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Han S, Wang M, Ma Z, Raza M, Zhao P, Liang J, Gao M, Li Y, Wang J, Hu D, Cai L. Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Stud Mycol 2023; 104:87-148. [PMID: 37351543 PMCID: PMC10282163 DOI: 10.3114/sim.2022.104.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/17/2023] [Indexed: 11/26/2023] Open
Abstract
Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.
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Affiliation(s)
- S.L. Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - M.M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - Z.Y. Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - M. Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - J.M. Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
| | - M. Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - Y.J. Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
| | - J.W. Wang
- Institute of Biology Co., Ltd., Henan Academy of Science, Zheng Zhou 450008, Henan, P. R. China;
| | - D.M. Hu
- College of Bioscience & Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, P. R. China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China;
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China;
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Steyn C, Jacobs A, Summerell B, Venter E. Fusarium diversity from the Golden Gate Highlands National Park. Front Microbiol 2023; 14:1149853. [PMID: 37125158 PMCID: PMC10133521 DOI: 10.3389/fmicb.2023.1149853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Members from the genus Fusarium can infect a broad range of plants and threaten agricultural and horticultural production. Studies on the diversity of Fusarium occurring in natural ecosystems have received less attention than the better known phytopathogenic members of the genus. This study identified Fusarium species from soils with low anthropogenic disturbance found in the Golden Gate Highlands National Park (GGHNP), a part of the Drakensberg system in South Africa. Selective techniques were implemented to obtain 257 individual isolates from the selected soil samples for which the translation elongation factor 1α (tef-1α) gene region was sequenced and compared against the Fusarium MLST and FUSARIUM-ID databases. Phylogenetic analyses, based on maximum likelihood and Bayesian inference, were used to determine species diversity in relation to reference isolates. Species level identifications were made within three of the seven species complexes and identified F. brachygibbosum, F. sporotrichioides, F. andiyazi, and F. gaditjirri based on the FUSARIUM-ID database, with F. transvaalense and F. lyarnte identified against the Fusarium MLST database. This indicated highly diverse populations of Fusarium from soils with low anthropogenic disturbance from the Afromontane grassland region found in mountain ranges.
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Affiliation(s)
- Carla Steyn
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Adriaana Jacobs
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
- ARC-Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - Brett Summerell
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
- Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
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3
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Seepe HA, Raphoko L, Amoo SO, Nxumalo W. Lantadene A and boswellic acid isolated from the leaves of Lantana camara L. have the potential to control phytopathogenic Fusarium species. Heliyon 2022; 8:e12216. [PMID: 36582687 PMCID: PMC9792760 DOI: 10.1016/j.heliyon.2022.e12216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/04/2022] [Accepted: 11/30/2022] [Indexed: 12/16/2022] Open
Abstract
Phytopathogenic Fusarium species are restricting factors causing diseases and yield loss in crop production. As part of exploration for pesticides from medicinal plants, this study aimed to isolate and characterize bioactive compounds from Lantana camara L. and evaluate their efficiency against Fusarium phytopathogens. Phytochemical investigation of ethyl acetate leaf extract led to separation of lantadene A (22-angeloyloxy-9-hydroxy-3-oxo-olean-12-en-28-oic acid) and boswellic acid (11-keto-β-boswellic acid). The chemical structures of the aforementioned compounds were confirmed using physical properties, spectroscopic analysis, and published data. Lantadene A exhibited significant antifungal activity against F. subglutinans, F. proliferatum, F. solani, F. graminearum, and F. semitectum with minimum inhibitory concentration (MIC) less than or equal to 0.63 mg/mL. Boswellic acid exhibited strong activity (MIC = 0.63 mg/mL) against F. subglutinans and F. semitectum. In terms of their toxicity towards Raw 264.7 cells, lantadene A and boswellic acid recorded half-maximal inhibitory concentration values of 84.2 μg/mL and 186.6 μg/mL, respectively. Both lantadene A and boswellic acid had no phytotoxic effect against seed germination and seedling root length. Lantadene A and boswellic acid have strong potential to be further investigated as lead natural fungicides (biopesticides) to control Fusarium crop diseases.
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Affiliation(s)
- Hlabana Alfred Seepe
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plants, Roodeplaat, Private Bag X293, Pretoria 0001, South Africa,Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga, 0727, Polokwane, South Africa,Döhne Agricultural Development Institute, Plant and Crops Production Research, Private Bag X 15, Stutterheim, 4930, South Africa,Corresponding author.
| | - Lerato Raphoko
- Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga, 0727, Polokwane, South Africa
| | - Stephen O. Amoo
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plants, Roodeplaat, Private Bag X293, Pretoria 0001, South Africa,Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa,Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
| | - Winston Nxumalo
- Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga, 0727, Polokwane, South Africa
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Abbas A, Mubeen M, Sohail MA, Solanki MK, Hussain B, Nosheen S, Kashyap BK, Zhou L, Fang X. Root rot a silent alfalfa killer in China: Distribution, fungal, and oomycete pathogens, impact of climatic factors and its management. Front Microbiol 2022; 13:961794. [PMID: 36033855 PMCID: PMC9403511 DOI: 10.3389/fmicb.2022.961794] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Alfalfa plays a significant role in the pasture ecosystems of China's north, northeast, and northwest regions. It is an excellent forage for livestock, improves soil structure, prevents soil erosion, and has ecological benefits. Presently root rot is a significant threat to the alfalfa productivity because of the survival of the pathogens as soil-borne and because of lack of microbial competition in the impoverished nutrient-deficient soils and resistant cultivars. Furthermore, these regions' extreme ecological and environmental conditions predispose alfalfa to root rot. Moisture and temperature, in particular, have a considerable impact on the severity of root rot. Pathogens such as Fusarium spp. and Rhizoctonia solani are predominant, frequently isolated, and of major concern. These pathogens work together as disease complexes, so finding a host genotype resistant to disease complexes is challenging. Approaches to root rot control in these regions include mostly fungicides treatments and cultural practices and very few reports on the usage of biological control agents. As seed treatment, fungicides such as carbendazim are frequently used to combat root rot; however, resistance to fungicides has arisen. However, breeding and transgenic approaches could be more efficient and sustainable long-term control strategies, especially if resistance to disease complexes may be identified. Yet, research in China is mainly limited to field investigation of root rot and disease resistance evaluation. In this review, we describe climatic conditions of pastoral regions and the role of alfalfa therein and challenges of root rot, the distribution of root rot in the world and China, and the impact of root rot pathogens on alfalfa in particular R. solani and Fusarium spp., effects of environmental factors on root rot and summarize to date disease management approach.
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Affiliation(s)
- Aqleem Abbas
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mustansar Mubeen
- Department of Plant Pathology, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Manoj Kumar Solanki
- Faculty of Natural Sciences, Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Babar Hussain
- Department of Plant Sciences, Karakoram International University, Gilgit, Gilgit Baltistan, Pakistan
| | - Shaista Nosheen
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, India
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiangling Fang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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5
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Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota). FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Montoya-Martínez AC, O'Donnell K, Busman M, Vaughan MM, McCormick SP, Santillán-Mendoza R, Pineda-Vaca D, Clapes-Garduño L, Fernández-Pavía SP, Ploetz RC, Benítez-Malvido J, Montero-Castro JC, Rodríguez-Alvarado G. Weeds Harbor Fusarium Species that Cause Malformation Disease of Economically Important Trees in Western Mexico. PLANT DISEASE 2022; 106:612-622. [PMID: 34569826 DOI: 10.1094/pdis-06-21-1339-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mango malformation disease (MMD) caused by Fusarium spp. is an important limiting factor in most production areas worldwide. Fusarium mexicanum and F. pseudocircinatum have been reported as causing MMD in Mexico. These two pathogens also cause a similar disease in Swietenia macrophylla (big-leaf mahogany malformation disease) in central western Mexico, and F. pseudocircinatum was recently reported as causing malformation disease in Tabebuia rosea (rosy trumpet) in the same region. These studies suggest that additional plant species, including weeds, might be hosts of these pathogens. The role that weed hosts might have in the disease cycle is unknown. The objectives of this work were to recover Fusarium isolates from understory vegetation in mango orchards with MMD, identify the Fusarium isolates through DNA sequence data, and determine whether F. mexicanum is capable of inducing disease in the weedy legume Senna uniflora (oneleaf senna). Additional objectives in this work were to compare Fusarium isolates recovered from weeds and mango trees in the same orchards by characterizing their phylogenetic relationships, assessing in vitro production of mycotoxins, and identifying their mating type idiomorph. A total of 59 Fusarium isolates from five species complexes were recovered from apical and lateral buds from four weed species. Two of the species within the F. fujikuroi species complex are known to cause MMD in Mexico. Trichothecene production was detected in five isolates, including F. sulawense and F. irregulare in the F. incarnatum-equiseti species complex and F. boothii in the F. sambucinum species complex. Both mating types were present among mango and weed isolates. This is the first report of herbaceous hosts harboring Fusarium species that cause mango malformation in Mexico. The information provided should prove valuable for further study of the epidemiological role of weeds in MMD and help manage the disease.
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Affiliation(s)
- Amelia C Montoya-Martínez
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Mark Busman
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Susan P McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Ricardo Santillán-Mendoza
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
- Campo Experimental Ixtacuaco, CIRGOC, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tlapacoyan, Veracruz, México
| | - Daniela Pineda-Vaca
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Lyana Clapes-Garduño
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Randy C Ploetz
- Department of Plant Pathology, Tropical Research and Education Center, University of Florida, Homestead, FL 33031-3314, U.S.A
| | - Julieta Benítez-Malvido
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán 58190, México
| | | | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
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7
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Navoda H, Dinushani Anupama D. Evaluation of antifungal plant extracts against cereal and legume seed-borne pathogens for effective management. STUDIES IN FUNGI 2022. [DOI: 10.48130/sif-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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8
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Antagonistic activity and characterization of indigenous soil isolates of bacteria and fungi against onion wilt incited by Fusarium sp. Arch Microbiol 2021; 204:68. [PMID: 34950974 DOI: 10.1007/s00203-021-02663-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 02/04/2023]
Abstract
Tuber rot disease due to phytopathogen Fusarium oxysporum f. sp. cepae (Foc) infection is one of the main factors causing the decreasing global onions production. This study aims to find bacteria and fungi candidates with Foc antagonistic activity through in vitro tests using dual culture techniques. A total of three bacterial isolates and three fungal isolates isolated from the rhizosphere of healthy onion plants showed the ability to inhibit Fusarium oxysporum growth. LC648364 isolate had an average inhibitory capability of 65.93%. At the same time, LC648367 and LC648368 fungal isolates can inhibit the growth of F. oxysporum by as much as 74.82% and 67.76%, respectively. Molecular analysis based on 16S rRNA markers showed three isolates belonging to the Bacillus. The LC648364 isolates are closely related to species Bacillus sp. strain LLB-17, LC648365 is closely related to B. subtilis strain S11 and LC648366 is closely related to B. cereus strain EM6. For the fungi, based on internal transcribed spacer (ITS) gene markers, there are three isolates. The LC648367 isolate is closely related to Aspergillus tubingensis, LC648368 is closely related to Trichoderma asperellum and LC648369 is closely related to Issatchenkia orientalis. This study can be used to develop indigenous microbial consortiums as biological control agents for phytopathogenic fungi Fusarium tuber rot on onion.
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Seepe HA, Nxumalo W, Amoo SO. Natural Products from Medicinal Plants against Phytopathogenic Fusarium Species: Current Research Endeavours, Challenges and Prospects. Molecules 2021; 26:molecules26216539. [PMID: 34770948 PMCID: PMC8587185 DOI: 10.3390/molecules26216539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Many Fusarium species are pathogenic, causing crop diseases during crop production and spoilage of agricultural products in both commercial and smallholder farming. Fusarium attack often results into food contamination, yield loss and increases in food insecurity and food prices. Synthetic fungicides have been used as a control strategy for the management of crop diseases caused by Fusarium pathogens. The negative effects associated with application of many synthetic pesticides has necessitated the need to search for alternative control strategies that are affordable and environmentally safe. Research on medicinal plants as control agents for Fusarium pathogens has received attention since plants are readily available and they contain wide variety of secondary metabolites that are biodegradable. The activities of solvent extracts, essential oils and compounds from medicinal plants have been tested against Fusarium phytopathogenic species. A summary of recent information on antifungal activity of plants against Fusarium species is valuable for the development of biopesticides. This paper reviews the antifungal research conducted on medicinal plants against Fusarium pathogens, over a 10-year period, from January 2012 to May 2021. We also highlight the challenges and opportunities of using natural products from medicinal plants in crop protection. Several databases (Science Direct and Web of Science) were used to obtain information on botanical products used to control Fusarium diseases on crops. Keywords search used included natural products, antifungal, Fusarium, crops diseases, phytopathogenic, natural compounds and essential oil.
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Affiliation(s)
- Hlabana A. Seepe
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plants, Roodeplaat, Private Bag X293, Pretoria 0001, South Africa
- Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga, Polokwane 0727, South Africa
- Correspondence: (H.A.S.); (W.N.); (S.O.A.); Tel.: +27-12-808-8000 (H.A.S.); +27-15-268-2331 (W.N.); +27-12-808-8000 (S.O.A.)
| | - Winston Nxumalo
- Department of Chemistry, University of Limpopo, Private Bag X1106, Sovenga, Polokwane 0727, South Africa
- Correspondence: (H.A.S.); (W.N.); (S.O.A.); Tel.: +27-12-808-8000 (H.A.S.); +27-15-268-2331 (W.N.); +27-12-808-8000 (S.O.A.)
| | - Stephen O. Amoo
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plants, Roodeplaat, Private Bag X293, Pretoria 0001, South Africa
- Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
- Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
- Correspondence: (H.A.S.); (W.N.); (S.O.A.); Tel.: +27-12-808-8000 (H.A.S.); +27-15-268-2331 (W.N.); +27-12-808-8000 (S.O.A.)
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10
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Leitão ST, Santos C, Araújo SDS, Rubiales D, Vaz Patto MC. Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit. HORTICULTURE RESEARCH 2021; 8:149. [PMID: 34193847 PMCID: PMC8245569 DOI: 10.1038/s41438-021-00583-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to "stress", "signaling", "cell wall", "hormone metabolism", and "secondary metabolism" functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.
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Affiliation(s)
- Susana T Leitão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Association BLC3 - Technology and Innovation Campus, Centre Bio R&D Unit, Lagares da Beira, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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11
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Structure and Abundance of Fusarium Communities Inhabiting the Litter of Beech Forests in Central Europe. FORESTS 2021. [DOI: 10.3390/f12060811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Members of the genus Fusarium and related genera are important components of many ecosystems worldwide and are responsible for many plant diseases. However, the structure of beech litter-inhabiting Fusarium communities and their potential role in reducing the natural regeneration of European beech are not well understood. To address this issue, we examined Fusarium communities in the litter of uneven-aged, old-growth beech-dominated forests in the Carpathians (Poland) and in the Alps (Austria), and in a managed beech stand (Poland). The fungi inhabiting beech litter were investigated using beechnuts and pine seedlings as bait. The pathogenicity of the most common species was investigated by inoculating beech germinants. Fusarium spp. were identified based on morphology and DNA sequence comparisons of RPB2 and TEF1-α genes, combined with phylogenetic analyses. Twelve fungal species were identified from 402 isolates, including nine known and three currently undescribed species. The isolates resided in three species complexes within the genus Fusarium. These were the F. oxysporum (one taxon), F. sambucinum (three taxa), and F. tricinctum (six taxa) species complexes. In addition, one isolate was assigned to the genus Neocosmospora, and one isolate could be placed within the genus Fusicolla. The most frequently isolated fungi from beechnuts and beech germinants were F. avenaceum (Fr.) Sacc., F. sporotrichioides Sherb. and Fusarium sp. B. The structure and abundance of species within Fusarium communities varied by beech forest type. The species richness of Fusarium spp. was greatest in old-growth beech-dominated stands, while abundances of Fusarium spp. were higher in managed beech-dominated stands. Pathogenicity tests showed that all four Fusarium species isolated from beechnuts and beech germinants could cause germinants to rot beech, suggesting that these fungi may play a negative role in the natural beech regeneration.
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Fusarium Species in Mangrove Soil in Northern Peninsular Malaysia and the Soil Physico-Chemical Properties. Microorganisms 2021; 9:microorganisms9030497. [PMID: 33652900 PMCID: PMC7996719 DOI: 10.3390/microorganisms9030497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 11/17/2022] Open
Abstract
Fusarium genus comprises important saprophytic and phytopathogenic fungi and is widespread in nature. The present study reports the occurrence of Fusarium spp. in soils from two mangrove forests in northern Peninsular Malaysia and analyzed physico-chemical properties of the mangrove soil. Based on TEF-1α sequences, nine Fusarium species were identified: Fusarium solani species complex (FSSC) (n = 77), Fusarium verticillioides (n = 20), Fusarium incarnatum (n = 10), Fusarium proliferatum (n = 7), Fusarium lateritium (n = 4), Fusarium oxysporum (n = 3), Fusarium rigidiuscula (n = 2), Fusarium chlamydosporum (n = 1), and Fusarium camptoceras (n = 1); FSSC isolates were the most prevalent. Phylogenetic analysis of the combined TEF-1α and ITS sequences revealed diverse phylogenetic affinities among the FSSC isolates and potentially new phylogenetic clades of FSSC. Soil analysis showed varied carbon content, pH, soil moisture, and salinity, but not nitrogen content, between sampling locations. Regardless of the physico-chemical properties, various Fusarium species were recovered from the mangrove soils. These were likely saprophytes; however, some were well-known plant pathogens and opportunistic human pathogens. Thus, mangrove soils might serve as inoculum sources for plant and human pathogenic Fusarium species. The present study demonstrates the occurrence of various Fusarium species in the extreme environment of mangrove soil, thereby contributing to the knowledge on species diversity in Fusarium.
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Laraba I, McCormick SP, Vaughan MM, Geiser DM, O’Donnell K. Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex. PLoS One 2021; 16:e0245037. [PMID: 33434214 PMCID: PMC7802971 DOI: 10.1371/journal.pone.0245037] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023] Open
Abstract
The Fusarium sambucinum species complex (FSAMSC) is one of the most taxonomically challenging groups of fusaria, comprising prominent mycotoxigenic plant pathogens and other species with various lifestyles. Among toxins produced by members of the FSAMSC, trichothecenes pose the most significant threat to public health. Herein a global collection of 171 strains, originating from diverse hosts or substrates, were selected to represent FSAMSC diversity. This strain collection was used to assess their species diversity, evaluate their potential to produce trichothecenes, and cause disease on wheat. Maximum likelihood and Bayesian analyses of a combined 3-gene dataset used to infer evolutionary relationships revealed that the 171 strains originally received as 48 species represent 74 genealogically exclusive phylogenetically distinct species distributed among six strongly supported clades: Brachygibbosum, Graminearum, Longipes, Novel, Sambucinum, and Sporotrichioides. Most of the strains produced trichothecenes in vitro but varied in type, indicating that the six clades correspond to type A, type B, or both types of trichothecene-producing lineages. Furthermore, five strains representing two putative novel species within the Sambucinum Clade produced two newly discovered type A trichothecenes, 15-keto NX-2 and 15-keto NX-3. Strains of the two putatively novel species together with members of the Graminearum Clade were aggressive toward wheat when tested for pathogenicity on heads of the susceptible cultivar Apogee. In planta, the Graminearum Clade strains produced nivalenol or deoxynivalenol and the aggressive Sambucinum Clade strains synthesized NX-3 and 15-keto NX-3. Other strains within the Brachygibbosum, Longipes, Novel, Sambucinum, and Sporotrichioides Clades were nonpathogenic or could infect the inoculated floret without spreading within the head. Moreover, most of these strains did not produce any toxin in the inoculated spikelets. These data highlight aggressiveness toward wheat appears to be influenced by the type of toxin produced and that it is not limited to members of the Graminearum Clade.
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Affiliation(s)
- Imane Laraba
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University, Peoria, IL, United States of America
| | - Susan P. McCormick
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University, Peoria, IL, United States of America
| | - Martha M. Vaughan
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University, Peoria, IL, United States of America
| | - David M. Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, PA, United States of America
| | - Kerry O’Donnell
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit. 1815 N. University, Peoria, IL, United States of America
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Mahmoud GAE. Biotic Stress to Legumes: Fungal Diseases as Major Biotic Stress Factor. SUSTAINABLE AGRICULTURE REVIEWS 2021:181-212. [DOI: 10.1007/978-3-030-68828-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Jha UC, Bohra A, Pandey S, Parida SK. Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes. Front Genet 2020; 11:1001. [PMID: 33193586 PMCID: PMC7644945 DOI: 10.3389/fgene.2020.01001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Fusarium wilt (FW) disease is the key constraint to grain legume production worldwide. The projected climate change is likely to exacerbate the current scenario. Of the various plant protection measures, genetic improvement of the disease resistance of crop cultivars remains the most economic, straightforward and environmental-friendly option to mitigate the risk. We begin with a brief recap of the classical genetic efforts that provided first insights into the genetic determinants controlling plant response to different races of FW pathogen in grain legumes. Subsequent technological breakthroughs like sequencing technologies have enhanced our understanding of the genetic basis of both plant resistance and pathogenicity. We present noteworthy examples of targeted improvement of plant resistance using genomics-assisted approaches. In parallel, modern functional genomic tools like RNA-seq are playing a greater role in illuminating the various aspects of plant-pathogen interaction. Further, proteomics and metabolomics have also been leveraged in recent years to reveal molecular players and various signaling pathways and complex networks participating in host-pathogen interaction. Finally, we present a perspective on the challenges and limitations of high-throughput phenotyping and emerging breeding approaches to expeditiously develop FW-resistant cultivars under the changing climate.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research, Uttar Pradesh, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research, Uttar Pradesh, India
| | - Shailesh Pandey
- Forest Protection Division, Forest Research Institute, Dehradun, India
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Menezes BS, Solidade LS, Conceição AA, Santos Junior MN, Leal PL, de Brito ES, Canuto KM, Mendonça S, de Siqueira FG, Marques LM. Pigment production by Fusarium solani BRM054066 and determination of antioxidant and anti-inflammatory properties. AMB Express 2020; 10:117. [PMID: 32613282 PMCID: PMC7329961 DOI: 10.1186/s13568-020-01054-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/23/2020] [Indexed: 12/31/2022] Open
Abstract
The fungal kingdom has been widely studied as a source of bioactive compounds of interest to the pharmaceutical and food industry. This paper studies the production of natural red pigments by Fusarium solani BRM054066 in the submerged fermentation system, using Doehlert experimental design to determine optimal cultivation conditions. The chemical composition of the red pigment was determined by Nuclear Magnetic Resonance spectroscopy (NMR) and Ultra-Performance Liquid Chromatography coupled to Mass Spectrometry (UPLC-MS). Antioxidant activity was assessed by the ability to sequester of free radical DPPH. In the analysis of anti-inflammatory activity, murine peritoneal macrophages activated by LPS were used, and the gene expression of TNF-α, IL-1β, IL-6, IL-10 and IL-17 was determined using qPCR. As a result, it was found that agitation at 200 rpm and glucose concentration ≥ 20 g/L promote the best results in the production of red pigment. The chemical compounds identified were two naphthoquinones, fusarubin and dihydrofusarubin, and an anthraquinone, a bostrycoidin, being fusarubin the majority compound. The red pigment showed antioxidant activity by scavenge 50% of the DPPH radical, in a concentration of 24 µg/mL. The pigment also showed an effective anti-inflammatory capacity by reducing the overexpression of the pro-inflammatory cytokines TNF-α, IL-1β and IL-6 and promoting the production of anti-inflammatory IL-10 and IL-17, in murine macrophages activated by LPS (p < 0.05). According to the results, the fungus F. solani BRM054066, under optimized conditions of cultivation, proved to be a promising source of biologically active natural pigments with wide industrial applicability.
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Isolation and Identification of Fusarium spp., the Causal Agents of Onion ( Allium cepa) Basal Rot in Northeastern Israel. BIOLOGY 2020; 9:biology9040069. [PMID: 32252245 PMCID: PMC7236657 DOI: 10.3390/biology9040069] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 11/16/2022]
Abstract
Over the past decade, there have been accumulating reports from farmers and field extension personnel on the increasing incidence and spread of onion (Allium cepa) bulb basal rot in northern Israel. The disease is caused mainly by Fusarium species. Rotting onion bulbs were sampled from fields in the Golan Heights in northeastern Israel during the summers of 2017 and 2018. Tissue from the sampled onion bulbs was used for the isolation and identification of the infecting fungal species using colony and microscopic morphology characterization. Final confirmation of the pathogens was performed with PCR amplification and sequencing using fungi-specific and Fusarium species-specific primers. Four Fusarium spp. isolates were identified in onion bulbs samples collected from the contaminated field: F. proliferatum, F. oxysporum f. sp. cepae, and two species less familiar as causative agents of this disease, F. acutatum and F. anthophilium. Phylogenetic analysis revealed that these species subdivided into two populations, a northern group isolated from white (Riverside cv.) onion bulbs, and a southern group isolated from red (565/505 cv.) bulbs. Pathogenicity tests conducted with seedlings and bulbs under moist conditions proved that all species could cause the disease symptoms, but with different degrees of virulence. Inoculating seeds with spore suspensions of the four species, in vitro, significantly reduced seedlings’ germination rate, hypocotyl elongation, and fresh biomass. Mature onion bulbs infected with the fungal isolates produced typical rot symptoms 14 days post-inoculation, and the fungus from each infected bulb was re-isolated and identified to satisfy Koch’s postulates. The onion bulb assay also reflected the degree of sensitivity of different onion cultivars to the disease. This work is the first confirmed report of the direct and primary cause of Fusarium onion basal rot disease in northeastern Israel. These findings are a necessary step towards uncovering the mycoflora of the diseased onion plants and developing a preventive program that would reduce the disease damage.
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Pollard AT, Okubara PA. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. J Microbiol Methods 2019; 157:21-30. [DOI: 10.1016/j.mimet.2018.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 10/27/2022]
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19
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Yang G, Li P, Meng L, Xv K, Dong F, Qiu Y, He L, Lin L. Diversity and communities of culturable endophytic fungi from different tree peonies (geoherbs and non-geoherbs), and their biosynthetic potential analysis. Braz J Microbiol 2018; 49 Suppl 1:47-58. [PMID: 30166266 PMCID: PMC6328841 DOI: 10.1016/j.bjm.2018.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 01/23/2023] Open
Abstract
To know more about the potential roles of endophytic fungi in the formation mechanism of Daodi medicinal material, diversity and communities of culturable endophytic fungi in three types of tree peonies were investigated. Endophytic fungi of three types of tree peonies were isolated and identified. The diversity was analyzed. Bayesian trees constructed by MrBayes 3.2.6 after phylogenetic analysis of the ITS sequences. The endophytic fungi potential for synthesis of natural products was assessed by means of detecting NRPS and PKS gene sequences. In total, 364 endophytic fungi isolates representing 26 genera were recovered from Paeonia ostii ‘Feng Dan’, Paeonia ostii ‘Luoyang Feng Dan’, and Paeonia suffruticosa ‘Luoyang Hong’. More culturable endophytic fungi appeared in P. suffruticosa ‘Luoyang Hong’ (206) compared with P. ostii ‘Feng Dan’ (60) and P. ostii ‘Luoyang Feng Dan’ (98). The fungal community of P. ostii ‘Feng Dan’ had the highest richness and diversity. PKSs and NRPS detection rates of endophytic fungi from P. ostii ‘Feng Dan’ are both the highest among the three types of tree peonies. Results indicate that endophytic fungus is an important factor of Daodi Cortex Moutan forming, and endophytic fungi in peony are related to genuineness of Cortex Moutan.
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Affiliation(s)
- Guodong Yang
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China.
| | - Peng Li
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China
| | - Lifen Meng
- Henan University of Science and Technology, College of Chemical Engineering and Pharmaceutics, Luoyang, Henan, People's Republic of China
| | - Keyi Xv
- Luoyang No.1 Senior High School, Class Nine, Grade Three, Luoyang, Henan, People's Republic of China
| | - Faming Dong
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China
| | - Yan Qiu
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China
| | - Lei He
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China
| | - Lin Lin
- Henan University of Science and Technology, College of Animal Science and Technology, Luoyang, Henan, People's Republic of China
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Sandoval-Denis M, Swart WJ, Crous PW. New Fusarium species from the Kruger National Park, South Africa. MycoKeys 2018; 34:63-92. [PMID: 29892206 PMCID: PMC5993860 DOI: 10.3897/mycokeys.34.25974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Three new Fusarium species, F. convolutans, F. fredkrugeri, and F. transvaalense (Ascomycota, Hypocreales, Nectriaceae) are described from soils collected in a catena landscape on a research supersite in the Kruger National Park, South Africa. The new taxa, isolated from the rhizosphere of three African herbaceous plants, Kyphocarpa angustifolia, Melhania acuminata, and Sida cordifolia, are described and illustrated by means of morphological and multilocus molecular analyses based on sequences from five DNA loci (CAL, EF-1 α, RPB1, RPB2 and TUB). According to phylogenetic inference based on Maximum-likelihood and Bayesian approaches, the newly discovered species are distributed in the Fusarium buharicum, F. fujikuroi, and F. sambucinum species complexes.
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Affiliation(s)
- Marcelo Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Wijnand J Swart
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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Zhang W, Zhang X, Li K, Wang C, Cai L, Zhuang W, Xiang M, Liu X. Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi. Mycology 2018; 9:176-188. [PMID: 30181924 PMCID: PMC6115877 DOI: 10.1080/21501203.2018.1478333] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/15/2018] [Indexed: 12/20/2022] Open
Abstract
Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.
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Affiliation(s)
- Weiwei Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genomics 2018; 19:269. [PMID: 29673315 PMCID: PMC5907747 DOI: 10.1186/s12864-018-4612-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to F. graminearum, the predicted gene count of 13,946 was slightly lower. The F. venenatum centromeres were found to be 25% smaller compared to F. graminearum. Chromosome length was 2.8% greater in F. venenatum, primarily due to an increased abundance of repetitive elements and transposons, but not transposon diversity. On chromosome 3 a major sequence rearrangement was found, but its overall gene content was relatively unchanged. Unlike homothallic F. graminearum, heterothallic F. venenatum possessed the MAT1-1 type locus, but lacked the MAT1-2 locus. The F. venenatum genome has the type A trichothecene mycotoxin TRI5 cluster, whereas F. graminearum has type B. From the F. venenatum gene set, 786 predicted proteins were species-specific versus NCBI. The annotated F. venenatum genome was predicted to possess more genes coding for hydrolytic enzymes and species-specific genes involved in the breakdown of polysaccharides than F. graminearum. Comparison of the two genomes reduced the previously defined F. graminearum-specific gene set from 741 to 692 genes. A comparison of the F. graminearum versus F. venenatum proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in F. venenatum. Five of the 15 F. graminearum-specific SMCs that were either absent or highly divergent in the F. venenatum genome showed increased in planta expression. In addition, two predicted F. graminearum transcription factors previously shown to be required for fungal virulence on wheat plants were absent or exhibited high sequence divergence. CONCLUSIONS This study identifies differences between the F. venenatum and F. graminearum genomes that may contribute to contrasting lifestyles, and highlights the repertoire of F. graminearum-specific candidate genes and SMCs potentially required for pathogenesis.
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Young E, Carey M, Meharg AA, Meharg C. Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing. MICROBIOME 2018; 6:48. [PMID: 29554982 PMCID: PMC5859661 DOI: 10.1186/s40168-018-0434-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/05/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plants can adapt to edaphic stress, such as nutrient deficiency, toxicity and biotic challenges, by controlled transcriptomic responses, including microbiome interactions. Traditionally studied in model plant species with controlled microbiota inoculation treatments, molecular plant-microbiome interactions can be functionally investigated via RNA-Seq. Complex, natural plant-microbiome studies are limited, typically focusing on microbial rRNA and omitting functional microbiome investigations, presenting a fundamental knowledge gap. Here, root and shoot meta-transcriptome analyses, in tandem with shoot elemental content and root staining, were employed to investigate transcriptome responses in the wild grass Holcus lanatus and its associated natural multi-species eukaryotic microbiome. A full factorial reciprocal soil transplant experiment was employed, using plant ecotypes from two widely contrasting natural habitats, acid bog and limestone quarry soil, to investigate naturally occurring, and ecologically meaningful, edaphically driven molecular plant-microbiome interactions. RESULTS Arbuscular mycorrhizal (AM) and non-AM fungal colonization was detected in roots in both soils. Staining showed greater levels of non-AM fungi, and transcriptomics indicated a predominance of Ascomycota-annotated genes. Roots in acid bog soil were dominated by Phialocephala-annotated transcripts, a putative growth-promoting endophyte, potentially involved in N nutrition and ion homeostasis. Limestone roots in acid bog soil had greater expression of other Ascomycete genera and Oomycetes and lower expression of Phialocephala-annotated transcripts compared to acid ecotype roots, which corresponded with reduced induction of pathogen defense processes, particularly lignin biosynthesis in limestone ecotypes. Ascomycota dominated in shoots and limestone soil roots, but Phialocephala-annotated transcripts were insignificant, and no single Ascomycete genus dominated. Fusarium-annotated transcripts were the most common genus in shoots, with Colletotrichum and Rhizophagus (AM fungi) most numerous in limestone soil roots. The latter coincided with upregulation of plant genes involved in AM symbiosis initiation and AM-based P acquisition in an environment where P availability is low. CONCLUSIONS Meta-transcriptome analyses provided novel insights into H. lanatus transcriptome responses, associated eukaryotic microbiota functions and taxonomic community composition. Significant edaphic and plant ecotype effects were identified, demonstrating that meta-transcriptome-based functional analysis is a powerful tool for the study of natural plant-microbiome interactions.
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Affiliation(s)
- Ellen Young
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Manus Carey
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Andrew A. Meharg
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
| | - Caroline Meharg
- Institute for Global Food Security, Queens University Belfast, David Keir Building, Belfast, BT9 5BN Northern Ireland, UK
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Edel-Hermann V, Sautour M, Gautheron N, Laurent J, Aho S, Bonnin A, Sixt N, Hartemann P, Dalle F, Steinberg C. A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals. Appl Environ Microbiol 2016; 82:6483-6489. [PMID: 27663024 PMCID: PMC5066365 DOI: 10.1128/aem.01939-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023] Open
Abstract
Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. IMPORTANCE We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution.
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Affiliation(s)
| | - Marc Sautour
- Parasitology and Mycology Laboratory, Plateau Technique de Biologie du CHU, Dijon, France UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | | | | | - Serge Aho
- Hospital Hygiene and Epidemiology Unit, Hôpital du Bocage, Dijon, France
| | - Alain Bonnin
- Parasitology and Mycology Laboratory, Plateau Technique de Biologie du CHU, Dijon, France UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - Nathalie Sixt
- Environmental Microbiology, Plateau Technique de Biologie du CHU, Dijon, France
| | - Philippe Hartemann
- Department Environment and Public Health, Nancy University, Hospital Hygiene Unit, Vandoeuvre-Nancy, France
| | - Frédéric Dalle
- Parasitology and Mycology Laboratory, Plateau Technique de Biologie du CHU, Dijon, France UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
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Muraosa Y, Schreiber AZ, Trabasso P, Matsuzawa T, Taguchi H, Moretti ML, Mikami Y, Kamei K. Development of cycling probe-based real-time PCR system to detect Fusarium species and Fusarium solani species complex (FSSC). Int J Med Microbiol 2014; 304:505-11. [PMID: 24704188 DOI: 10.1016/j.ijmm.2014.03.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 01/23/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022] Open
Abstract
In the present study, we developed a new real-time PCR system based on the cycling probe technology (CPT), which is composed of two single tube real-time PCR assays: the Fusarium genus-specific assay and the Fusarium solani species complex (FSSC)-specific assay with primers targeting the 28s ribosomal RNA gene. The Fusarium genus-specific assay was shown to be highly specific, detecting all reference Fusarium strains with no cross-reaction with other reference fungal strains, such as Aspergillus spp. and human DNA. The FSSC-specific assay also reacted very specifically with FSSC, except for a cross-reaction with Fusarium lunatum. To validate the real-time PCR system, we tested 87 clinical isolates of Fusarium spp. Identification results from the real-time PCR system were found to be 100% concordant with those from DNA sequencing of EF-1α gene. The sensitivity testing also demonstrated high sensitivity, enabling detection of one copy of standard DNA with good reproducibility. Furthermore, both assays were shown to be extremely sensitive even when fungal cells were mixed with human cells, detecting 3 germinated conidia spiked in 3mL of human blood. To apply our new real-time PCR system to the molecular diagnosis of fusariosis, we evaluated its efficacy using a mouse model of invasive F. solani infection. Plasma and whole blood samples of infected mice were tested using the real-time PCR system. The sensitivity of the real-time PCR system was found to be 100% (n=4) in plasma samples. In contrast, no amplification signal was detected in whole blood samples. This system could provide a rapid and precise diagnostic tool for early diagnosis, which is necessary for appropriate treatment and improvement of prognosis of disseminated fusariosis.
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Affiliation(s)
- Yasunori Muraosa
- Medical Mycology Research Center, Chiba University, Chiba, Japan.
| | | | - Plínio Trabasso
- Infectious Diseases Division, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | | | - Hideaki Taguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Maria Luiza Moretti
- Infectious Diseases Division, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Yuzuru Mikami
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
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Pottorff MO, Li G, Ehlers JD, Close TJ, Roberts PA. Genetic mapping, synteny, and physical location of two loci for Fusarium oxysporum f. sp. tracheiphilum race 4 resistance in cowpea [ Vignaunguiculata (L.) Walp]. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:779-791. [PMID: 24659904 PMCID: PMC3956937 DOI: 10.1007/s11032-013-9991-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 11/13/2013] [Indexed: 05/20/2023]
Abstract
Fusarium wilt is a vascular disease caused by the fungus Fusariumoxysporum f.sp. tracheiphilum (Fot) in cowpea [Vignaunguiculata (L.) Walp]. In this study, we mapped loci conferring resistance to Fot race 4 in three cowpea RIL populations: IT93K-503-1 × CB46, CB27 × 24-125B-1, and CB27 × IT82E-18/Big Buff. Two independent loci which confer resistance to Fot race 4 were identified, Fot4-1 and Fot4-2. Fot4-1 was identified in the IT93K-503-1 (resistant) × CB46 (susceptible) population and was positioned on the cowpea consensus genetic map, spanning 21.57-29.40 cM on linkage group 5. The Fot4-2 locus was validated by identifying it in both the CB27 (resistant) × 24-125B-1 (susceptible) and CB27 (resistant) × IT82E-18/Big Buff (susceptible) populations. Fot4-2 was positioned on the cowpea consensus genetic map on linkage group 3; the minimum distance spanned 71.52-71.75 cM whereas the maximum distance spanned 64.44-80.23 cM. These genomic locations of Fot4-1 and Fot4-2 on the cowpea consensus genetic map, relative to Fot3-1 which was previously identified as the locus conferring resistance to Fot race 3, established that all three loci were independent. The Fot4-1 and Fot4-2 syntenic loci were examined in Glycine max, where several disease-resistance candidate genes were identified for both loci. In addition, Fot4-1 and Fot4-2 were coarsely positioned on the cowpea physical map. Fot4-1 and Fot4-2 will contribute to molecular marker development for future use in marker-assisted selection, thereby expediting introgression of Fot race 4 resistance into future cowpea cultivars.
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Affiliation(s)
- Marti O. Pottorff
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA USA
| | - Guojing Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, People’s Republic of China
| | - Jeffery D. Ehlers
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA USA
- Bill and Melinda Gates Foundation, Seattle, WA USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA USA
| | - Philip A. Roberts
- Department of Nematology, University of California Riverside, Riverside, CA USA
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Liu JK, Phookamsak R, Doilom M, Wikee S, Li YM, Ariyawansha H, Boonmee S, Chomnunti P, Dai DQ, Bhat JD, Romero AI, Zhuang WY, Monkai J, Jones EBG, Chukeatirote E, Ko Ko TW, Zhao YC, Wang Y, Hyde KD. Towards a natural classification of Botryosphaeriales. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0207-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Udayanga D, Liua X, Mckenzie EH, Chukeatirote E, Hyde KD. Multi-locus Phylogeny Reveals Three new Species of Diaporthe from Thailand. CRYPTOGAMIE MYCOL 2012. [DOI: 10.7872/crym.v33.iss3.2012.295] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Laurence MH, Burgess LW, Summerell BA, Liew ECY. High levels of diversity in Fusarium oxysporum from non-cultivated ecosystems in Australia. Fungal Biol 2011; 116:289-97. [PMID: 22289774 DOI: 10.1016/j.funbio.2011.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 12/22/2022]
Abstract
The Fusarium oxysporum species complex (FOSC) is a ubiquitous ascomycetous group that includes both pathogenic and non-pathogenic strains, the former being responsible for disease in over 100 cultivated plant species. Previous phylogenetic studies have uncovered at least four major clades within the FOSC, with Clade 1 hypothesised as being ancestral. However, the origin of these clades and pathogenic strains is poorly understood. Due to an emphasis on agricultural isolates in previous studies, the underlying diversity of this species complex in non-cultivated soils is largely unknown. To address this imbalance an extensive survey of isolates associated with native vegetation geographically isolated from cultivation throughout the Australian continent was conducted. A multi-gene phylogenetic analysis of the translation elongation factor (EF-1α) and the mitochondrial small subunit (mtSSU) rDNA loci did not recover any novel clades. However, the Australian isolates had high levels of intra-Clade diversity based on EF-1α sequence type (ST) comparison with a global dataset. The ST diversity was not equally distributed across the four clades, with the majority of novel STs recovered from Clade 1. Implications on the origin of the FOSC are discussed.
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Affiliation(s)
- Matthew H Laurence
- Food and Natural Resources, The University of Sydney, NSW 2006, Australia.
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Liu JK, Phookamsak R, Jones EBG, Zhang Y, Ko-Ko TW, Hu HL, Boonmee S, Doilom M, Chukeatirote E, Bahkali AH, Wang Y, Hyde KD. Astrosphaeriella is polyphyletic, with species in Fissuroma gen. nov., and Neoastrosphaeriella gen. nov. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0142-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wang X, Chen G, Huang F, Zhang J, Hyde KD, Li H. Phyllosticta species associated with citrus diseases in China. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0140-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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