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Bashyal BM, Yadav GK, Parmar P, Sunani SK, Aggarwal S, Gopala Krishnan S, Kumar A, Zaidi NW, Aggarwal R. High-Quality Genome Resource of Ustilaginoidea virens (UV2_4G), Causal Agent of an Emerging False Smut Disease in Rice. PLANT DISEASE 2023; 107:896-898. [PMID: 36265154 DOI: 10.1094/pdis-05-22-1193-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ustilaginoidea virens is the fungal pathogen causing an emerging false smut disease that affects crop yield as well as deteriorates quality of the grains by producing mycotoxins. A high quality genome of U. virens isolate UV2_4G was sequenced using Nanopore and Illumina HiSeq 2,000 sequencing platforms. The total assembled genome of Indian isolate UV2_4G was 35.9 Mb, which comprised 89 scaffolds with N50 of 700,296 bp. A total of 358,697 variants were identified in the genome, out of which 355,173 were SNPs and 3,524 were INDELS. Further, 7,390 SSRs belonging to different repeat types were also identified in the genome. Out of 7,444 proteins predicted, 7,206 were functionally annotated. A total of 1,307 CAZymes, 501 signal peptides, 1,876 effectors, and 2,709 genes involved in host-pathogen interactions were identified. Comparative analysis revealed isolate UV2_4G is distinct with 31 unique clusters and placed distantly in phylogenetic analysis. Taken together, this high-quality genome assembly and sequence annotation resource can give an improved insight for characterizing the biological and pathogenic mechanisms of U. virens.
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Affiliation(s)
- Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gaurav Kumar Yadav
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pooja Parmar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sunil Kumar Sunani
- ICAR-Indian Institute of Pulse Research, Regional station, Khordha, Bhubaneswar, Odisha 752055, India
| | - Shweta Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Rashmi Aggarwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Fu R, Chen C, Wang J, Liu Y, Zhao L, Lu D. Diversity Analysis of the Rice False Smut Pathogen Ustilaginoidea virens in Southwest China. J Fungi (Basel) 2022; 8:1204. [PMID: 36422026 PMCID: PMC9694781 DOI: 10.3390/jof8111204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 04/10/2024] Open
Abstract
Rice false smut caused by Ustilaginoidea virens is a destructive disease in rice cropping areas of the world. The present study is focused on the morphology, pathogenicity, mating-type loci distribution, and genetic characterization of different isolates of U. virens. A total of 221 strains of U. virens were collected from 13 rice-growing regions in southwest China. The morphological features of these strains exhibited high diversity, and the pathogenicity of the smut fungus showed significant differentiation. There was no correlation between pathogenicity and sporulation. Mating-type locus (MAT) analysis revealed that all 221 isolates comprised heterothallic and homothallic forms, wherein 204 (92.31%) and 17 (7.69%) isolates belonged to heterothallic and homothallic mating types, respectively. Among 204 strains of heterothallic mating types, 62 (28.05%) contained MAT1-1-1 idiomorphs, and 142 isolates (64.25%) had the MAT1-2-1 idiomorph. Interestingly, strains isolated from the same fungus ball had different mating types. The genetic structure of the isolates was analyzed using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs). All isolates were clustered into five genetic groups. The values of Nei's gene diversity (H) and Shannon's information index (I) indicated that all strains as a group had higher genetic diversity than strains from a single geographical population. The pairwise population fixation index (FST) values also indicated significant genetic differentiation among all compared geographical populations. The analysis of molecular variation (AMOVA) indicated greater genetic variation within individual populations and less genetic variation among populations. The results showed that most of the strains were not clustered according to their geographical origin, showing the rich genetic diversity and the complex and diverse genetic background of U. virens in southwest China. These results should help to better understand the biological and genetic diversity of U. virens in southwest China and provide a theoretical basis for building effective management strategies.
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Affiliation(s)
- Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
| | - Yao Liu
- Crop Research Institute, Sichuan Academy of Agricultural Science, Chengdu 610066, China
| | - Liyu Zhao
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 20# Jingjusi Rd., Chengdu 610066, China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu 610066, China
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Pan X, Wang X, Yu J, Yu M, Cao H, Yong M, Song T, Qi Z, Du Y, Zhang R, Liu Y. Loop-Mediated Isothermal Amplification for Rapid Detection of Mating Types of Villosiclava virens. PLANT DISEASE 2022; 106:1128-1133. [PMID: 34739329 DOI: 10.1094/pdis-09-21-1943-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
Rice false smut (RFS), caused by Villosiclava virens, is an important fungal disease in panicles of rice. V. virens is a heterothallic ascomycete controlled by two opposite idiomorphs, MAT1-1 and MAT1-2. Previous study showed that sexual reproduction of V. virens plays an important role in the epidemic of RFS. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay to detect the mating type of V. virens easily and rapidly by using specific primers based on the mating type genes MAT1-1-2 and MAT1-2-1, respectively. The LAMP assay used only a water/dry bath and could recognize the mating type of V. virens in just 45 min. The LAMP assay was so sensitive that it could detect small amounts of V. virens genomic DNA (as low as 2.0 pg of MAT1-1 and 200.0 pg of MAT1-2) and was 10 times more sensitive than PCR. In addition, we demonstrated the application of mating type via LAMP assay by assessing the genomic DNA of V. virens isolated from rice fields. The high efficiency and specificity of this LAMP assay suggest that it can be used as a rapid testing tool in mating type recognition of V. virens isolates in the field.
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Affiliation(s)
- Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xiao Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Mingli Yong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Bashyal BM, Rohith M, Parmar P, Darshan K, Sunani SK, Aggarwal R. Biology and Management of Ustilaginoidea virens Causing False Smut Disease of Rice (Oryza sativa L.). Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wilson AM, Wilken PM, Wingfield MJ, Wingfield BD. Genetic Networks That Govern Sexual Reproduction in the Pezizomycotina. Microbiol Mol Biol Rev 2021; 85:e0002021. [PMID: 34585983 PMCID: PMC8485983 DOI: 10.1128/mmbr.00020-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Sexual development in filamentous fungi is a complex process that relies on the precise control of and interaction between a variety of genetic networks and pathways. The mating-type (MAT) genes are the master regulators of this process and typically act as transcription factors, which control the expression of genes involved at all stages of the sexual cycle. In many fungi, the sexual cycle typically begins when the mating pheromones of one mating type are recognized by a compatible partner, followed by physical interaction and fertilization. Subsequently, highly specialized sexual structures are formed, within which the sexual spores develop after rounds of meiosis and mitosis. These spores are then released and germinate, forming new individuals that initiate new cycles of growth. This review provides an overview of the known genetic networks and pathways that are involved in each major stage of the sexual cycle in filamentous ascomycete fungi.
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Affiliation(s)
- Andi M. Wilson
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - P. Markus Wilken
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Brenda D. Wingfield
- Forestry and Agricultural Biotechnology Institute, Department of Biochemistry, Genetics, and Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Bao J, Wang R, Gao S, Wang Z, Fang Y, Wu L, Wang M. High-Quality Genome Sequence Resource of a Rice False Smut Fungus Ustilaginoidea virens Isolate, UV-FJ-1. PHYTOPATHOLOGY 2021; 111:1889-1892. [PMID: 34732059 DOI: 10.1094/phyto-01-21-0007-a] [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
Ustilaginoidea virens is the fungal pathogen causing rice false smut, resulting in not only yield lost but also grain pollution with toxic mycotoxins. Here we deployed PacBio Sequel II HIFI-read sequencing technology to generate a near-complete genome assembly for the U. virens isolate UV-FJ-1 (38.48 Mb), which was isolated from Fujian province, China. The genome assembly contains 116 contigs with N50 of 0.65 Mb and a maximum length of 2.10 Mb, and the genome completeness is ≥98% assessed by benchmarking universal single-copy orthologs (BUSCOs) and the mapping rate of Illumina short reads. Excluding 35.78% repeat sequences, we identified a total of 7,164 protein-coding genes, of which 5,818 were functionally annotated and 223 encode putative effector proteins. Moreover, 21 secondary metabolite biosynthesis gene clusters were found in UV-FJ-1 genome. Taken together, this high-quality genome assembly and gene annotation resource will provide a better insight for characterizing the biological and pathogenic mechanisms of U. virens.
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Affiliation(s)
- Jiandong Bao
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rong Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Shilei Gao
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhe Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lv Wu
- Gongzhuling Sub-center for New Plant Variety Tests, Ministry of Agriculture and Rural Affairs, Jilin Academy of Agricultural Sciences, Changchun, 136100, China
| | - Mo Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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Sharanabasav H, Pramesh D, Prasannakumar MK, Chidanandappa E, Yadav MK, Ngangkham U, Parivallal B, Raghavendra BT, Manjunatha C, Sharma SK, Karthik N. Morpho-molecular and mating-type locus diversity of Ustilaginoidea virens: an incitant of false smut of rice from Southern parts of India. J Appl Microbiol 2021; 131:2372-2386. [PMID: 33772985 DOI: 10.1111/jam.15087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/17/2021] [Accepted: 03/21/2021] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the geo-distinct isolates of Ustilaginoidea virens for morpho-molecular and mating-type locus diversity. METHODS AND RESULTS Sixty-one isolates of U. virens collected from Southern India exhibited significant diversity in mycelial width (3·45-5·50 µm), colony colour (yellow, pale yellow, and white), and growth pattern (thick leather mat, raised-fluffy, flat-fluffy, and raised). Field-borne chlamydospores of each isolate were significantly smaller in size (3·34-5·26 µm2 ) compared to those formed on culture media (18·6-100·89 µm2 ). The phylogenetic study based on internal transcribed sequences revealed two clusters; however, most isolates (n = 54) were grouped in cluster-I, indicating common ancestral origin. We also identified 42 haplotypes; among them, Hap_3 has the highest number of isolates (n = 19). Mating-type locus (MAT1) analysis revealed all sixty-one isolates as heterothallic, wherein 37 and 24 isolates belonging to MAT1-1-1 and MAT1-2-1 heterothallic mating types, respectively. The microsynteny analysis of MAT1 loci of one of the Indian strain (Uv-Gvt) along with Uv-8b (China) strain revealed synteny conservation at MAT1 locus, which is flanked by conserved genes SLA2 and a hypothetical protein in the upstream and APN2, COX12 and APC5 in the downstream of the locus. CONCLUSIONS Morpho-molecular study revealed the significant diversity among geo-distinct isolates, and MAT1 loci analysis indicated the distribution of heterothallic mating types in south Indian paddy fields. And also, complete synteny conservation between Indian and Chinese strain was observed at the MAT1 locus. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report describing the sexuality of Indian strains of the U. virens, which would help better understand the genetic diversity of the U. virens prevailing in Southern India and aid in developing resistant rice cultivars against this pathogen population.
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Affiliation(s)
- H Sharanabasav
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - D Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - E Chidanandappa
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India
| | - M K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - U Ngangkham
- ICAR-Research Complex for NEH Region Umia, Meghalaya, India
| | - B Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - B T Raghavendra
- Department of Plant Pathology, University of Agricultural Sciences, Raichur, India
| | - C Manjunatha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S K Sharma
- ICAR-Research Complex for NEH Region, Imphal Center, Manipur, India
| | - N Karthik
- University of Madras, Chennai, India
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Sun W, Fan J, Fang A, Li Y, Tariqjaveed M, Li D, Hu D, Wang WM. Ustilaginoidea virens: Insights into an Emerging Rice Pathogen. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:363-385. [PMID: 32364825 DOI: 10.1146/annurev-phyto-010820-012908] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
False smut of rice, caused by Ustilaginoidea virens, has become one of the most important diseases in rice-growing regions worldwide. The disease causes a significant yield loss and imposes health threats to humans and animals by producing mycotoxins. In this review, we update our understanding of the pathogen, including the disease cycle and infection strategies, the decoding of the U. virens genome, comparative/functional genomics, and effector biology. Whereas the decoding of the U. virens genome unveils specific adaptations of the pathogen in successfully occupying rice flowers, progresses in comparative/functional genomics and effector biology have begun to uncover the molecular mechanisms underlying U. virens virulence and pathogenicity. We highlight the identification and characterization of the produced mycotoxins and their biosynthetic pathways in U. virens.The management strategies for this disease are also discussed. The flower-specific infection strategy makes the pathogen a unique tool to unveil novel mechanisms for the interactions between nonobligate biotrophic pathogens and their hosts.
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Affiliation(s)
- Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Anfei Fang
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yuejiao Li
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Muhammad Tariqjaveed
- College of Plant Protection and the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, China Agricultural University, Beijing 100193, China
| | - Dayong Li
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
| | - Dongwei Hu
- State Key Laboratory of Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
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Yong M, Yu J, Pan X, Yu M, Cao H, Qi Z, Du Y, Zhang R, Song T, Yin X, Chen Z, Liu W, Liu Y. MAT1-1-3, a Mating Type Gene in the Villosiclava virens, Is Required for Fruiting Bodies and Sclerotia Formation, Asexual Development and Pathogenicity. Front Microbiol 2020; 11:1337. [PMID: 32714294 PMCID: PMC7344243 DOI: 10.3389/fmicb.2020.01337] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/25/2020] [Indexed: 12/29/2022] Open
Abstract
Villosiclava virens is the prevalent causative pathogen of rice false smut, a destructive rice disease. Mating-type genes play a vital role in the evolution of mating systems in fungi. Some fungi have lost MAT1-1-3, one of the mating-type genes, during evolution, whereas others still retain MAT1-1-3. However, how MAT1-1-3 regulates the sexual development of heterothallic V. virens remains unknown. Here, we generated the MAT1-1-3 mutants, which exhibited defects in vegetative growth, stress response, pathogenicity, sclerotia formation and fruiting body maturation. An artificial outcrossing inoculation assay showed that the Δmat1-1-3 mutant was unable to produce sclerotia. Unexpectedly, the Δmat1-1-3 mutant could form immature fruiting bodies without mating on potato sucrose agar medium (PSA) compared with the wild-type strain, most likely by activating the truncated MAT1-2-1 transcription to regulate the sexual development. Moreover, RNA-seq data showed that knockout of MAT1-1-3 results in misregulation of a subset of genes involved in sexual development, MAPK signaling, cell wall integrity, autophagy, epigenetic modification, and transcriptional regulation. Collectively, this study reveals that MAT1-1-3 is required for asexual and sexual development, and pathogenicity of V. virens, thereby provides new insights into the function of mating-type genes in the fungi life cycle and infection process.
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Affiliation(s)
- Mingli Yong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaole Yin
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhiyi Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Mating genes in Calonectria and evidence for a heterothallic ancestral state. Persoonia - Molecular Phylogeny and Evolution of Fungi 2020; 45:163-176. [PMID: 34456375 PMCID: PMC8375350 DOI: 10.3767/persoonia.2020.45.06] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/14/2020] [Indexed: 11/25/2022]
Abstract
The genus Calonectria includes many important plant pathogens with a wide global distribution. In order to better understand the reproductive biology of these fungi, we characterised the structure of the mating type locus and flanking genes using the genome sequences for seven Calonectria species. Primers to amplify the mating type genes in other species were also developed. PCR amplification of the mating type genes and multi-gene phylogenetic analyses were used to investigate the mating strategies and evolution of mating type in a collection of 70 Calonectria species residing in 10 Calonectria species complexes. Results showed that the organisation of the MAT locus and flanking genes is conserved. In heterothallic species, a novel MAT gene, MAT1-2-12 was identified in the MAT1-2 idiomorph; the MAT1-1 idiomorph, in most cases, contained the MAT1-1-3 gene. Neither MAT1-1-3 nor MAT1-2-12 was found in homothallic Calonectria (Ca.) hongkongensis, Ca. lateralis, Ca. pseudoturangicola and Ca. turangicola. Four different homothallic MAT locus gene arrangements were observed. Ancestral state reconstruction analysis provided evidence that the homothallic state was basal in Calonectria and this evolved from a heterothallic ancestor.
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Yu J, Yu M, Song T, Cao H, Pan X, Yong M, Qi Z, Du Y, Zhang R, Yin X, Liu Y. A Homeobox Transcription Factor UvHOX2 Regulates Chlamydospore Formation, Conidiogenesis, and Pathogenicity in Ustilaginoidea virens. Front Microbiol 2019; 10:1071. [PMID: 31281290 PMCID: PMC6596325 DOI: 10.3389/fmicb.2019.01071] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/29/2019] [Indexed: 12/21/2022] Open
Abstract
Rice false smut fungus (teleomorph: Villosiclava virens; anamorph: Ustilaginoidea virens) can generate chlamydospores and survive winter under field conditions. The chlamydospore is considered as an important infection source of the disease. However, little is known about the regulatory mechanism of the chlamydospore production. In this study, we identified a defective homeobox transcription factor (designated as UvHOX2) gene in a U. virens random insertional mutant B-766 that could not form chlamydospores. To confirm the regulatory function of UvHOX2, an Agrobacterium tumefaciens mediated transformation- and CRISPR/Cas9- based targeted gene replacement method was developed. The UvHox2 deletion mutants completely failed to produce chlamydospores, showed reduced conidia production and decreased virulence, and was hyper-sensitive to oxidative, osmotic, and cell wall stresses. We confirmed that UvHOX2 is located in the nuclei of U. virens, and the expression of UvHox2 was the strongest during the early stage of chlamydospore and conidium formation. Global transcription pattern of UvHOX2 was also determined by RNA-seq in this study, and several genes that might be down-stream of UvHOX2 regulation were identified. The results will better our understanding of the molecular mechanism of chlamydospore formation in U. virens as a model fungus.
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Affiliation(s)
- Junjie Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mina Yu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianqiao Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huijuan Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mingli Yong
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhongqiang Qi
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Du
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongsheng Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaole Yin
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,School of the Environment and Safety Engineering, Jiangsu University, Zhengjiang, China
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Wilken PM, Steenkamp ET, Wingfield MJ, de Beer ZW, Wingfield BD. Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fan J, Yang J, Wang Y, Li G, Li Y, Huang F, Wang W. Current understanding on Villosiclava virens, a unique flower-infecting fungus causing rice false smut disease. MOLECULAR PLANT PATHOLOGY 2016; 17:1321-1330. [PMID: 26720072 PMCID: PMC6638446 DOI: 10.1111/mpp.12362] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 12/25/2015] [Accepted: 12/27/2015] [Indexed: 05/13/2023]
Abstract
Villosiclava virens (Vv) is an ascomycete fungal pathogen that causes false smut disease in rice. Recent reports have revealed some interesting aspects of the enigmatic pathogen to address the question of why it specifically infects rice flowers and converts a grain into a false smut ball. Comparative and functional genomics have suggested specific adaptation of Vv in the colonization of rice flowers. Anatomical studies have disclosed that Vv specifically infects rice stamen filaments before heading and intercepts seed formation. In addition, Vv can occupy the whole inner space of a spikelet embracing all floral organs and activate the rice grain-filling network, presumably for nutrient acquisition to support the development of the false smut ball. This profile provides a general overview of the rice false smut pathogen, and summarizes advances in the Vv life cycle, genomics and genetics, and the molecular Vv-rice interaction. Current understandings of the Vv-rice pathosystem indicate that it is a unique and interesting system which can enrich the study of plant-pathogen interactions. Taxonomy: Ustilaginoidea virens is the anamorph form of the pathogen (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Incertae sedis; Order Incertae sedis; Family Incertae sedis; Genus Ustilaginoidea). The teleomorph form is Villosiclava virens (Kingdom Fungi; Phylum Ascomycota; Class Ascomycetes; Subclass Sordariomycetes; Order Hypocreales; Family Clavicipitaceae; Genus Villosiclava). Disease symptoms: The only visible symptom is the replacement of rice grains by ball-shaped fungal mycelia, namely false smut balls. When maturing, the false smut ball is covered with powdery chlamydospores, and the colour changes to yellowish, yellowish orange, green, olive green and, finally, to greenish black. Sclerotia are often formed on the false smut balls in autumn. Identification and detection: Vv conidia are round to elliptical, measuring 3-5 μm in diameter. Chlamydospores are ornamented with prominent irregularly curved spines, which are 200-500 nm in length. The sclerotia are black, horseshoe-shaped and irregular oblong or flat, ranging from 2 to 20 mm. Nested polymerase chain reaction (PCR) and quantitative PCR have been developed to specifically detect Vv presence in rice tissues and other biotic and abiotic samples in fields. Host range: Rice is the primary host for Vv. Natural infection by Vv has been found on several paddy field weeds, including Digitaria marginata, Panicum trypheron, Echinochloa crusgalli and Imperata cylindrica. However, the occurrence of infection in these potential alternative hosts is very rare. Life cycle: Vv infects rice spikelets at the late rice booting stage, and produces false smut balls covered with dark-green chlamydospores. Occasionally, sclerotia form on the surface of false smut balls in late autumn when the temperature fluctuates greatly between day and night. Both chlamydospores and sclerotia may serve as primary infection sources. Rainfall at the rice booting stage is a major environmental factor resulting in epidemics of rice false smut disease. Disease control: The use of fungicides is the major approach for the control of Vv. Several fungicides, such as cuproxat SC, copper oxychloride, tebuconazole, propiconazole, difenoconazole and validamycin, are often applied. However, the employment of resistant rice cultivars and genes has been limited, because of the poor understanding of rice resistance to Vv. Useful websites: Villosiclava virens genome sequence: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=JHTR01#contigs.
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Affiliation(s)
- Jing Fan
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Juan Yang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Yu‐Qiu Wang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Guo‐Bang Li
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Yan Li
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
| | - Fu Huang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
- College of Agronomy & Institute of Agricultural EcologySichuan Agricultural UniversityChengdu611130China
| | - Wen‐Ming Wang
- Rice Research Institute & Key Laboratory for Major Crop DiseasesSichuan Agricultural UniversityChengdu611130China
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Comparative genomics of Beauveria bassiana: uncovering signatures of virulence against mosquitoes. BMC Genomics 2016; 17:986. [PMID: 27905873 PMCID: PMC5134283 DOI: 10.1186/s12864-016-3339-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence. RESULTS A high-quality, near-complete genome assembly was achieved for the highly virulent isolate Bb8028, which was compared to the assemblies of the four other isolates. Whole genome analysis showed a high level of genetic diversity between the five isolates (2.85-16.8 SNPs/kb), which grouped into two distinct phylogenetic clusters. Mating type gene analysis revealed the presence of either the MAT1-1-1 or the MAT1-2-1 gene. Moreover, a putative new MAT gene (MAT1-2-8) was detected in the MAT1-2 locus. Comparative genome analysis revealed that Bb8028 contains 163 genes exclusive for this isolate. These unique genes have a tendency to cluster in the genome and to be often located near the telomeres. Among the genes unique to Bb8028 are a Non-Ribosomal Peptide Synthetase (NRPS) secondary metabolite gene cluster, a polyketide synthase (PKS) gene, and five genes with homology to bacterial toxins. A survey of candidate virulence genes for B. bassiana is presented. CONCLUSIONS Our results indicate several genes and molecular processes that may underpin virulence towards mosquitoes. Thus, the genome sequences of five isolates of B. bassiana provide a better understanding of the natural variation in virulence and will offer a major resource for future research on this important biological control agent.
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Comparative transcriptome analysis of fruiting body and sporulating mycelia of Villosiclava virens reveals genes with putative functions in sexual reproduction. Curr Genet 2016; 62:575-84. [DOI: 10.1007/s00294-015-0563-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/23/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
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