flow between Cauca valley H. e. chestertonii and west Pacific slope populations of H. erato.
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Affiliation(s)
- Astrid G Muñoz
- Instituto de Genética, Departamento de Ciencias Biologicas-Facultad de Ciencias, Universidad de los Andes, Carrera 1 No 18A-70, Bogotá, DC, Colombia.
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Zhang Y, Yu ZF, Xu J, Zhang KQ. Divergence and dispersal of the nematode-trapping fungus Arthrobotrys oligospora from China. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:763-773. [PMID: 23761368 DOI: 10.1111/j.1758-2229.2011.00297.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Nematode-trapping fungi are of significant agricultural, forestry and ecological importance. However, relatively little is known about the patterns of genetic variation for any nematode-trapping fungus through its broad geographic and ecological contexts. Here, we analysed DNA sequence variation among strains of the nematode-trapping fungus Arthrobotrys oligospora from China. Our analyses revealed that the Chinese A. oligospora is a species complex with at least three divergent lineages (cryptic species). In addition, there was significant geographic structuring with unambiguous evidence for localized recombination within two of the three lineages in nature. However, evidence for clonal reproduction was also found. We discuss the implications of our results to the conservation and biocontrol application of A. oligospora in agriculture and forestry.
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Affiliation(s)
- Ying Zhang
- Laboratory for Conservation and Utilization of Bio-resources, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, Yunnan 650091, China. Department of Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4K1, Canada
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Fávaro LCDL, de Melo FL, Aguilar-Vildoso CI, Araújo WL. Polyphasic analysis of intraspecific diversity in Epicoccum nigrum warrants reclassification into separate species. PLoS One 2011; 6:e14828. [PMID: 21853017 PMCID: PMC3154903 DOI: 10.1371/journal.pone.0014828] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 12/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Epicoccum nigrum Link (syn. E. purpurascens Ehrenb. ex Schlecht) is a saprophytic ascomycete distributed worldwide which colonizes a myriad of substrates. This fungus has been known as a biological control agent for plant pathogens and produces a variety of secondary metabolites with important biological activities as well as biotechnological application. E. nigrum produces darkly pigmented muriform conidia on short conidiophores on sporodochia and is a genotypically and phenotypically highly variable species. Since different isolates identified as E. nigrum have been evaluated as biological control agents and used for biocompound production, it is highly desirable that this species name refers to only one lineage. However, according to morphological and genetic variation, E. nigrum present two genotypes that may comprise more than one species. METHODOLOGY/PRINCIPAL FINDINGS We report the application of combined molecular (ITS and β-tubulin gene sequence analysis, PCR-RFLP and AFLP techniques), morphometric, physiological, genetic compatibility and recombination analysis to study the taxonomic relationships within an endophytic population that has been identified as E. nigrum. This combined analysis established two genotypes showing morphological, physiological and genetic divergence as well as genetic incompatibility characterized by colony inhibition, strongly indicating that these genotypes correspond to different species. Genotype 1 corresponds to E. nigrum while genotype 2 represents a new species, referred to in this study as Epicoccum sp. CONCLUSIONS/SIGNIFICANCE This research contributes to the knowledge of the Epicoccum genus and asserts that the classification of E. nigrum as a single variable species should be reassessed. In fact, based on the polyphasic approach we suggest the occurrence of cryptic species within E. nigrum and also that many of the sequences deposited as E. nigrum in GenBank and culture collection of microbial strains should be reclassified, including the reference strain CBS 161.73 sequenced in this work. In addition, this study provides valuable tools for differentiation of Epicoccum species.
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Affiliation(s)
| | | | | | - Welington Luiz Araújo
- Laboratory of Molecular Biology and Microbial Ecology, NIB, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil
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Grünwald NJ, Goss EM. Evolution and population genetics of exotic and re-emerging pathogens: novel tools and approaches. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:249-267. [PMID: 21370974 DOI: 10.1146/annurev-phyto-072910-095246] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species, allowing for the unprecedented reconstruction of the demographic history of pathogens. Specifically, recent advances in the application of coalescent, maximum likelihood (ML), and Bayesian methods to population genetic data combined with increasing availability of affordable sequencing and parallel computing have created the opportunity to apply these methods to a broad range of questions regarding the evolution of emerging pathogens. These approaches are particularly powerful when used to test multiple competing hypotheses. We provide several examples illustrating how coalescent analysis provides critical insights into understanding migration pathways as well as processes of divergence, speciation, and recombination.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon 97330, USA.
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Frenkel O, Peever TL, Chilvers MI, Özkilinc H, Can C, Abbo S, Shtienberg D, Sherman A. Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp. (Chickpea). Appl Environ Microbiol 2010; 76:30-9. [PMID: 19897759 PMCID: PMC2798644 DOI: 10.1128/aem.01181-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 10/31/2009] [Indexed: 11/20/2022] Open
Abstract
For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.
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Affiliation(s)
- Omer Frenkel
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Tobin L. Peever
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Martin I. Chilvers
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Hilal Özkilinc
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Canan Can
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Shahal Abbo
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Dani Shtienberg
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Amir Sherman
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
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Genetic diversity of Labyrinthula terrestris, a newly emergent plant pathogen, and the discovery of new Labyrinthulid organisms. ACTA ACUST UNITED AC 2009; 113:1192-9. [DOI: 10.1016/j.mycres.2009.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 07/15/2009] [Accepted: 08/05/2009] [Indexed: 11/21/2022]
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Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. THE NEW PHYTOLOGIST 2009; 183:513-529. [PMID: 19563451 DOI: 10.1111/j.1469-8137.2009.02927.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.
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Affiliation(s)
- Luke G Barrett
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joel M Kniskern
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Natacha Bodenhausen
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
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