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Xiao S, Wang J, Bai Z, Pan Y, Li Q, Zhao D, Zhang D, Yang Z, Zhu J. Alternaria solani effectors AsCEP19 and AsCEP20 reveal novel functions in pathogenicity and conidiogenesis. Microbiol Spectr 2024:e0421423. [PMID: 38912810 DOI: 10.1128/spectrum.04214-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/15/2024] [Indexed: 06/25/2024] Open
Abstract
Previous work identified a pair of specific effectors AsCEP19 and AsCEP20 in Alternaria solani as contributors to the virulence of A. solani. Here, we constructed AsCEP19 and AsCEP20 deletion mutants in A. solani strain HWC168 to further reveal the effects of these genes on the biology and pathogenicity of A. solani. Deletion of AsCEP19 and AsCEP20 did not affect vegetative growth but did affect conidial maturation, with an increase in the percentage of abnormal conidia produced. Furthermore, we determined the expression patterns of genes involved in the conidiogenesis pathway and found that the regulatory gene abaA was significantly upregulated and chsA, a positive regulator for conidiation, was significantly downregulated in the mutant strains compared to the wild-type strain. These results suggest that AsCEP19 and AsCEP20 indirectly affect the conidial development and maturation of A. solani. Pathogenicity assays revealed significantly impaired virulence of ΔAsCEP19, ΔAsCEP20, and ΔAsCEP19 + AsCEP20 mutants on potato and tomato plants. Moreover, we performed localization assays with green fluorescent protein-tagged proteins in chili pepper leaves. We found that AsCEP19 can specifically localize to the chloroplasts of chili pepper epidermal cells, while AsCEP20 can localize to both chloroplasts and the plasma membrane. Weighted gene co-expression network analysis revealed enrichment of genes of this module in the photosynthesis pathway, with many hub genes associated with chloroplast structure and photosynthesis. These results suggest that chloroplasts are the targets for AsCEP19 and AsCEP20. IMPORTANCE Alternaria solani is an important necrotrophic pathogen causing potato early blight. Previous studies have provide preliminary evidence that specific effectors AsCEP19 and AsCEP20 contribute to virulence, but their respective functions, localization, and pathogenic mechanisms during the infection process of A. solani remain unclear. Here, we have systematically studied the specific effectors AsCEP19 and AsCEP20 for the first time, which are essential for conidial maturation. The deletion of AsCEP19 and AsCEP20 can significantly impair fungal pathogenicity. Additionally, we preliminarily revealed that AsCEP19 and AsCEP20 target the chloroplasts of host cells. Our findings further enhance our understanding of the molecular mechanisms underlying the virulence of necrotrophic pathogens.
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Affiliation(s)
- Siyu Xiao
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Jinhui Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei, China
| | - Zihan Bai
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Yang Pan
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Qian Li
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Dongmei Zhao
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Dai Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhihui Yang
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei, China
| | - Jiehua Zhu
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
- Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Baoding, Hebei, China
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Wei H, Zhong Z, Li Z, Zhang Y, Stukenbrock EH, Tang B, Yang N, Baroncelli R, Peng L, Liu Z, He X, Yang Y, Yuan Z. Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte. PLANT COMMUNICATIONS 2024; 5:100672. [PMID: 37563834 PMCID: PMC10811371 DOI: 10.1016/j.xplc.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.
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Affiliation(s)
- Huanshen Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118 Kiel, Germany; Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
| | - Ningning Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Long Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhuo Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuzhan Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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Chen Y, Cao Y, Jiao C, Sun X, Gai Y, Zhu Z, Li H. The Alternaria alternata StuA transcription factor interacting with the pH-responsive regulator PacC for the biosynthesis of host-selective toxin and virulence in citrus. Microbiol Spectr 2023; 11:e0233523. [PMID: 37812002 PMCID: PMC10715145 DOI: 10.1128/spectrum.02335-23] [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: 06/04/2023] [Accepted: 08/19/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE In this study, we used Alternaria alternata as a biological model to report the role of StuA in phytopathogenic fungi. Our findings indicated that StuA is required for Alternaria citri toxin (ACT) biosynthesis and fungal virulence. In addition, StuA physically interacts with PacC. Disruption of stuA or pacC led to decreased expression of seven toxin biosynthetic genes (ACCT) and toxin production. PacC could recognize and bind to the promoter regions of ACTT6 and ACTTR. Our results revealed a previously unrecognized (StuA-PacC)→ACTTR module for the biosynthesis of ACT in A. alternata, which also provides a framework for the study of StuA in other fungi.
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Affiliation(s)
- Yanan Chen
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Yingzi Cao
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chen Jiao
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang Agriculture & Forestry University, Hangzhou, China
| | - Yunpeng Gai
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zengrong Zhu
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
| | - Hongye Li
- The Key Laboratory of Molecular Biology of Crop Pathogens and Insects of Ministry of Agriculture, The Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Xiao Q, Chen Z, Ma M, Xie X, Weng H, Zhang Y, Chen J, Xiao A. Synthesis, characterization, antibacterial and emulsifying properties of agar benzoate. Int J Biol Macromol 2023; 239:124254. [PMID: 37003393 DOI: 10.1016/j.ijbiomac.2023.124254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Agar benzoate (AB) with different degrees of substitution (DS) was synthesized by the esterification of agar and benzoic anhydride in aqueous solution. The DS could be regulated by adjusting composition ratio, pH, and temperature. Its chemical structure was determined by Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy (NMR). 13C NMR spectrum of the AB suggested the main substitution occurred at the C-6 in the d-galactopyranose. Cryo-scanning electron microscopy (Cryo-SEM) showed that the aperture of AB was larger than that of agar. The thermal performance of AB decreased slightly, but this did not affect its performance. AB showed the highest relative antibacterial activity against Escherichia coli, S. aureus and Alternaria alternata, reaching 100 % (AB 20 g/L), 100 % (AB 40 g/L) and 19.35 % (7 d incubation), respectively. Moreover, the obtained AB possessed good emulsion stability. These antibacterial AB have broad application prospects in the field of fruit and vegetable preservation.
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Affiliation(s)
- Qiong Xiao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
| | - Zizhou Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
| | - Mingze Ma
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
| | - Xiangji Xie
- Sanming Inspection & Testing Center for Product Quality, Sanming 365000, China
| | - Huifen Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
| | - Yonghui Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China
| | - Jun Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China.
| | - Anfeng Xiao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China; National R&D Center for Red Alga Processing Technology, Xiamen, Fujian Province 361021, China; Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Xiamen, Fujian Province 361021, China; Xiamen Key Laboratory of Marine Functional Food, Xiamen 361021, China.
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Luo X, Wang H, Wang M. Genomic Sequence Data of Alternaria alternata hznu325 Causing Black Leaf Spot on Chrysanthemum morifolium. PLANT DISEASE 2022; 106:2506-2510. [PMID: 35895327 DOI: 10.1094/pdis-11-21-2517-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Xiujun Luo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
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Montezano Fernandes F, Vieira de Queiroz M, Lopes da Silva L, Maria Queiroz Azevedo D, Luis Badel J, Couto Alfenas A. Chromosomal polymorphism of the Ceratocystis fimbriata species complex in Brazil. Fungal Genet Biol 2022; 162:103728. [PMID: 35932991 DOI: 10.1016/j.fgb.2022.103728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 11/04/2022]
Abstract
Ceratocystis fimbriata is an important pathogen that causes wilt in several plant species. Despite the importance of this pathogen, knowledge about its karyotypic polymorphism and genomic architecture is limited. The main objective of this study was to investigate the karyotype of isolates of the C. fimbriata species complex from different host plants and geographical origins in Brazil. First, the identity of the isolates was confirmed conducting multilocus sequence analysis (MLSA) phylogeny using β-tubulin (TUBB), translation elongation factor 1α (TEF-1α) and mating-type (MAT1 and MAT2) gene sequences. To investigate the chromosomal polymorphism, two conditions of pulsed-field gel electrophoresis (PFGE) were used and the karyotypes of the isolates obtained. The retrotransposon-microsatellite amplified polymorphism (REMAP) molecular marker was utilized to assess the genetic variability among isolates. In the MLSA utilizing the concatenated gene sequences, Ceratocystis cacaofunesta and C. fimbriata formed separate clades, but considerable variation among C. fimbriata isolates was observed. Polymorphism in chromosome number and size was found, indicating the existence of genomic differences among isolates and occurrence of chromosomal rearrangements in the species complex. The number of chromosomes varied from seven to nine and the estimated minimum chromosome sizes were estimated to be between 2.7 to 6.0 Mbp. Small polymorphic chromosomes ranging from 1.2 to 1.8 Mbp were observed in all isolates, raising the hypothesis that they could be supernumerary chromosomes. REMAP analysis revealed a high genetic variability and that isolates from the same host tend to group together in a same cluster. Our results bring new insights into the chromosomal diversity and genome organization of the C. fimbriata complex.
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Affiliation(s)
- Fernando Montezano Fernandes
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Marisa Vieira de Queiroz
- Laboratory of Molecular Genetics of Microorganisms, Department of Microbiology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Leandro Lopes da Silva
- Laboratory of Molecular Genetics of Microorganisms, Department of Microbiology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Daiana Maria Queiroz Azevedo
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Jorge Luis Badel
- Laboratory of Molecular Phytobacteriology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Acelino Couto Alfenas
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil.
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Zaccaron AZ, Chen LH, Samaras A, Stergiopoulos I. A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome. Microb Genom 2022; 8:000819. [PMID: 35471194 PMCID: PMC9453070 DOI: 10.1099/mgen.0.000819] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 03/29/2022] [Indexed: 01/25/2023] Open
Abstract
Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the 'two-speed genome' model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.
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Affiliation(s)
- Alex Z. Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, USA
| | - Li-Hung Chen
- Department of Plant Pathology, University of California Davis, Davis, USA
- Present address: Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Anastasios Samaras
- Department of Plant Pathology, University of California Davis, Davis, USA
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Ma H, Li L, Gai Y, Zhang X, Chen Y, Zhuo X, Cao Y, Jiao C, Gmitter FG, Li H. Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata. Front Microbiol 2021; 12:783633. [PMID: 34880849 PMCID: PMC8645686 DOI: 10.3389/fmicb.2021.783633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/02/2021] [Indexed: 01/16/2023] Open
Abstract
Histone acetylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by HATs and HDACs. This study determined the function of 6 histone acetyltransferases (HATs) (Gcn5, RTT109, Elp3, Sas3, Sas2, Nat3) and 6 histone deacetylases (HDACs) (Hos2, Rpd3, Hda1, Hos3, Hst2, Sir2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. Our data provide evidence that HATs and HDACs are both required for mycelium growth, cell development and pathogenicity as many gene deletion mutants (ΔGcn5, ΔRTT109, ΔElp3, ΔSas3, ΔNat3, ΔHos2, and ΔRpd3) displayed reduced growth, conidiation or virulence at varying degrees. In addition, HATs and HDACs are involved in the resistance to multiple stresses such as oxidative stress (Sas3, Gcn5, Elp3, RTT109, Hos2), osmotic stress (Sas3, Gcn5, RTT109, Hos2), cell wall-targeting agents (Sas3, Gcn5, Hos2), and fungicide (Gcn5, Hos2). ΔGcn5, ΔSas3, and ΔHos2 displayed severe growth defects on sole carbon source medium suggesting a vital role of HATs and HDACs in carbon source utilization. More SNPs were generated in ΔGcn5 in comparison to wild-type when they were exposed to ultraviolet ray. Moreover, ΔRTT109, ΔGcn5, and ΔHos2 showed severe defects in resistance to DNA-damaging agents, indicating the critical role of HATs and HDACs in DNA damage repair. These phenotypes correlated well with the differentially expressed genes in ΔGcn5 and ΔHos2 that are essential for carbon sources metabolism, DNA damage repair, ROS detoxification, and asexual development. Furthermore, Gcn5 is required for the acetylation of H3K4. Overall, our study provides genetic evidence to define the central role of HATs and HDACs in the pathological and biological functions of A. alternata.
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Affiliation(s)
- Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China.,Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Zhang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaokang Zhuo
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Yingzi Cao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fred G Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Fontaine K, Fourrier-Jeandel C, Armitage AD, Boutigny AL, Crépet M, Caffier V, Gnide DC, Shiller J, Le Cam B, Giraud M, Ioos R, Aguayo J. Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ 2021; 9:e12496. [PMID: 34917421 PMCID: PMC8643104 DOI: 10.7717/peerj.12496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 11/20/2022] Open
Abstract
Leaf blotch caused by Alternaria spp. is a common disease in apple-producing regions. The disease is usually associated with one phylogenetic species and one species complex, Alternaria alternata and the Alternaria arborescens species complex (A. arborescens SC), respectively. Both taxa may include the Alternaria apple pathotype, a quarantine or regulated pathogen in several countries. The apple pathotype is characterized by the production of a host-selective toxin (HST) which is involved in pathogenicity towards the apple. A cluster of genes located on conditionally dispensable chromosomes (CDCs) is involved in the production of this HST (namely AMT in the case of the apple pathotype). Since 2016, leaf blotch and premature tree defoliation attributed to Alternaria spp. have been observed in apple-producing regions of central and south-eastern France. Our study aimed to identify the Alternaria species involved in apple tree defoliation and assess the presence of the apple pathotype in French orchards. From 2016 to 2018, 166 isolates were collected and identified by multi-locus sequence typing (MLST). This analysis revealed that all these French isolates belonged to either the A. arborescens SC or A. alternata. Specific PCR detection targeting three genes located on the CDC did not indicate the presence of the apple pathotype in France. Pathogenicity was assessed under laboratory conditions on detached leaves of Golden Delicious and Gala apple cultivars for a representative subset of 28 Alternaria isolates. All the tested isolates were pathogenic on detached leaves of cultivars Golden Delicious and Gala, but no differences were observed between the pathogenicity levels of A. arborescens SC and A. alternata. However, the results of our pathogenicity test suggest that cultivar Golden Delicious is more susceptible than Gala to Alternaria leaf blotch. Implications in the detection of the Alternaria apple pathotype and the taxonomic assignment of Alternaria isolates involved in Alternaria leaf blotch are discussed.
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Affiliation(s)
- Kévin Fontaine
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Céline Fourrier-Jeandel
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Anne-Laure Boutigny
- ANSES, Laboratoire de la Santé des Végétaux, Unité Bactériologie, Virologie et OGM, Angers, France
| | | | - Valérie Caffier
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Dossi Carine Gnide
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Jason Shiller
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Bruno Le Cam
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Michel Giraud
- Centre opérationnel de Lanxade, CTIFL, Prigonrieux, France
| | - Renaud Ioos
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
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10
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Gai Y, Li L, Liu B, Ma H, Chen Y, Zheng F, Sun X, Wang M, Jiao C, Li H. Distinct and essential roles of bZIP transcription factors in the stress response and pathogenesis in Alternaria alternata. Microbiol Res 2021; 256:126915. [PMID: 34953292 DOI: 10.1016/j.micres.2021.126915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/05/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022]
Abstract
The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata under metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We investigated the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A.alternata by analyzing targeted gene disrupted mutants. Morphological analysis provides evidence that the bZIP transcription factors (Gcn4, MeaB, Atf1, the ER stress regulator Hac1, and the all development altered-1 gene Ada1) are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover,the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings reveal that bZIP transcription factors function as key regulators of fungal morphogenesis, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.
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Affiliation(s)
- Yunpeng Gai
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Lei Li
- Department of Plant Pathology, South China Agricultural University, Guangzhou 510640, China
| | - Bing Liu
- Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Haijie Ma
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Yanan Chen
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fang Zheng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xuepeng Sun
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chen Jiao
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hongye Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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11
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Dettman JR, Eggertson Q. Phylogenomic analyses of Alternaria section Alternaria: A high-resolution, genome-wide study of lineage sorting and gene tree discordance. Mycologia 2021; 113:1218-1232. [PMID: 34637684 DOI: 10.1080/00275514.2021.1950456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The genus Alternaria contains a diversity of saprobic and pathogenic species that can be found in a wide range of environments. Alternaria is currently divided into 26 subgeneric sections, and the "small-spored" Alternaria section Alternaria includes many species that are economically important agricultural pathogens. Recognizing that a stable framework for systematics and species identification is essential for management and regulation purposes, this section has experienced much taxonomic debate and systematic revision in recent years. Molecular phylogenetic studies have challenged the reliability of using morphological characteristics to differentiate Alternaria species but have also suggested that commonly used molecular markers for fungal phylogenetics may not be sufficiently informative at this taxonomic level. To allow the assessment of molecular variation and evolutionary history at a genome-wide scale, we present an overview and analysis of phylogenomic resources for Alternaria section Alternaria. We review the currently available genomic resources and report five newly sequenced genomes. We then perform multiple comparative genomic analyses, including macrosynteny assessment and inference of phylogenetic relationships using a variety of data sets and analysis methods. Fine-scale, genome-wide phylogenetic reconstruction revealed incomplete lineage sorting and the genomic distribution of gene/species tree discordance. Based on these patterns, we propose a list of candidate genes that may be developed into informative markers that are diagnostic for the main lineages. This overview identifies gaps in knowledge and can guide future genome sequencing efforts for this important group of plant pathogenic fungi.
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Affiliation(s)
- Jeremy R Dettman
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Quinn Eggertson
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
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12
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Huang K, Tang J, Zou Y, Sun X, Lan J, Wang W, Xu P, Wu X, Ma R, Wang Q, Wang Z, Liu J. Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. Front Microbiol 2021; 12:713462. [PMID: 34616379 PMCID: PMC8488381 DOI: 10.3389/fmicb.2021.713462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/16/2021] [Indexed: 02/05/2023] Open
Abstract
Alternaria alternata is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of A. alternata (Y784-BC03) was isolated and identified from “Hongyang” kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. The assembled genome is composed of 33,869,130bp (32.30Mb) comprising 10 chromosomes and 11,954 genes. A total of 2,180 virulence factors were predicted to be present in the obtained genome sequence. The virulence factors comprised genes encoding secondary metabolites, including non-host-specific toxins, cell wall-degrading enzymes, and major transcriptional regulators. The predicted gene clusters encoding genes for the biosynthesis and export of secondary metabolites in the genome of Y784-BC03 were associated with non-host-specific toxins, including cercosporin, dothistromin, and versicolorin B. Major transcriptional regulators of different mycotoxin biosynthesis pathways were identified, including the transcriptional regulators, polyketide synthase, P450 monooxygenase, and major facilitator superfamily transporters.
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Affiliation(s)
- Ke Huang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China.,Institute of Microbial Ecology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jianming Tang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yong Zou
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiangcheng Sun
- College of Life Sciences, Northwest A&F University, Yangling, China.,West China Biopharm Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Jianbin Lan
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Wei Wang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China.,Institute of Microbial Ecology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Panpan Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | | | - Rui Ma
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia Liu
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
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13
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Gai Y, Ma H, Chen Y, Li L, Cao Y, Wang M, Sun X, Jiao C, Riely BK, Li H. Chromosome-Scale Genome Sequence of Alternaria alternata Causing Alternaria Brown Spot of Citrus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:726-732. [PMID: 33689393 DOI: 10.1094/mpmi-10-20-0278-sc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Haijie Ma
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yingzi Cao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mingshuang Wang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xuepeng Sun
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A
| | - Brendan K Riely
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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14
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Witte TE, Villeneuve N, Boddy CN, Overy DP. Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens. Front Microbiol 2021; 12:664276. [PMID: 33968000 PMCID: PMC8102738 DOI: 10.3389/fmicb.2021.664276] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic "crosstalk" with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies of Alternaria pathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes in Fusarium species offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.
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Affiliation(s)
- Thomas E. Witte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Villeneuve
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David P. Overy
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
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15
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Wang M, Luo X, Wang H. First Draft Genome Sequence Resource of Colletotrichum liriopes Causing Leaf Anthracnose on Ophiopogon japonicus. PLANT DISEASE 2021; 105:1179-1182. [PMID: 33258434 DOI: 10.1094/pdis-11-20-2326-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Leaf anthracnose of Ophiopogon japonicus is an important disease that can significantly reduce the quality and economic value of this traditional Chinese medicinal plant. The disease is caused by Colletotrichum liriopes, a necrotrophic fungus that belongs to the Glomerellaceae family of the Sordariomycetes class. Here, we present the draft whole-genome sequence of the C. liriopes strain A2 that caused leaf anthracnose on O. japonicus. The assembly consists of 407 contigs with an estimated genome size of 53.1 Mb. Furthermore, we identified 670 carbohydrate-active enzymes, 1,377 secreted proteins, and 60 secondary metabolite gene clusters, which may be associated with the pathogenicity of this pathogen. This genome resource will provide a valuable resource for future research on the pathogenesis of C. liriopes and comparative genome analyses within genus Colletotrichum.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiujun Luo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
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16
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Li L, Ma H, Zheng F, Chen Y, Wang M, Jiao C, Li H, Gai Y. The transcription regulator ACTR controls ACT-toxin biosynthesis and pathogenicity in the tangerine pathotype of Alternaria alternata. Microbiol Res 2021; 248:126747. [PMID: 33740671 DOI: 10.1016/j.micres.2021.126747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
The host-selective ACT toxin is essential for the pathogenesis of the citrus fungal pathogen Alternaria alternata. However, the mechanism of ACT-toxin gene clusters ACT-toxin biosynthesis regulated by is still poorly understood. The biosynthesis of ACT toxin is mainly regulated by multiple ACT toxin genes located in the secondary metabolite gene cluster. In this study, we reported a transcription regulator ACTR contributes ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 in Alternaria alternata. We generated ACTR-disrupted and -silenced mutants in the tangerine pathotype of A. alternata. Phenotype analysis showed that the ACTR mutants displayed a significant loss of ACT toxin production and a decreased virulence on citrus leaves whereas the vegetative growth and sporulation were not affected, indicating an essential role of ACTR in both ACT toxin biosynthesis and pathogenicity. To elucidate the transcription network of ACTR, we performed RNA-Seq experiments on wild-type and ACTR null mutant and identified genes that were differentially expressed between two genotypes. Transcriptome profiling and RT-qPCR analysis demonstrated that the ACT toxin biosynthetic gene ACTS4 is down-regulated in ACTR mutant. We generated ACTS4 knock-down mutant and found that the pathogenicity of ACTS4 mutant was severely impaired. Interestingly, both ACTR and ACTS4 are not involved in the response to different abiotic stresses including oxidative stress, salt stress, cell-wall disrupting regents, and metal ion stress, indicating the function of these two genes is highly specific. In conclusion, our results highlight the important regulatory role of ACTR in ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 and underline the essential role of in the tangerine pathotype of A. alternata.
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Affiliation(s)
- Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Haijie Ma
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Fang Zheng
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meiqin Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; Boyce Thompson Institute, Ithaca, NY, USA
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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17
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Wang M, Hou X, Wang H. Genomic Sequence Resource of Alternaria alternata Strain B3 Causing Leaf Blight on Ophiopogon japonicus. PLANT DISEASE 2021; 105:684-687. [PMID: 32865479 DOI: 10.1094/pdis-07-20-1454-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Black spot of Ophiopogon japonicus is an economically important disease, which can result in significant losses of both yield and quality of this traditional Chinese medicinal plant. The disease is caused by the small-spored fungal pathogen Alternaria alternata, a necrotrophic fungus that is ubiquitously distributed in the environment. Here, we present the draft whole-genome sequence of A. alternata strain B3 that caused black spot on O. japonicus. The assembly consists of 76 contigs with an estimated genome size of 33.8 Mb. Furthermore, we identified genes that may be associated with the pathogenicity, such as carbohydrate-active enzymes, secreted proteins, and secondary metabolite gene clusters. This genome resource will provide a useful source for future research on the evolution of pathogenicity of A. alternata and phylogenomic analysis in delineating phylogenetic lineages within the genus Alternaria.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Xin Hou
- College of Plant Protection, Shandong Agricultural University, Shandong Key Laboratory of Agricultural Microbiology, Tai'an 271018, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
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18
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The critical role of MetR/ MetB/ MetC/ MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata. Appl Environ Microbiol 2021; 87:AEM.01911-20. [PMID: 33277273 PMCID: PMC7851696 DOI: 10.1128/aem.01911-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Methionine is a unique sulfur-containing amino acid, which plays an important role in biological protein synthesis and various cellular processes. Here, we characterized the biological functions of AaMetB, AaMetC, and AaMetX in the tangerine pathotype of Alternaria alternata Morphological analysis showed that the mutants lacking AaMetB, AaMetC, or AaMetX resulted in less aerial hypha and fewer conidia in artificial media. Pathogenicity analysis showed that AaMetB, AaMetC, and AaMetX are required for full virulence. The defects in vegetative growth, conidiation and virulence of ΔMetB, ΔMetC, and ΔMetX can be restored by exogenous methionine and homocysteine, indicating that AaMetB, AaMetC, and AaMetX are required for methionine biosynthesis. However, exogenous cysteine only restored the growth and virulence defects of ΔMetR but not ΔMetB/C/X, suggesting that AaMetR is essential for cysteine biosynthesis. Oxidant sensitivity assay showed that only ΔMetR is sensitive to H2O2 and many ROS-generating compounds, indicating that AaMetR is essential for oxidative tolerance. Interestingly, fungicides indoor bioassays showed that only the ΔMetR mutants are susceptive to chlorothalonil, a fungicide that could bind to the cysteine of glyceraldehyde-3-phosphate dehydrogenase. Comparative transcriptome analysis showed that the inactivation of MetB, MetC, MetX, or MetR significantly affected the expression of methionine metabolism-related genes. Moreover, the inactivation of AaMetR significantly affected the expression of many genes related to glutathione metabolism, which is essential for ROS tolerance. Taken together, our study provides genetic evidence to define the critical roles of AaMetB, AaMetC, AaMetX, and AaMetR in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata IMPORTANCE The transcription factor METR regulating methionine metabolism is essential for reactive oxygen species (ROS) tolerance and virulence in many phytopathogenic fungi. However, the underlying regulatory mechanism of METR involved in this process is still unclear. In the present study, we generated AaMetB, AaMetC and AaMetX deletion mutants and compared these mutants with AaMetR disrupted mutants. Interestingly, we found that AaMetB, AaMetC and AaMetX are required for vegetative growth, conidiation, and pathogenicity in Alternaria alternata, but not for ROS tolerance and cysteine metabolism. Furthermore, we found that METR is involved in the biosynthesis of cysteine, which is an essential substrate for the biosynthesis of methionine and glutathione. This study emphasizes the critical roles of MetR, MetB, MetC, MetX in the regulation of cysteine and methionine metabolism, as well as the cross-link with glutathione-mediated ROS tolerance in phytopathogenic fungi, which provides a foundation for future investigations.
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Wang M, Fu H, Ruan R. A Small Horizontally Transferred Gene Cluster Contributes to the Sporulation of Alternaria alternata. Genome Biol Evol 2020; 11:3436-3444. [PMID: 31764979 PMCID: PMC6916707 DOI: 10.1093/gbe/evz257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2019] [Indexed: 12/17/2022] Open
Abstract
Horizontal gene transfer (HGT) has been identified as an important source of genomic innovation in fungi. However, how HGT drove the evolution of Alternaria alternata, a necrotrophic fungus which can be ubiquitously isolated from soil and various plants and decaying plant materials is largely known. In this study, we identified 12 protein-encoding genes that are likely acquired from lineages outside Pezizomycotina. Phylogenetic trees and approximately unbiased comparative topology tests strongly supported the evolutionary origin of these genes. According to their predicted functions, these HGT candidates are involved in nitrogen and carbohydrate metabolism. Especially, five genes of them were likely transferred as a physically linked cluster from Tremellales (Basidiomycota). Functionally knocking out the five-gene cluster in an A. alternata isolate causing citrus brown spot resulted in an 80% decrease in asexual spore production in the deletion mutant. We further knocked out each of these five genes in this cluster and the resultant single-gene deletion mutants exhibited a various degree of reduction in spore production. Except for conidiation, functions of these genes associated with vegetative growth, stress tolerance, and virulence are very limited. Our results provide new evidence that HGT has played important roles over the course of the evolution of filamentous fungi.
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Affiliation(s)
- Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huilan Fu
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruoxin Ruan
- Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Hangzhou Academy of Agricultural Sciences, Hangzhou, China
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