1
|
Shanmugaraj C, Kamil D, Gogoi R, Das A, Kumar GMS, Hussain Z, Singh PK, Iquebal MA. Characterizing genetic diversity of Sclerotium rolfsii isolates by biomapping of mycelial compatibility groupings and multilocus sequence analysis. World J Microbiol Biotechnol 2024; 40:251. [PMID: 38910228 DOI: 10.1007/s11274-024-04049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing targeted strategies for disease management in affected crops. In our study, a comprehensive genetic analysis was conducted on 50 isolates of S. rolfsii, collected from various geographic regions and host plants. Two specific genes, TEF1α and RPB2, were utilized to assess the genetic diversity and relationships among these isolates. Notably, out of 1225 pairings examined, only 154 exhibited a compatible reaction, while the majority displayed antagonistic reactions, resulting in the formation of a barrier zone. The isolates were grouped into 10 distinct MCGs. These MCGs were further characterized using genetic sequencing. TEF1α sequences distinguished the isolates into 17 distinct clusters, and RPB2 sequences classified them into 20 clusters. Some MCGs shared identical gene sequences within each gene, while others exhibited unique sequences. Intriguingly, when both TEF1α and RPB2 sequences were combined, all 10 MCGs were effectively differentiated, even those that appeared identical with single-gene analysis. This combined approach provided a comprehensive understanding of the genetic diversity and relationships among the S. rolfsii isolates, allowing for precise discrimination between different MCGs. The results shed light on the population structure and genetic variability within this plant pathogenic fungus, providing valuable insights for disease management and control strategies. This study highlights the significance of comprehending the varied virulence characteristics within S. rolfsii isolates, categorizing them into specific virulence groups based on disease severity index (DSI) values. The association with MCGs provides additional insights into the genetic underpinnings of virulence in this pathogen. Furthermore, the identification of geographical patterns in virulence implies the influence of region-specific factors, with potential implications for disease control and crop protection strategies.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [G. M. Sandeep] Last name [Kumar]. Author 2 Given name: [Praveen Kumar] Last name [Singh]. Also, kindly confirm the details in the metadata are correct.I confirm that the given names are accurate and presented in the correct sequence.
Collapse
Affiliation(s)
- C Shanmugaraj
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Robin Gogoi
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Amrita Das
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - G M Sandeep Kumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, India
| | - Zakir Hussain
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Praveen Kumar Singh
- Division of Centre for Protected Cultivation Technology (CPCT), ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - M A Iquebal
- Center for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| |
Collapse
|
2
|
Patra GK, Acharya GK, Panigrahi J, Mukherjee AK, Rout GR. The soil-borne fungal pathogen Athelia rolfsii: past, present, and future concern in legumes. Folia Microbiol (Praha) 2023; 68:677-690. [PMID: 37615849 DOI: 10.1007/s12223-023-01086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Legumes are ubiquitous, low-cost meals that are abundant in protein, vitamins, minerals, and calories. Several biotic constraints are to blame for the global output of legumes not meeting expectations. Fungi, in particular, are substantial restrictions that not only hinder production but also pose a serious health risk to both human and livestock consumption. Athelia rolfsii (Syn. Sclerotium rolfsii) is a dangerous pathogenic fungus that attacks most crops, causing massive yield losses. Legumes are no longer immune to this dreadful fungus, which can potentially result in a 100% yield loss. The initial disease symptoms based on the formation of brown color lesions at the point of infection and further development of mycelia, followed by yellowing and wilting of the whole plant. To tackle such situation, various strategies, i.e., management in cultural practices, disease-free plant growth, genetic changes, crop hybridization and in vitro culture techniques have been undertaken. This present review encapsulates the entire situation, from sclerotial dissemination through infection development and control in legume crops, with the goal of developing a tangible understanding of sustainable legume production improvements. Further study in this area might be led in an integrated manner as a result of this information, which could contribute to a better understanding of the processes of disease incidence, resistance mechanism, and its control, and fostering greater inventiveness in the production of legumes.
Collapse
Affiliation(s)
- Gyanendra K Patra
- Department of Agril. Biotechnology, College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar, India
| | - Gobinda K Acharya
- Central Horticultural Experiment Station, ICAR-IIHR, Bhubaneswar, India
| | - J Panigrahi
- Department of Biotechnology, Berhampur University, Berhampur, India
| | | | - Gyana R Rout
- Department of Molecular Biology & Biotechnology, Institute of Agricultural Sciences, S'O'A Deemed to be University, Bhubaneswar, Odisha, India.
| |
Collapse
|
3
|
Paul SK, Gupta DR, Mahapatra CK, Rani K, Islam T. Morpho-molecular, cultural and pathological characterization of Athelia rolfsii causing southern blight disease on common bean. Heliyon 2023; 9:e16136. [PMID: 37234650 PMCID: PMC10208843 DOI: 10.1016/j.heliyon.2023.e16136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 05/06/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Common bean (Phaseolus vulgaris), is a winter legume crop in Bangladesh and is considered an important vegetable with export potential. However, the production of common bean is severely affected by a newly reported soilborne fungal pathogen, Athelia rolfsii. This study aimed to characterize this new pathogen by morphological, molecular, cultural, and pathological analyses and determine the host range. The disease incidence in the affected field ranged between 6 and 13%. Initial disease symptoms were observed as brown sunken lesions at the point of infection and development of mycelia, followed by yellowing and quick wilting of the whole plant. A total of 10 fungal isolates were recovered from the infected plant samples, which were morphologically similar and produced white to brown mycelia and numerous brown sclerotia on the PDA medium. Two of them viz. BTCBSr3 and BTCBSr4 were used for the detailed study. Based on morphology and phylogenetic analyses of the sequenced data of internal transcribed spacer (ITS) and translation elongation factor 1 alpha (EF-1α), the pathogen was identified as A. rolfsii. Mycelial growth rate (3.6 cm/day) and fresh weight (107 mg) were higher in the PDA medium, whereas the number of sclerotia production (328/plate) was higher in OMA media. The isolates could grow in a wider range of incubation temperatures (15-35 °C) and media pH (3-9). In the cross-inoculation assay, both isolates were pathogenic on tomato, brinjal, and chickpea, but not on chili, soybean, and cowpea. This study has laid a foundation for further pathological research on the fungus in aid to develop an effective management practice against the pathogen.
Collapse
Affiliation(s)
- Swapan Kumar Paul
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | | | - Kanistha Rani
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| |
Collapse
|
4
|
Liu J, Liang M, Lin T, Zhao Q, Wang H, Yang S, Guo Q, Wang X, Guo H, Cui L, Yan Y, Hieno A, Kageyama K, Suga H, Li M. A LAMP-Based Toolbox Developed for Detecting the Major Pathogens Affecting the Production and Quality of the Chinese Medicinal Crop Aconitum carmichaelii. PLANT DISEASE 2023; 107:658-666. [PMID: 35852903 DOI: 10.1094/pdis-05-22-1092-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aconitum carmichaelii Debeaux is a traditional Chinese medicinal herb that has been utilized for approximately 2,000 years. However, as cultivation has increased, there have been more reports of A. carmichaelii infections caused by four major pathogenic fungal species, Fusarium oxysporum, F. solani, Mucor circinelloides, and Sclerotium rolfsii, resulting in increased disease incidences and limited production and quality. To detect these infections, we developed a LAMP-based toolbox in this study. The cytochrome c oxidase subunit 1 (cox1) gene, translation elongation factor-1α (EF-1α), internal transcribed spacer (ITS) regions of rDNA, and alcohol dehydrogenase 1 (ADH1) gene, respectively, were used to design species-specific LAMP primer sets for F. oxysporum, F. solani, S. rolfsii, and M. circinelloides. The results showed that the LAMP-based toolbox was effective at detecting pathogens in soil and plant materials. We also used this toolbox to investigate pathogen infection in the main planting regions of A. carmichaelii. Before harvesting, F. oxysporum, M. circinelloides, and S. rolfsii were commonly found in the planting fields and in infected A. carmichaelii plants. Therefore, the toolbox we developed will be useful for tracking these infections, as well as for disease control in A. carmichaelii.
Collapse
Affiliation(s)
- Jingzhe Liu
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Huiqin Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shunyuan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xinyi Wang
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Hua Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Langjun Cui
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Yaping Yan
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Mingzhu Li
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| |
Collapse
|
5
|
Chen J, Cong L, Zhou R, Li Z, Piao J, Hao N. Identification and Characterization of Sclerotium delphinii Causing Southern Blight on Aconitum kusnezoffii in Northeast China. PLANT DISEASE 2022; 106:2031-2038. [PMID: 35124993 DOI: 10.1094/pdis-10-21-2281-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: 06/14/2023]
Abstract
Aconitum kusnezoffii is a perennial medicinal plant that belongs to the Ranunculaceae family and is distributed mainly in Northeast and North China. In July 2018, a typical southern blight disease of A. kusnezoffii was observed in commercial fields of Qingyuan County, Fushun City, Liaoning Province, China. The fungus mainly infected stem base and tuberous roots of the plant by wrapping the hyphae and absorbing nutrition, resulting in tuberous root wilted or whole plant death. Morphological characteristics of colony and sclerotia of three representative strains isolated from the diseased plants differed from those of Sclerotium rolfsii isolated from A. carmichaelii. Sclerotia were large (0.8 to 5.1 mm), reddish-brown, and irregular and had pitted surfaces, and the hyphae were white, compact, or fluffy, with a growth rate ranging from 8.0 to 10.1 mm/day. Phylogenetic analysis of the internal transcribed spacer and the large subunit sequences of Akln6, Akln9, and Akln15 showed that three strains isolated from A. kusnezoffii formed a unique and well-supported clade that groups with the reference isolates of S. delphinii. Based on phylogenetic analysis and cultural and morphological characteristics, the three isolates of A. kusnezoffii were identified as S. delphinii. The optimum temperature for mycelial growth of the three tested isolates was 30°C, and sclerotia formed and matured more easily at 20°C. Light promoted the growth of mycelial, whereas dark was beneficial to the formation and maturation of sclerotia. The pathogenicity of S. delphinii showed stronger than S. rolfsii at low temperature (20°C). This is the first report of S. delphinii causing southern blight on A. kusnezoffii in China, and this finding provides a basis for disease-accurate diagnosis and the development of effective management strategies.
Collapse
Affiliation(s)
- Jipeng Chen
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Liyuan Cong
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Rujun Zhou
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Zibo Li
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jingzi Piao
- Department of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Ning Hao
- Department of Cultivation and Identification of Medicinal Herbs, College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| |
Collapse
|
6
|
The Biogenically Efficient Synthesis of Silver Nanoparticles Using the Fungus Trichoderma harzianum and Their Antifungal Efficacy against Sclerotinia sclerotiorum and Sclerotium rolfsii. J Fungi (Basel) 2022; 8:jof8060597. [PMID: 35736080 PMCID: PMC9225611 DOI: 10.3390/jof8060597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Silver nanoparticles (AgNs) are known as a promising alternative tool to control fungal diseases. AgNs were biologically synthesized using Trichoderma harzianum filtrate as an ecofriendly approach. The presence of AgNs was confirmed by changing the color to brown, followed by UV-Vis spectroscopy, transmission electron microscopy (TEM), and Energy-dispersive spectra (EDS). TEM studies showed that the size of AgNs average was 31.13 nm and the shape was spherical. In vitro assays of AgNs showed a significant inhibitory effect on the growth of Sclerotinia sclerotiorum (S. sclerotiorum) and Sclerotium rolfsii (S. rolfsii). The percentage inhibition on mycelial linear growth, dry weight, and sclerotia formation of S. sclerotiorum and S. rolfsii at 100−L were 87.8, 82.7, 96.4, 52.8, 55.1, and 85.4%, respectively. The obtained results suggested that the biosynthesized AgNs have antifungal activity against S. sclerotiorum and S. rolfsii. Foliar spray of bean and sunflower plants with AgNs caused a decrease in disease severity, which promoted the plant protection against S. sclerotiorum and S. rolfsii, respectively. Substantially, this study will extend our understanding of the AgNs antifungal action for suppressing fungal diseases.
Collapse
|
7
|
Paul NC, Hwang EJ, Nam SS, Lee HU, Lee JS, Yu GD, Kang YG, Lee KB, Go S, Yang JW. Phylogenetic Placement and Morphological Characterization of Sclerotium rolfsii (Teleomorph: Athelia rolfsii) Associated with Blight Disease of Ipomoea batatas in Korea. MYCOBIOLOGY 2017; 45:129-138. [PMID: 29138617 PMCID: PMC5673508 DOI: 10.5941/myco.2017.45.3.129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/14/2017] [Accepted: 06/26/2017] [Indexed: 06/01/2023]
Abstract
In this study, we aimed to characterize fungal samples from necrotic lesions on collar regions observed in different sweetpotato growing regions during 2015 and 2016 in Korea. Sclerotia appeared on the root zone soil surface, and white dense mycelia were observed. At the later stages of infection, mother roots quickly rotted, and large areas of the plants were destroyed. The disease occurrence was monitored at 45 and 84 farms, and 11.8% and 6.8% of the land areas were found to be infected in 2015 and 2016, respectively. Fungi were isolated from disease samples, and 36 strains were preserved. Based on the cultural and morphological characteristics of colonies, the isolates resembled the reference strain of Sclerotium rolfsii. Representative strains were identified as S. rolfsii (teleomorph: Athelia rolfsii) based on phylogenetic analysis of the internal transcribed spacer and large subunit genes along with morphological observations. To test the pathogenicity, sweetpotato storage roots were inoculated with different S. rolfsii strains. 'Yulmi' variety displayed the highest disease incidence, whereas 'Pungwonmi' resulted in the least. These findings suggested that morphological characteristics and molecular phylogenetic analysis were useful for identification of S. rolfsii.
Collapse
Affiliation(s)
- Narayan Chandra Paul
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Eom-Ji Hwang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Sang-Sik Nam
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Hyeong-Un Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Joon-Seol Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Gyeong-Dan Yu
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Yong-Gu Kang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Kyeong-Bo Lee
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - San Go
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| | - Jung-Wook Yang
- Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan 58545, Korea
| |
Collapse
|
8
|
Ji L, Liu C, Zhang L, Liu A, Yu J. Variation of rDNA Internal Transcribed Spacer Sequences in Rhizoctonia cerealis. Curr Microbiol 2017; 74:877-884. [PMID: 28474105 DOI: 10.1007/s00284-017-1258-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 04/26/2017] [Indexed: 11/24/2022]
Abstract
Fifty-four single protoplast isolates (SPIs) were regenerated from three Rhizoctonia cerealis strains. A total of 169 rDNA-ITS regions were cloned and sequenced from these 54 SPIs. Variations in the ITS1 and ITS2 regions that flank the 5.8S gene were found within clones from the same strain, as well as within clones from the same SPI. These include variations in GC content and ITS length, and single-nucleotide polymorphisms (SNPs). The different strains and SPIs GC contents range from 40.25 to 41.74% and from 42.40 to 45.02%, in the ITS1 and ITS2 regions, respectively. All SNPs occur in the ITS1 and ITS2 regions, with 3-6 and 4-6 polymorphic sites in each region, respectively, in the different strains. SNP variation is relatively stable within the same strain. For example, the 89 ITS sequences generated from isolate WK-207, regardless of SPI or clone, predominantly cluster into two separate clades on a phylogenetic tree, suggesting that nuclei genetic heterogeneity is related to ITS variation in R. cerealis. Although rDNA-ITS sequences from the three strains and different SPIs are somewhat variable, all of our ITS sequences cluster together in anastomosis subgroup AG-DI during phylogenetic analysis. The ITS variation we observed does not negatively influence R. cerealis anastomosis group or subgroup classification.
Collapse
Affiliation(s)
- Lei Ji
- Department of Plant Pathology, Shandong Agriculture University, Taian, 271018, China
| | - Chunju Liu
- Shandong Gaomi Tobacco Monopoly Bureau, Gaomi, 261500, China
| | - Li Zhang
- Department of Plant Pathology, Shandong Agriculture University, Taian, 271018, China
| | - Aixin Liu
- Department of Plant Pathology, Shandong Agriculture University, Taian, 271018, China.
| | - Jinfeng Yu
- Department of Plant Pathology, Shandong Agriculture University, Taian, 271018, China.
| |
Collapse
|
9
|
Matheny PB, Curtis JM, Hofstetter V, Aime MC, Moncalvo JM, Ge ZW, Yang ZL, Slot JC, Ammirati JF, Baroni TJ, Bougher NL, Hughes KW, Lodge DJ, Kerrigan RW, Seidl MT, Aanen DK, DeNitis M, Daniele GM, Desjardin DE, Kropp BR, Norvell LL, Parker A, Vellinga EC, Vilgalys R, Hibbett DS. Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832627] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Judd M. Curtis
- Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
| | - Valérie Hofstetter
- Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708
| | - M. Catherine Aime
- USDA-ARS, Systematic Botany and Mycology Laboratory, Room 304, Building 011A, 10300 Baltimore Avenue, Beltsville, Maryland 20705-2350
| | - Jean-Marc Moncalvo
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum and Department of Botany, University of Toronto, Toronto, Ontario, M5S 2C6 Canada
| | | | - Zhu-Liang Yang
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, P.R. China
| | - Jason C. Slot
- Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts, 01609
| | - Joseph F. Ammirati
- University of Washington, Biology Department, Box 355325, Seattle, Washington 98195
| | - Timothy J. Baroni
- Department of Biological Sciences, SUNY Cortland, Box 2000, Cortland, New York 13045-0900
| | - Neale L. Bougher
- Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia
| | - Karen W. Hughes
- Botany Department, 437 Hesler Biology Building, University of Tennessee, Knoxville, Tennessee 37996-1100
| | - D. Jean Lodge
- International Institute of Tropical Forestry, USDA Forest Service – FPL, PO Box 1377 Luqillo, PR 00773-1377
| | | | - Michelle T. Seidl
- Environmental Microbiology Laboratory Inc., 1400 12th Avenue SE, Bellevue, Washington 98004
| | - Duur K. Aanen
- Laboratory of Genetics, Arboretumlaan 4, 6703 BD, Wageningen, The Netherlands
| | | | - Graciela M. Daniele
- Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina
| | - Dennis E. Desjardin
- Department of Biology, San Francisco State University, San Francisco, California 94132
| | | | - Lorelei L. Norvell
- Pacific Northwest Mycology Service, 6720 NW Skyline Boulevard, Portland, Oregon 97229-1309
| | - Andrew Parker
- 127 Raven Way, Metaline Falls, Washington 99153-9720
| | - Else C. Vellinga
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, California 94720-3102
| | - Rytas Vilgalys
- Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708
| | - David S. Hibbett
- Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts, 01610
| |
Collapse
|
10
|
Pannecoucque J, Höfte M. Detection of rDNA ITS polymorphism inRhizoctonia solaniAG 2-1 isolates. Mycologia 2017; 101:26-33. [DOI: 10.3852/08-084] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Monica Höfte
- Ghent University, Department of Crop Protection, Laboratory of Phytopathology, Coupure Links 653, B-9000 Ghent, Belgium
| |
Collapse
|
11
|
Vialle A, Feau N, Allaire M, Didukh M, Martin F, Moncalvo JM, Hamelin RC. Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Mol Ecol Resour 2013; 9 Suppl s1:99-113. [PMID: 21564970 DOI: 10.1111/j.1755-0998.2009.02637.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Our study evaluated in silico the potential of 14 mitochondrial genes encoding the subunits of the respiratory chain complexes, including cytochrome c oxidase I (CO1), as Basidiomycota DNA barcode. Fifteen complete and partial mitochondrial genomes were recovered and characterized in this study. Mitochondrial genes showed high values of molecular divergence, indicating a potential for the resolution of lower-level relationships. However, numerous introns occurred in CO1 as well as in six other genes, potentially interfering with polymerase chain reaction amplification. Considering these results and given the minimal length of 600-bp that is optimal for a fungal barcode, the genes encoding for the ATPase subunit 6, the cytochrome oxidase subunit 3 and the NADH dehydrogenase subunit 6 have the most promising characteristics for DNA barcoding among the mitochondrial genes studied. However, biological validation on two fungal data sets indicated that no single mitochondrial gene gave a better taxonomic resolution than the ITS, the region already widely used in fungal taxonomy.
Collapse
Affiliation(s)
- Agathe Vialle
- Centre d'étude de la forêt, Université Laval, QC, Canada
| | | | | | | | | | | | | |
Collapse
|
12
|
The heterogeneity of the rDNA-ITS sequence and its phylogeny in Rhizoctonia cerealis, the cause of sharp eyespot in wheat. Curr Genet 2013; 60:1-9. [DOI: 10.1007/s00294-013-0397-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 11/25/2022]
|
13
|
Xing X, Ma X, Hart MM, Wang A, Guo S. Genetic diversity and evolution of Chinese traditional medicinal fungus Polyporus umbellatus (Polyporales, Basidiomycota). PLoS One 2013; 8:e58807. [PMID: 23554929 PMCID: PMC3598919 DOI: 10.1371/journal.pone.0058807] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polyporus umbellatus is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of P. umbellatus. METHODOLOGY/PRINCIPAL FINDINGS The objective of this research was to assess genetic differences of P. umbellatus from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in P. umbellatus was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, P. umbellatus may spread from a center (Shaanxi, Henan and Gansu province) to other regions. CONCLUSIONS/SIGNIFICANCE We found sclerotial samples of P. umbellatus contained levels of intraspecific genetic diversity. These findings suggested that P. umbellatus populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly.
Collapse
Affiliation(s)
- Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xueting Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Miranda M. Hart
- Biology, University of British Columbia Okanagan, Kelowna, Canada
| | - Airong Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| |
Collapse
|
14
|
Le CN, Mendes R, Kruijt M, Raaijmakers JM. Genetic and Phenotypic Diversity of Sclerotium rolfsii in Groundnut Fields in Central Vietnam. PLANT DISEASE 2012; 96:389-397. [PMID: 30727129 DOI: 10.1094/pdis-06-11-0468] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Groundnut (Arachis hypogaea) is an economically important legume crop in Vietnam and many other countries worldwide. Stem and pod rot, caused by the soilborne fungus Sclerotium rolfsii, is a major yield-limiting factor in groundnut cultivation. To develop sustainable measures to control this disease, fundamental knowledge of the epidemiology and diversity of S. rolfsii populations is essential. In this study, disease incidence was monitored in eight groundnut areas in central Vietnam with a total of 240 observational field plots. The results showed that 5 to 25% of the field-grown groundnut plants were infected by S. rolfsii. Based on internal transcribed spacer (ITS) ribosomal DNA sequence analyses, three distinct groups were identified among a total of 103 randomly selected S. rolfsii field isolates, with the majority of the isolates (n = 90) in one ITS group. S. rolfsii isolates originating from groundnut, tomato, and taro were all pathogenic on groundnut and relatively sensitive to the fungicide tebuconazole but displayed substantial diversity of various genetic and phenotypic traits, including mycelial compatibility, growth rate, and sclerotial characteristics.
Collapse
Affiliation(s)
- C N Le
- Laboratory of Phytopathology, Wageningen University, The Netherlands, and Department of Plant Protection, Hue University of Agriculture and Forestry (HUAF), Vietnam
| | - R Mendes
- Laboratory of Phytopathology, Wageningen University
| | - M Kruijt
- Laboratory of Phytopathology, Wageningen University
| | | |
Collapse
|
15
|
Genetic Differentiation of Colletotrichum gloeosporioides and C. truncatum Associated with Anthracnose Disease of Papaya (Carica papaya L.) and Bell Pepper (Capsium annuum L.) Based on ITS PCR-RFLP Fingerprinting. Mol Biotechnol 2011; 50:237-49. [DOI: 10.1007/s12033-011-9434-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
16
|
Ota Y, Hattori T. Relationships among three Japanese Laetiporus taxa based on phylogenetic analysis and incompatibility tests. MYCOSCIENCE 2008. [DOI: 10.1007/s10267-007-0403-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Xu Z, Gleason ML, Mueller DS, Esker PD, Bradley CA, Buck JW, Benson DM, Dixon PM, Monteiro JEBA. Overwintering of Sclerotium rolfsii and S. rolfsii var. delphinii in Different Latitudes of the United States. PLANT DISEASE 2008; 92:719-724. [PMID: 30769591 DOI: 10.1094/pdis-92-5-0719] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Previously known only from the southern United States, hosta petiole rot recently appeared in the northern United States. Sclerotium rolfsii var. delphinii is believed to be the predominant petiole rot pathogen in the northern United States, whereas S. rolfsii is most prevalent in the southern United States. In order to test the hypothesis that different tolerance to climate extremes affects the geographic distribution of these fungi, the survival of S. rolfsii and S. rolfsii var. delphinii in the northern and southeastern United States was investigated. At each of four locations, nylon screen bags containing sclerotia were placed on the surface of bare soil and at 20-cm depth. Sclerotia were recovered six times from November 2005 to July 2006 in North Dakota and Iowa, and from December 2005 to August 2006 in North Carolina and Georgia. Survival was estimated by quantifying percentage of sclerotium survival on carrot agar. Sclerotia of S. rolfsii var. delphinii survived until at least late July in all four states. In contrast, no S. rolfsii sclerotia survived until June in North Dakota or Iowa, whereas 18.5% survived until August in North Carolina and 10.3% survived in Georgia. The results suggest that inability to tolerate low temperature extremes limits the northern range of S. rolfsii.
Collapse
Affiliation(s)
- Z Xu
- Department of Plant Pathology, Iowa State University, Ames 50011
| | - M L Gleason
- Department of Plant Pathology, Iowa State University, Ames 50011
| | - D S Mueller
- Department of Plant Pathology, Iowa State University, Ames 50011
| | - P D Esker
- Department of Plant Pathology, Iowa State University, Ames 50011
| | - C A Bradley
- Department of Plant Pathology, North Dakota State University, Fargo 58105
| | - J W Buck
- Department of Plant Pathology, University of Georgia, Griffin 30223
| | - D M Benson
- Department of Plant Pathology, North Carolina State University, Raleigh 27695
| | - P M Dixon
- Department of Statistics, Iowa State University, Ames 50011
| | - J E B A Monteiro
- Department of Exact Sciences, ESALQ, University of Sao Paulo, Piracicaba, Brazil
| |
Collapse
|
18
|
de Fine Licht HH, Boomsma JJ, Aanen DK. Presumptive horizontal symbiont transmission in the fungus-growing termite Macrotermes natalensis. Mol Ecol 2006; 15:3131-8. [PMID: 16968259 DOI: 10.1111/j.1365-294x.2006.03008.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
All colonies of the fungus-growing termite Macrotermes natalensis studied so far are associated with a single genetically variable lineage of Termitomyces symbionts. Such limited genetic variation of symbionts and the absence of sexual fruiting bodies (mushrooms) on M. natalensis mounds would be compatible with clonal vertical transmission, as is known to occur in Macrotermes bellicosus. We investigated this hypothesis by analysing DNA sequence polymorphisms as codominant SNP markers of four single-copy gene fragments of Termitomyces isolates from 31 colonies of M. natalensis. A signature of free recombination was found, indicative of frequent sexual horizontal transmission. First, all 31 strains had unique multilocus genotypes. Second, SNP markers (n = 55) were largely in Hardy-Weinberg equilibrium (90.9%) and almost all possible pairs of SNPs between genetically unlinked loci were in linkage equilibrium (96.7%). Finally, extensive intragenic recombination was found, especially in the EF1alpha fragment. Substantial genetic variation and a freely recombining population structure can only be explained by frequent horizontal and sexual transmission of Termitomyces. The apparent variation in symbiont transmission mode among Macrotermes species implies that vertical symbiont transmission can evolve rapidly. The unexpected finding of horizontal transmission makes the apparent absence of Termitomyces mushrooms on M. natalensis mounds puzzling. To our knowledge, this is the first detailed study of the genetic population structure of a single lineage of Termitomyces.
Collapse
Affiliation(s)
- H H de Fine Licht
- Department of Population Biology, Institute of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | | | | |
Collapse
|
19
|
Wang DM, Yao YJ. Intrastrain internal transcribed spacer heterogeneity inGanodermaspecies. Can J Microbiol 2005; 51:113-21. [PMID: 16091769 DOI: 10.1139/w04-118] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intrastrain internal transcribed spacer (ITS) heterogeneity is first reported from Ganoderma, a fungal genus within Basidiomycetes. ITS amplification products from 4 strains, representing 4 Ganoderma species, were cloned and sequenced. Two to five different ITS types were found within a single strain. The clone sequences were analyzed along with other sequences from Ganoderma retrieved from GenBank. The results show that sequence variation within strains varies considerably with species and the heterogeneity may occur in the 3 parts (ITS1, ITS2, and 5.8S) of the ITS region.Key words: intragenomic ITS heterogeneity, polymorphism, Ganoderma.
Collapse
Affiliation(s)
- D-M Wang
- Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
| | | |
Collapse
|