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Yang X, Cao S, Sun H, Deng Y, Zhang X, Li Y, Ma D, Chen H, Li W. The critical roles of the Zn 2Cys 6 transcription factor Fp487 in the development and virulence of Fusarium pseudograminearum: A potential target for Fusarium crown rot control. Microbiol Res 2024; 285:127784. [PMID: 38824820 DOI: 10.1016/j.micres.2024.127784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
Fusarium crown rot (FCR) caused by Fusarium pseudograminearum poses a significant threat to wheat production in the Huang-Huai-Hai region of China. However, the pathogenic mechanism of F. pseudograminearum is still poorly understood. Zn2Cys6 transcription factors, which are exclusive to fungi, play pivotal roles in regulating fungal development, drug resistance, pathogenicity, and secondary metabolism. In this study, we present the functional characterization of a Zn2Cys6 transcription factor F. pseudograminearum, designated Fp487. In F. pseudograminearum, Fp487 is shown to be required for mycelial growth through gene knockout and phenotypic analyses. Compared with wild-type CF14047, the ∆Fp487 mutant displayed a slight reduction in growth rate but a significant decrease in conidiogenesis, pathogenicity and 3-acetyl-deoxynivalenol (3AcDON) production. Moreover, the mutant exhibited heightened sensitivity to oxidative and cytomembrane stress. Furthermore, we synthesized dsRNA from the Fp487 gene in vitro, resulting in a reduction in the growth rate of F. pseudograminearum and its virulence on barley leaves through spray-induced gene silencing (SIGS). Notably, this study makes the first instance of inducing the expression of abundant dsRNA from F. pseudograminearum by engineering the Escherichia coli strain HT115 (DE3) and utilizing the SIGS technique to evaluate the virulence effect of dsRNA on F. pseudograminearum. In conclusion, our findings revealed the crucial role of Fp487 in regulating pathogenicity, stress responses, DON production, and conidiogenesis in F. pseudograminearum. Furthermore, Fp487 is a potential RNAi-based target for FCR control.
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Affiliation(s)
- Xiaoyue Yang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Haiyan Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yuanyu Deng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xin Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Yan Li
- Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Dongfang Ma
- Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, Hubei 434025, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu 225009, China.
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2
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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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Li S, Zhu H, He Y, Hong N, Wang G, Wang L. BdCV1-Encoded P3 Silencing Suppressor Identification and Its Roles in Botryosphaeria dothidea, Causing Pear Ring Rot Disease. Cells 2023; 12:2386. [PMID: 37830600 PMCID: PMC10571871 DOI: 10.3390/cells12192386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Pear ring rot disease is an important branch disease, caused by Botryosphaeria dothidea. With the discovery of fungal viruses, the use of their attenuated properties for biological control provides a new strategy for the biological control of fungal disease. RNA silencing is a major antiviral defense mechanism in plants, insects, and fungi. Viruses encode and utilize RNA silencing suppressors to suppress host defenses. Previous studies revealed that Botryosphaeria dothidea chrysovirus 1 (BdCV1) exhibited weak pathogenicity and could activate host gene silencing by infecting B. dothidea. The aim of our study was to investigate whether BdCV1 can encode a silencing suppressor and what effect it has on the host. In this study, the capability of silencing inhibitory activity of four BdCV1-encoded proteins was analyzed, and the P3 protein was identified as a BdCV1 RNA silencing suppressor in the exotic host Nicotiana benthamiana line 16c. In addition, we demonstrated that P3 could inhibit local silencing, block systemic RNA silencing, and induce the necrosis reaction of tobacco leaves. Furthermore, overexpression of P3 could slow down the growth rate and reduce the pathogenicity of B. dothidea, and to some extent affect the expression level of RNA silencing components and virus-derived siRNAs (vsiRNAs). Combined with transcriptomic analysis, P3 had an effect on the gene expression and biological process of B. dothidea. The obtained results provide new theoretical information for further study of interaction between BdCV1 P3 as a potential silencing suppressor and B. dothidea.
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Affiliation(s)
- Shanshan Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Haodong Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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Wang D, Zhang Y, Zhou S, Zhang X, Liu S, Li X, Liu Z. Gcc1 homologs regulate growth, oxidative stress, conidiation and appressorium formation in Colletotrichum siamense and Colletotrichum graminicola. Microb Pathog 2023; 182:106249. [PMID: 37437644 DOI: 10.1016/j.micpath.2023.106249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
The Zn2Cys6 transcription factor is a fungal-specific zinc finger protein, which plays an important role in regulating growth, development and pathogenicity of pathogenic fungi. In this study, we characterized two Zn2Cys6 transcription factors, CsGcc1 and CgrGcc1 in Colletotrichum siamense and C. graminicola, respectively, which are homologous to Gcc1 in Magnaporthe oryzae. Both CsGcc1 and CgrGcc1 contain a typical GAL4 DNA-binding domain. Deletion of CsGCC1 or CgrGCC1 decreased the growth rate and lowered the tolerance to H2O2. In addition, disrupting CsGCC1 reduced conidial yield and lowered the germination rate and appressorium formation rate of C. siamense. Cellophane assays showed that deletion of CsGCC1 also weakened the penetration ability of appressoria. In C. graminicola, CgrGcc1 did not affect the production and germination of oval conidia, but its deletion significantly decreased the yield of the falcate conidium, and led to abnormal appressorium formation. In terms of pathogenicity, CsGcc1 slightly reduced the virulence of C. siamense, while deleting CgrGcc1 did not affect virulence of C. graminicola. In conclusion, the Zn2Cys6 transcription factors CsGcc1 and CgrGcc1 are involved in the regulation of vegetative growth, oxidative stress, conidial/falcate conidial production and appressorium formation in C. siamense and C. graminicola.
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Affiliation(s)
- Diguang Wang
- School of Life Sciences, Hainan University, Haikou, China
| | - Ying Zhang
- School of Life Sciences, Hainan University, Haikou, China
| | | | - Xingyuan Zhang
- School of Life Sciences, Hainan University, Haikou, China
| | - Shayu Liu
- School of Life Sciences, Hainan University, Haikou, China
| | - Xiaoyu Li
- School of Life Sciences, Hainan University, Haikou, China; One Health Institute, Hainan University, Haikou, China.
| | - Zhiqiang Liu
- School of Life Sciences, Hainan University, Haikou, China; One Health Institute, Hainan University, Haikou, China.
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Diao Y, Jin J, Xiong X, Yu C, Tian Y, Li D, Liu H. Transcription Factor VM1G_06867: A Requirement for Growth, Pathogenicity, Development, and Maintenance of Cell Wall Integrity in Valsa mali. J Fungi (Basel) 2023; 9:692. [PMID: 37367628 DOI: 10.3390/jof9060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
Apple canker disease, caused by Valsa mali, is one of the most serious apple tree diseases in China. VmSom1 is an important transcription factor that acts on the cyclic adenosine signaling pathway (cAMP/PKA), regulating the growth, development, morphological differentiation, and pathogenic forces of the pathogen. We perform transcriptome analysis of the VmSom1 deletion mutant and the wild-type strain 11-175 and identify a significantly differentially expressed gene, VM1G_06867, a zinc finger motif transcription factor in V. mali. In this study, we obtain the VM1G_06867 gene using the single deletion mutant via homologous recombination. To determine the relationship between VmSom1 and VM1G_06867, we also obtain a double deletion mutant ΔVmSom1/06867. Compared to the wild-type strain 11-175, the single deletion mutant VM1G_06867 shows a drastic reduction in growth rate and forms more pycnidia on the PDA medium. Additionally, the growth of the mutant is inhibited by SDS, Congo red, and fluorescent brighteners. In comparison to the single deletion mutant VmSom1, the double deletion mutant ΔVmSom1/06867 shows no significant change in growth or conidiation and is unable to produce conidia. The growth rate is significantly increased in Congo red, NaCl, and Sorbitol mediums. These results demonstrate that VM1G_06867 plays important roles in growth, pathogenicity, asexual development, and maintenance of cell wall integrity. VM1G_06867 can recover osmotic stress and cell wall integrity defects caused by the deletion of VmSom1, as well as restore the loss of pathogenicity caused by the deletion of the VmSom1 gene, but not completely.
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Affiliation(s)
- Yufei Diao
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Jiyang Jin
- Mountain Tai Forest Ecosystem Research Station of State Forestry Administration, Forestry College, Shandong Agricultural University, Tai'an 271018, China
| | - Xiong Xiong
- Mountain Tai Forest Ecosystem Research Station of State Forestry Administration, Forestry College, Shandong Agricultural University, Tai'an 271018, China
| | - Chengming Yu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Yehan Tian
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Duochuan Li
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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6
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See PT, Moffat CS. Profiling the Pyrenophora tritici-repentis secretome: The Pf2 transcription factor regulates the secretion of the effector proteins ToxA and ToxB. Mol Microbiol 2023; 119:612-629. [PMID: 37059688 DOI: 10.1111/mmi.15058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 02/13/2023] [Accepted: 03/19/2023] [Indexed: 04/16/2023]
Abstract
The global wheat disease tan spot is caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr) which secretes necrotrophic effectors to facilitate host plant colonization. We previously reported a role of the Zn2 Cys6 binuclear cluster transcription factor Pf2 in the regulation of the Ptr effector ToxA. Here, we show that Pf2 is also a positive regulator of ToxB, via targeted deletion of PtrPf2 which resulted in reduced ToxB expression and defects in conidiation and pathogenicity. To further investigate the function of Ptr Pf2 in regulating protein secretion, the secretome profiles of two Δptrpf2 mutants of two Ptr races (races 1 and 5) were evaluated using a SWATH-mass spectrometry (MS) quantitative approach. Analysis of the secretomes of the Δptrpf2 mutants from in vitro culture filtrate identified more than 500 secreted proteins, with 25% unique to each race. Of the identified proteins, less than 6% were significantly differentially regulated by Ptr Pf2. Among the downregulated proteins were ToxA and ToxB, specific to race 1 and race 5 respectively, demonstrating the role of Ptr Pf2 as a positive regulator of both effectors. Significant motif sequences identified in both ToxA and ToxB putative promoter regions were further explored via GFP reporter assays.
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Affiliation(s)
- Pao Theen See
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australian, 6102, Australia
| | - Caroline S Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australian, 6102, Australia
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7
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Transcription factor lineages in plant-pathogenic fungi, connecting diversity with fungal virulence. Fungal Genet Biol 2022; 161:103712. [PMID: 35667520 DOI: 10.1016/j.fgb.2022.103712] [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: 12/16/2021] [Revised: 05/18/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022]
Abstract
Plant-pathogenic fungi span diverse taxonomic lineages. Their host-infection strategies are often specialised and require the coordinated regulation of molecular virulence factors. Transcription factors (TFs) are fundamental regulators of gene expression, yet relatively few virulence-specific regulators are characterised in detail and their evolutionary trajectories are not well understood. Hence, this study compared the full range of TFs across taxonomically-diverse fungal proteomes and classified their lineages through an orthology analysis. The primary aims were to characterise differences in the range and profile of TF lineages broadly linked to plant-host association or pathogenic lifestyles, and to better characterise the evolutionary origin and trajectory of experimentally-validated virulence regulators. We observed significantly fewer TFs among obligate, host-associated pathogens, largely attributed to contractions in several Zn2Cys6 TF-orthogroup lineages. We also present novel insight into the key virulence-regulating TFs Ste12, Pf2 and EBR1, providing evidence for their ancestral origins, expansion and/or loss. Ultimately, the analysis presented here provides both primary evidence for TF evolution in fungal phytopathogenicity, as well as a practical phylogenetic resource to guide further detailed investigation on the regulation of virulence within key pathogen lineages.
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Li Y, Li S, Liang Z, Cai Q, Zhou T, Zhao C, Wu X. RNA-seq Analysis of Rhizoctonia solani AG-4HGI Strain BJ-1H Infected by a New Viral Strain of Rhizoctonia solani Partitivirus 2 Reveals a Potential Mechanism for Hypovirulence. PHYTOPATHOLOGY 2022; 112:1373-1385. [PMID: 34965159 DOI: 10.1094/phyto-08-21-0349-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizoctonia solani partitivirus 2 (RsPV2), in the genus Alphapartitivirus, confers hypovirulence on R. solani AG-1-IA, the causal agent of rice sheath blight. In this study, a new strain of RsPV2 obtained from R. solani AG-4HGI strain BJ-1H, the causal agent of black scurf on potato, wasidentified and designated as Rhizoctonia solani partitivirus 2 strain BJ-1H (RsPV2-BJ). An RNA sequencing analysis of strain BJ-1H and the virus RsPV2-BJ-free strain BJ-1H-VF derived from strain BJ-1H was conducted to investigate the potential molecular mechanism of hypovirulence induced by RsPV2-BJ. In total, 14,319 unigenes were obtained, and 1,341 unigenes were identified as differentially expressed genes (DEGs), with 570 DEGs being down-regulated and 771 being up-regulated. Notably, several up-regulated DEGs were annotated to cell wall degrading enzymes, including β-1,3-glucanases. Strain BJ-1H exhibited increased expression of β-1,3-glucanase after RsPV2-BJ infection, suggesting that cell wall autolysis activity in R. solani AG-4HGI strain BJ-1H might be promoted by RsPV2-BJ, inducing hypovirulence in its host fungus R. solani AG-4HGI. To the best of our knowledge, this is the first report on the potential mechanism of hypovirulence induced by a mycovirus in R. solani.
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Affiliation(s)
- Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Zhijian Liang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Qingnian Cai
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
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He F, Kange AM, Yang J, Xiao J, Wang R, Yang L, Jia Y, Fu ZQ, Zhao Y, Liu F. The Transcription Factor VpxlnR Is Required for the Growth, Development, and Virulence of the Fungal Pathogen Valsa pyri. Front Microbiol 2022; 13:784686. [PMID: 35308334 PMCID: PMC8928461 DOI: 10.3389/fmicb.2022.784686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Pears (Pyrus sp.) are widely cultivated in China, and their yield accounts for more than 60% of global pear production. The fungal pathogen Valsa pyri is a major causal agent of pear canker disease, which results in enormous losses of pear production in northern China. In this study, we characterized a Zn2Cys6 transcription factor that contains one GAL4 domain and a fungal-trans domain, which are present in VpxlnR. The vpxlnR gene expression was upregulated in the invasion stage of V. pyri. To investigate its functions, we constructed gene deletion mutants and complementary strains. We observed that the growth of the vpxlnR mutants was reduced on potato dextrose agar (PDA), Czapek plus glucose or sucrose compared with that of the wild-type strain. Additionally, vpxlnR mutants exhibited loss of function in fruiting body formation. Moreover, vpxlnR mutants were more susceptible to hydrogen peroxide (H2O2) and salicylic acid (SA) and were reduced in their virulence at the early infection stage. According to a previous study, VpxlnR-interacting motifs containing NRHKGNCCGM were searched in the V. pyri genome, and we obtained 354 target genes, of which 148 genes had Clusters of Orthologous Groups (COG) terms. PHI-BLAST was used to identify virulence-related genes, and we found 28 hits. Furthermore, eight genes from the 28 PHI-BLAST hits were further assessed by yeast one-hybrid (Y1H) assays, and five target genes, salicylate hydroxylase (VP1G_09520), serine/threonine-protein kinase (VP1G_03128), alpha-xylosidase (VP1G_06369), G-protein beta subunit (VP1G_02856), and acid phosphatase (VP1G_03782), could interact with VpxlnR in vivo. Their transcript levels were reduced in one or two vpxlnR mutants. Taken together, these findings imply that VpxlnR is a key regulator of growth, development, stress, and virulence through controlling genes involved in signaling pathways and extracellular enzyme activities in V. pyri. The motifs interacting with VpxlnR also provide new insights into the molecular mechanism of xlnR proteins.
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Affiliation(s)
- Feng He
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Alex-Machio Kange
- Department of Agriculture and Natural Resource, Bomet University College, Bomet, Kenya
| | - Jie Yang
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jiaxin Xiao
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Rongbo Wang
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, China
| | - Lu Yang
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yifan Jia
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- *Correspondence: Yancun Zhao,
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Fengquan Liu,
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10
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Piombo E, Dubey M. Computational Analysis of HTS Data and Its Application in Plant Pathology. Methods Mol Biol 2022; 2536:275-307. [PMID: 35819611 DOI: 10.1007/978-1-0716-2517-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Piombo E, Vetukuri RR, Broberg A, Kalyandurg PB, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M. Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions. Microbiol Spectr 2021; 9:e0109921. [PMID: 34549988 PMCID: PMC8557909 DOI: 10.1128/spectrum.01099-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Dicer-like proteins (DCLs) play a vital role in RNA interference (RNAi), by cleaving RNA filament into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in mycoparasitic interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and characterize the functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced secondary metabolite production, antagonism toward the plant-pathogenic fungus Botrytis cinerea, and reduced ability to control Fusarium foot rot disease on wheat, caused by Fusarium graminearum. Transcriptome sequencing of the in vitro interaction between the C. rosea Δdcl2 strain and B. cinerea or F. graminearum identified the downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes, and secondary metabolites biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild-type interaction. A total of 61 putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 were downregulated in the Δdcl2 mutant. In addition to putative endogenous gene targets, these milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Δdcl2 mutant incapable of producing the targeting milRNAs. In summary, this study constitutes the first step in elucidating the role of RNAi in mycoparasitic interactions, with important implications for biological control of plant diseases, and poses the base for future studies focusing on the role of cross-species RNAi regulating mycoparasitic interactions. IMPORTANCE Small RNAs mediated RNA interference (RNAi) known to regulate several biological processes. Dicer-like endoribonucleases (DCLs) play a vital role in the RNAi pathway by generating sRNAs. In this study, we investigated a role of DCL-mediated RNAi in interference interactions between mycoparasitic fungus Clonostachys rosea and the two fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohosts). We found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohosts, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and poses a base for future works studying the role of DCL-based cross-species RNAi in fungal interactions.
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Affiliation(s)
- Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pruthvi B. Kalyandurg
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sandeep Kushwaha
- Department of Plant Breeding, Horticum, Swedish University of Agricultural Sciences, Lomma, Sweden
- National Institute of Animal Biotechnology, Hyderabad, Telangana, India
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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12
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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13
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Zuriegat Q, Zheng Y, Liu H, Wang Z, Yun Y. Current progress on pathogenicity-related transcription factors in Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2021; 22:882-895. [PMID: 33969616 PMCID: PMC8232035 DOI: 10.1111/mpp.13068] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 05/03/2023]
Abstract
Fusarium oxysporum is a well-known soilborne plant pathogen that causes severe vascular wilt in economically important crops worldwide. During the infection process, F. oxysporum not only secretes various virulence factors, such as cell wall-degrading enzymes (CWDEs), effectors, and mycotoxins, that potentially play important roles in fungal pathogenicity but it must also respond to extrinsic abiotic stresses from the environment and the host. Over 700 transcription factors (TFs) have been predicted in the genome of F. oxysporum, but only 26 TFs have been functionally characterized in various formae speciales of F. oxysporum. Among these TFs, a total of 23 belonging to 10 families are required for pathogenesis through various mechanisms and pathways, and the zinc finger TF family is the largest family among these 10 families, which consists of 15 TFs that have been functionally characterized in F. oxysporum. In this review, we report current research progress on the 26 functionally analysed TFs in F. oxysporum and sort them into four groups based on their roles in F. oxysporum pathogenicity. Furthermore, we summarize and compare the biofunctions, involved pathways, putative targets, and homologs of these TFs and analyse the relationships among them. This review provides a systematic analysis of the regulation of virulence-related genes and facilitates further mechanistic analysis of TFs important in F. oxysporum virulence.
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Affiliation(s)
- Qussai Zuriegat
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yuru Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Institute for Food and Drug Quality ControlFuzhouChina
| | - Hong Liu
- College of Resources and EnvironmentFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Yingzi Yun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsCollege of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
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Chambers KR, Van de Wouw AP, Gardiner DM, Elliott CE, Idnurm A. A conserved Zn 2Cys 6 transcription factor, identified in a spontaneous mutant from in vitro passaging, is involved in pathogenicity of the blackleg fungus Leptosphaeria maculans. Fungal Biol 2021; 125:541-550. [PMID: 34140150 DOI: 10.1016/j.funbio.2021.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022]
Abstract
Continuous passaging in vitro can lead to the accumulation of changes in DNA sequence that potentially affect the properties of microbes, making them different from the original isolates. The identification of such genetic alterations is rare in fungi. A set of insertional mutants in the plant pathogenic fungus Leptosphaeria maculans, all derived from the same transformation experiment, had independent Agrobacterium T-DNA insertions and reduced pathogenicity on canola (Brassica napus). None of the insertions co-segregated in progeny from crosses with the reduction in pathogenicity. Genome sequences of three strains were analysed, and a mutation identified in a gene (ptf1, for pathogenicity-associated transcription factor 1) encoding a putative Zn2(II)Cys6 transcription factor. Homologs are found in other ascomycetes, and are required for pathogenicity by Fusarium graminearum, Fusarium oxysporum and Magnaporthe oryzae. The mutation in the L. maculans ptf1 gene co-segregates in progeny from crosses with the reduction in pathogenicity, a strain with an independent mutant allele isolated using CRISPR-Cas9 editing has reduced pathogenicity, and addition of wild type copies of the gene restores pathogenicity. Thus, this work defines a base pair substitution that occurred during in vitro passaging of a fungus that contributed to an attenuation of pathogenicity.
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Affiliation(s)
- Kylie R Chambers
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia; Department of Primary Industries and Regional Development, Northam, WA, 6401, Australia
| | | | - Donald M Gardiner
- CSIRO Agriculture and Food, St Lucia, Brisbane, QLD, 4067, Australia
| | - Candace E Elliott
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia.
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15
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Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics. Microorganisms 2020; 8:microorganisms8020305. [PMID: 32098375 PMCID: PMC7075021 DOI: 10.3390/microorganisms8020305] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 01/19/2023] Open
Abstract
Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics.
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Kange AM, Xia A, Si J, Li B, Zhang X, Ai G, He F, Dou D. The Fungal-Specific Transcription Factor VpFSTF1 Is Required for Virulence in Valsa pyri. Front Microbiol 2020; 10:2945. [PMID: 31998257 PMCID: PMC6965324 DOI: 10.3389/fmicb.2019.02945] [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] [Received: 09/09/2019] [Accepted: 12/06/2019] [Indexed: 01/12/2023] Open
Abstract
Valsa pyri is the causal agent of pear canker disease, which leads to enormous losses of pear production in eastern Asian, especially China. In this study, we identified a fungal-specific transcription factor 1 (termed as VpFSTF1) from V. pyri, which is highly conserved in fungi. To characterize its functions, we generated mutant and complementation strains in V. pyri and found that ΔVpFSTF1 mutants lost the ability to form fruiting bodies along with the reduced virulence. The radial growth of ΔVpFSTF1 mutant was sensitive to increasing concentrations of hydrogen peroxide (H2O2) and salicylic acid (SA). Moreover, RNA-sequencing (RNA-Seq) analysis of wild-type (WT) and ΔVpFSTF1 mutant strains was performed, and the results revealed 1,993 upregulated, and 2006 downregulated differentially expressed genes (DEGs) in the mutant. The DEGs were corresponding to the genes that are involved in amino acid metabolism, starch, and sucrose metabolism, gluconeogenesis, citrate cycle, and carbon metabolism. Interestingly, pathogen host interaction (PHI) analysis showed that 69 downregulated genes were related to virulence, suggesting that they might function downstream of VpFSTF1. Nine DEGs were further validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and the results were consistent with RNA-seq analysis. Furthermore, promoter regions were predicted, and VpFSTF1 binding activity was assessed. We demonstrated that five promoters are directly or indirectly targeted by VpFSTF1, including catalase-related peroxidase (VPIG_01209) and P450 family genes. Taken together, these findings indicate that VpFSTF1 is crucial for the virulence of V. pyri via direct or indirect regulation of downstream genes expression and lay an important foundation for understanding the molecular mechanism of V. pyri infection.
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Affiliation(s)
- Alex Machio Kange
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai Xia
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jierui Si
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Bingxin Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xiong Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Gan Ai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Feng He
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,School of Life Sciences, Anhui Normal University, Wuhu, China
| | - Daolong Dou
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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17
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Transcription Factors Controlling Primary and Secondary Metabolism in Filamentous Fungi: The β-Lactam Paradigm. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Sun ZB, Wang Q, Zhang J, Jiang WZ, Wang Q, Li SD, Ma GZ, Sun MH. The transcription factor-encoding gene crtf is involved in Clonostachys chloroleuca mycoparasitism on Sclerotinia sclerotiorum. Microbiol Res 2018; 210:6-11. [PMID: 29625660 DOI: 10.1016/j.micres.2018.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/28/2018] [Accepted: 03/03/2018] [Indexed: 10/17/2022]
Abstract
Clonostachys chloroleuca 67-1 (formerly C. rosea 67-1) is a potential biocontrol fungus active against various fungal plant pathogens. From transcriptome sequencing of 67-1 parasitizing sclerotia of Sclerotinia sclerotiorum, we identified the transcription factor-encoding gene crtf that is significantly up-regulated during mycoparasitism. Transcription factors are widely distributed in fungi and involved in multiple biological processes. However, their role and regulatory mechanisms in mycoparasitism remain poorly understood. In this study, the function of crtf during 67-1 mycoparasitism was verified through gene knockout and complementation. The results showed that deletion of crtf did not influence fungal morphological characteristics, but the ability of the Δcrtf mutant to parasitize sclerotia and suppress soybean Sclerotinia white mold in the greenhouse was markedly diminished compared with the wild type strain. The biocontrol activity of Δcrtf recovered wild type levels when complemented with a plasmid expressing the crtf gene. These findings suggest that crtf plays a crucial role in C. chloroleuca mycoparasitism and provide insight into the molecular mechanisms underlying C. chloroleuca mycoparasitism on plant pathogenic fungi.
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Affiliation(s)
- Zhan-Bin Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qi Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; School of Marine Science and Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Jun Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei-Zhi Jiang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qi Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Gui-Zhen Ma
- School of Marine Science and Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Targeted and random genetic modification of the black Sigatoka pathogen Pseudocercospora fijiensis by Agrobacterium tumefaciens-mediated transformation. J Microbiol Methods 2018; 148:127-137. [PMID: 29654806 DOI: 10.1016/j.mimet.2018.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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20
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Zhang W, Gui Y, Short DPG, Li T, Zhang D, Zhou L, Liu C, Bao Y, Subbarao KV, Chen J, Dai X. Verticillium dahliae transcription factor VdFTF1 regulates the expression of multiple secreted virulence factors and is required for full virulence in cotton. MOLECULAR PLANT PATHOLOGY 2018; 19:841-857. [PMID: 28520093 PMCID: PMC6638078 DOI: 10.1111/mpp.12569] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/11/2017] [Accepted: 05/13/2017] [Indexed: 05/05/2023]
Abstract
Fungal transcription factors (TFs) implicated in the regulation of virulence gene expression have been identified in a number of plant pathogens. In Verticillium dahliae, despite its agricultural importance, few regulators of transcription have been characterized. In this study, a T-DNA insertion mutant with significantly reduced virulence towards cotton was identified. The T-DNA was traced to VdFTF1, a gene encoding a TF containing a Fungal_trans domain. Transient expression in onion epidermal cells indicated that VdFTF1 is localized to the nucleus. The VdFTF1-deletion strains displayed normal vegetative growth, mycelial pigmentation and conidial morphology, but exhibited significantly reduced virulence on cotton, suggesting that VdFTF1 is required exclusively for pathogenesis. Comparisons of global transcription patterns of wild-type and VdFTF1-deletion strains indicated that VdFTF1 affected the expression of 802 genes, 233 of which were associated with catalytic processes. These genes encoded 69 potentially secreted proteins, 43 of which contained a carbohydrate enzyme domain known to participate in pathogenesis during infection of cotton. Targeted gene deletion of one VdFTF1-regulated gene resulted in significantly impaired vascular colonization, as measured by quantitative polymerase chain reaction, as well as aggressiveness and symptom severity in cotton. In conclusion, VdFTF1, which encodes a TF containing a Fungal_trans domain, regulates the gene expression of plant cell wall degradation enzymes in V. dahliae, which are required for full virulence on cotton.
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Affiliation(s)
- Wen‐Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Yue‐Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA 95616USA
| | - Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Chun Liu
- BGI‐ShenzhenShenzhenGuangdong 518083China
| | - Yu‐Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | | | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
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21
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Zhang S, Zheng X, Reiter RJ, Feng S, Wang Y, Liu S, Jin L, Li Z, Datla R, Ren M. Melatonin Attenuates Potato Late Blight by Disrupting Cell Growth, Stress Tolerance, Fungicide Susceptibility and Homeostasis of Gene Expression in Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2017; 8:1993. [PMID: 29209352 PMCID: PMC5702310 DOI: 10.3389/fpls.2017.01993] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/06/2017] [Indexed: 05/18/2023]
Abstract
Phytophthora infestans (P. infestans) is the causal agent of potato late blight, which caused the devastating Irish Potato Famine during 1845-1852. Until now, potato late blight is still the most serious threat to potato growth and has caused significant economic losses worldwide. Melatonin can induce plant innate immunity against pathogen infection, but the direct effects of melatonin on plant pathogens are poorly understood. In this study, we investigated the direct effects of melatonin on P. infestans. Exogenous melatonin significantly attenuated the potato late blight by inhibiting mycelial growth, changing cell ultrastructure, and reducing stress tolerance of P. infestans. Notably, synergistic anti-fungal effects of melatonin with fungicides on P. infestans suggest that melatonin could reduce the dose levels and enhance the efficacy of fungicide against potato late blight. A transcriptome analysis was carried out to mine downstream genes whose expression levels were affected by melatonin. The analysis of the transcriptome suggests that 66 differentially expressed genes involved in amino acid metabolic processes were significantly affected by melatonin. Moreover, the differentially expressed genes associated with stress tolerance, fungicide resistance, and virulence were also affected. These findings contribute to a new understanding of the direct functions of the melatonin on P. infestans and provide a potential ecofriendly biocontrol approach using a melatonin-based paradigm and application to prevent potato late blight.
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Affiliation(s)
- Shumin Zhang
- School of Life Sciences, Chongqing University, Chongqing, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, China
| | - Xianzhe Zheng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Shun Feng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Ying Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Sen Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liang Jin
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Raju Datla
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, SK, Canada
| | - Maozhi Ren
- School of Life Sciences, Chongqing University, Chongqing, China
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22
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Verma S, Gazara RK, Verma PK. Transcription Factor Repertoire of Necrotrophic Fungal Phytopathogen Ascochyta rabiei: Predominance of MYB Transcription Factors As Potential Regulators of Secretome. FRONTIERS IN PLANT SCIENCE 2017; 8:1037. [PMID: 28659964 PMCID: PMC5470089 DOI: 10.3389/fpls.2017.01037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/30/2017] [Indexed: 06/02/2023]
Abstract
Transcription factors (TFs) are the key players in gene expression and their study is highly significant for shedding light on the molecular mechanisms and evolutionary history of organisms. During host-pathogen interaction, extensive reprogramming of gene expression facilitated by TFs is likely to occur in both host and pathogen. To date, the knowledge about TF repertoire in filamentous fungi is in infancy. The necrotrophic fungus Ascochyta rabiei, that causes destructive Ascochyta blight (AB) disease of chickpea (Cicer arietinum), demands more comprehensive study for better understanding of Ascochyta-legume pathosystem. In the present study, we performed the genome-wide identification and analysis of TFs in A. rabiei. Taking advantage of A. rabiei genome sequence, we used a bioinformatic approach to predict the TF repertoire of A. rabiei. For identification and classification of A. rabiei TFs, we designed a comprehensive pipeline using a combination of BLAST and InterProScan software. A total of 381 A. rabiei TFs were predicted and divided into 32 fungal specific families of TFs. The gene structure, domain organization and phylogenetic analysis of abundant families of A. rabiei TFs were also carried out. Comparative study of A. rabiei TFs with that of other necrotrophic, biotrophic, hemibiotrophic, symbiotic, and saprotrophic fungi was performed. It suggested presence of both conserved as well as unique features among them. Moreover, cis-acting elements on promoter sequences of earlier predicted A. rabiei secretome were also identified. With the help of published A. rabiei transcriptome data, the differential expression of TF and secretory protein coding genes was analyzed. Furthermore, comprehensive expression analysis of few selected A. rabiei TFs using quantitative real-time polymerase chain reaction revealed variety of expression patterns during host colonization. These genes were expressed in at least one of the time points tested post infection. Overall, this study illustrates the first genome-wide identification and analysis of TF repertoire of A. rabiei. This work would provide the basis for further studies to dissect role of TFs in the molecular mechanisms during A. rabiei-chickpea interactions.
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Affiliation(s)
| | | | - Praveen K. Verma
- Plant Immunity Laboratory, National Institute of Plant Genome ResearchNew Delhi, India
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Wang S, Zhang J, Li P, Qiu D, Guo L. Transcriptome-Based Discovery of Fusarium graminearum Stress Responses to FgHV1 Infection. Int J Mol Sci 2016; 17:ijms17111922. [PMID: 27869679 PMCID: PMC5133918 DOI: 10.3390/ijms17111922] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/25/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023] Open
Abstract
Fusarium graminearum hypovirus 1 (FgHV1), which is phylogenetically related to Cryphonectria hypovirus 1 (CHV1), is a virus in the family Hypoviridae that infects the plant pathogenic fungus F. graminearum. Although hypovirus FgHV1 infection does not attenuate the virulence of the host (hypovirulence), it results in defects in mycelial growth and spore production. We now report that the vertical transmission rate of FgHV1 through asexual spores reached 100%. Using RNA deep sequencing, we performed genome-wide expression analysis to reveal phenotype-related genes with expression changes in response to FgHV1 infection. A total of 378 genes were differentially expressed, suggesting that hypovirus infection causes a significant alteration of fungal gene expression. Nearly two times as many genes were up-regulated as were down-regulated. A differentially expressed gene enrichment analysis identified a number of important pathways. Metabolic processes, the ubiquitination system, and especially cellular redox regulation were the most affected categories in F. graminearum challenged with FgHV1. The p20, encoded by FgHV1 could induce H2O2 accumulation and hypersensitive response in Nicotiana benthamiana leaves. Moreover, hypovirus FgHV1 may regulate transcription factors and trigger the RNA silencing pathway in F. graminearum.
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Affiliation(s)
- Shuangchao Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100081, China.
- Walloon Centre of Industrial Biology, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, Gembloux 5030, Belgium.
| | - Jingze Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Pengfei Li
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100081, China.
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Niño-Sánchez J, Casado-Del Castillo V, Tello V, De Vega-Bartol JJ, Ramos B, Sukno SA, Díaz Mínguez JM. The FTF gene family regulates virulence and expression of SIX effectors in Fusarium oxysporum. MOLECULAR PLANT PATHOLOGY 2016; 17:1124-39. [PMID: 26817616 PMCID: PMC6638452 DOI: 10.1111/mpp.12373] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/15/2016] [Accepted: 01/18/2016] [Indexed: 05/08/2023]
Abstract
The FTF (Fusarium transcription factor) gene family comprises a single copy gene, FTF2, which is present in all the filamentous ascomycetes analysed, and several copies of a close relative, FTF1, which is exclusive to Fusarium oxysporum. An RNA-mediated gene silencing system was developed to target mRNA produced by all the FTF genes, and tested in two formae speciales: F. oxysporum f. sp. phaseoli (whose host is common bean) and F. oxysporum f. sp. lycopersici (whose host is tomato). Quantification of the mRNA levels showed knockdown of FTF1 and FTF2 in randomly isolated transformants of both formae speciales. The attenuation of FTF expression resulted in a marked reduction in virulence, a reduced expression of several SIX (Secreted In Xylem) genes, the best studied family of effectors in F. oxysporum, and lower levels of SGE1 (Six Gene Expression 1) mRNA, the presumptive regulator of SIX expression. Moreover, the knockdown mutants showed a pattern of colonization of the host plant similar to that displayed by strains devoid of FTF1 copies (weakly virulent strains). Gene knockout of FTF2 also resulted in a reduction in virulence, but to a lesser extent. These results demonstrate the role of the FTF gene expansion, mostly the FTF1 paralogues, as a regulator of virulence in F. oxysporum and suggest that the control of effector expression is the mechanism involved.
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Affiliation(s)
- Jonathan Niño-Sánchez
- Instituto Hispano-Luso de Investigaciones Agrarias (Ciale), Departamento de Microbiología y Genética, Universidad de Salamanca, C/Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Virginia Casado-Del Castillo
- Instituto Hispano-Luso de Investigaciones Agrarias (Ciale), Departamento de Microbiología y Genética, Universidad de Salamanca, C/Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - Vega Tello
- Instituto Hispano-Luso de Investigaciones Agrarias (Ciale), Departamento de Microbiología y Genética, Universidad de Salamanca, C/Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - José J De Vega-Bartol
- Instituto de Biologia Experimental e Tecnológica/Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (IBET/ITQB-UNL), Av. República, 2784-505, Oeiras, Portugal
| | - Brisa Ramos
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid-INIA, Campus de Monteganceno, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Serenella A Sukno
- Instituto Hispano-Luso de Investigaciones Agrarias (Ciale), Departamento de Microbiología y Genética, Universidad de Salamanca, C/Río Duero 12, Villamayor, 37185, Salamanca, Spain
| | - José María Díaz Mínguez
- Instituto Hispano-Luso de Investigaciones Agrarias (Ciale), Departamento de Microbiología y Genética, Universidad de Salamanca, C/Río Duero 12, Villamayor, 37185, Salamanca, Spain
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Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 2016; 17:670. [PMID: 27552804 PMCID: PMC4994206 DOI: 10.1186/s12864-016-2941-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Wageningen UR, Wageningen, The Netherlands
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Luo K, Rocheleau H, Qi PF, Zheng YL, Zhao HY, Ouellet T. Indole-3-acetic acid in Fusarium graminearum: Identification of biosynthetic pathways and characterization of physiological effects. Fungal Biol 2016; 120:1135-45. [PMID: 27567719 DOI: 10.1016/j.funbio.2016.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
Abstract
Fusarium graminearum is a devastating pathogenic fungus causing fusarium head blight (FHB) of wheat. This fungus can produce indole-3-acetic acid (IAA) and a very large amount of IAA accumulates in wheat head tissues during the first few days of infection by F. graminearum. Using liquid culture conditions, we have determined that F. graminearum can use tryptamine (TAM) and indole-3-acetonitrile (IAN) as biosynthetic intermediates to produce IAA. It is the first time that F. graminearum is shown to use the l-tryptophan-dependent TAM and IAN pathways rather than the indole-3-acetamide or indole-3-pyruvic acid pathways to produce IAA. Our experiments also showed that exogenous IAA was metabolized by F. graminearum. Exogenous IAA, TAM, and IAN inhibited mycelial growth; IAA and IAN also affected the hyphae branching pattern and delayed macroconidium germination. IAA and TAM had a small positive effect on the production of the mycotoxin 15-ADON while IAN inhibited its production. Our results showed that IAA and biosynthetic intermediates had a significant effect on F. graminearum physiology and suggested a new area of exploration for fungicidal compounds.
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Affiliation(s)
- Kun Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi 712100, PR China; Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
| | - Hélène Rocheleau
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
| | - Peng-Fei Qi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Hui-Yan Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi 712100, PR China.
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.
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27
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Kettle AJ, Carere J, Batley J, Manners JM, Kazan K, Gardiner DM. The Fdb3 transcription factor of the Fusarium Detoxification of Benzoxazolinone gene cluster is required for MBOA but not BOA degradation in Fusarium pseudograminearum. Fungal Genet Biol 2016; 88:44-53. [PMID: 26828593 DOI: 10.1016/j.fgb.2016.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/20/2016] [Accepted: 01/28/2016] [Indexed: 11/20/2022]
Abstract
A number of cereals produce the benzoxazolinone class of phytoalexins. Fusarium species pathogenic towards these hosts can typically degrade these compounds via an aminophenol intermediate, and the ability to do so is encoded by a group of genes found in the Fusarium Detoxification of Benzoxazolinone (FDB) cluster. A zinc finger transcription factor encoded by one of the FDB cluster genes (FDB3) has been proposed to regulate the expression of other genes in the cluster and hence is potentially involved in benzoxazolinone degradation. Herein we show that Fdb3 is essential for the ability of Fusarium pseudograminearum to efficiently detoxify the predominant wheat benzoxazolinone, 6-methoxy-benzoxazolin-2-one (MBOA), but not benzoxazoline-2-one (BOA). Furthermore, additional genes thought to be part of the FDB gene cluster, based upon transcriptional response to benzoxazolinones, are regulated by Fdb3. However, deletion mutants for these latter genes remain capable of benzoxazolinone degradation, suggesting that they are not essential for this process.
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Affiliation(s)
- Andrew J Kettle
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland 4067, Australia; University of Queensland (UQ), School of Agriculture and Food Sciences, St. Lucia, Queensland 4067, Australia
| | - Jason Carere
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland 4067, Australia
| | - Jacqueline Batley
- University of Queensland (UQ), School of Agriculture and Food Sciences, St. Lucia, Queensland 4067, Australia; University of Western Australia, School of Plant Biology, Crawley, Western Australia 6009, Australia
| | - John M Manners
- CSIRO Agriculture, Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland 4067, Australia; UQ, Queensland Alliance for Agriculture & Food Innovation, St. Lucia, Brisbane, Queensland 4067, Australia
| | - Donald M Gardiner
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland 4067, Australia.
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28
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van der Lee TAJ, Medema MH. Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet Biol 2016; 89:29-36. [PMID: 26775250 DOI: 10.1016/j.fgb.2016.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/20/2022]
Abstract
Fungal natural products possess biological activities that are of great value to medicine, agriculture and manufacturing. Recent metagenomic studies accentuate the vastness of fungal taxonomic diversity, and the accompanying specialized metabolic diversity offers a great and still largely untapped resource for natural product discovery. Although fungal natural products show an impressive variation in chemical structures and biological activities, their biosynthetic pathways share a number of key characteristics. First, genes encoding successive steps of a biosynthetic pathway tend to be located adjacently on the chromosome in biosynthetic gene clusters (BGCs). Second, these BGCs are often are located on specific regions of the genome and show a discontinuous distribution among evolutionarily related species and isolates. Third, the same enzyme (super)families are often involved in the production of widely different compounds. Fourth, genes that function in the same pathway are often co-regulated, and therefore co-expressed across various growth conditions. In this mini-review, we describe how these partly interlinked characteristics can be exploited to computationally identify BGCs in fungal genomes and to connect them to their products. Particular attention will be given to novel algorithms to identify unusual classes of BGCs, as well as integrative pan-genomic approaches that use a combination of genomic and metabolomic data for parallelized natural product discovery across multiple strains. Such novel technologies will not only expedite the natural product discovery process, but will also allow the assembly of a high-quality toolbox for the re-design or even de novo design of biosynthetic pathways using synthetic biology approaches.
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Affiliation(s)
- Theo A J van der Lee
- Biointeractions & Plant Health, Plant Research International, Wageningen UR, Wageningen, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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29
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Fan HW, Noda H, Xie HQ, Suetsugu Y, Zhu QH, Zhang CX. Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle. Genome Biol Evol 2015; 7:2623-34. [PMID: 26338189 PMCID: PMC4607526 DOI: 10.1093/gbe/evv169] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change.
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Affiliation(s)
- Hai-Wei Fan
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - Hiroaki Noda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | | | | | | | - Chuan-Xi Zhang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
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30
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Niño-Sánchez J, Tello V, Casado-Del Castillo V, Thon MR, Benito EP, Díaz-Mínguez JM. Gene expression patterns and dynamics of the colonization of common bean (Phaseolus vulgaris L.) by highly virulent and weakly virulent strains of Fusarium oxysporum. Front Microbiol 2015; 6:234. [PMID: 25883592 PMCID: PMC4383042 DOI: 10.3389/fmicb.2015.00234] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The dynamics of root and hypocotyl colonization, and the gene expression patterns of several fungal virulence factors and plant defense factors have been analyzed and compared in the interaction of two Fusarium oxysporum f. sp. phaseoli strains displaying clear differences in virulence, with a susceptible common bean cultivar. The growth of the two strains on the root surface and the colonization of the root was quantitatively similar although the highly virulent (HV) strain was more efficient reaching the central root cylinder. The main differences between both strains were found in the temporal and spatial dynamics of crown root and hypocotyl colonization. The increase of fungal biomass in the crown root was considerably larger for the HV strain, which, after an initial stage of global colonization of both the vascular cylinder and the parenchymal cells, restricted its growth to the newly differentiated xylem vessels. The weakly virulent (WV) strain was a much slower and less efficient colonizer of the xylem vessels, showing also growth in the intercellular spaces of the parenchyma. Most of the virulence genes analyzed showed similar expression patterns in both strains, except SIX1, SIX6 and the gene encoding the transcription factor FTF1, which were highly upregulated in root crown and hypocotyl. The response induced in the infected plant showed interesting differences for both strains. The WV strain induced an early and strong transcription of the PR1 gene, involved in SAR response, while the HV strain preferentially induced the early expression of the ethylene responsive factor ERF2.
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Affiliation(s)
- Jonathan Niño-Sánchez
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Vega Tello
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Virginia Casado-Del Castillo
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Michael R Thon
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
| | - José María Díaz-Mínguez
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca Salamanca, Spain
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31
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Lanver D, Berndt P, Tollot M, Naik V, Vranes M, Warmann T, Münch K, Rössel N, Kahmann R. Plant surface cues prime Ustilago maydis for biotrophic development. PLoS Pathog 2014; 10:e1004272. [PMID: 25033195 PMCID: PMC4102580 DOI: 10.1371/journal.ppat.1004272] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
Infection-related development of phytopathogenic fungi is initiated by sensing and responding to plant surface cues. This response can result in the formation of specialized infection structures, so-called appressoria. To unravel the program inducing filaments and appressoria in the biotrophic smut fungus Ustilago maydis, we exposed cells to a hydrophobic surface and the cutin monomer 16-hydroxy hexadecanoic acid. Genome-wide transcriptional profiling at the pre-penetration stage documented dramatic transcriptional changes in almost 20% of the genes. Comparisons with the U. maydis sho1 msb2 double mutant, lacking two putative sensors for plant surface cues, revealed that these plasma membrane receptors regulate a small subset of the surface cue-induced genes comprising mainly secreted proteins including potential plant cell wall degrading enzymes. Targeted gene deletion analysis ascribed a role to up-regulated GH51 and GH62 arabinofuranosidases during plant penetration. Among the sho1/msb2-dependently expressed genes were several secreted effectors that are essential for virulence. Our data also demonstrate specific effects on two transcription factors that redirect the transcriptional regulatory network towards appressorium formation and plant penetration. This shows that plant surface cues prime U. maydis for biotrophic development. A basic requirement for pathogens to infect their hosts and to cause disease is to detect that they are in contact with the host surface. Plant pathogenic fungi typically respond to leaf surface contact with the development of specialized infection structures enabling the fungus to penetrate the leaf cuticle and to enter the plant tissue. In this study we analyzed the response of the corn smut fungus Ustilago maydis to two plant surface cues, such as hydrophobic surface and cutin monomers. Based on genome-wide gene expression analysis we found that these cues trigger the production of secreted plant cell wall degrading enzymes helping the fungus to penetrate the plant surface. In addition, genes were activated that code for a group of secreted proteins, so-called effectors, that affect virulence after penetration. These results demonstrate that plant surface cues trigger fungal penetration of the plant surface and also prime the fungus for later development inside plant tissue. These specific responses required two cell surface proteins that likely function as plant surface sensors.
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Affiliation(s)
- Daniel Lanver
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Patrick Berndt
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Marie Tollot
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Vikram Naik
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Miroslav Vranes
- Karlsruhe Institute of Technology (KIT), Institute for Applied Biosciences, Department of Genetics, Karlsruhe, Germany
| | - Tobias Warmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Karin Münch
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Department of Organismic Interactions, Marburg, Germany
- * E-mail:
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32
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Jonkers W, Xayamongkhon H, Haas M, Olivain C, van der Does HC, Broz K, Rep M, Alabouvette C, Steinberg C, Kistler HC. EBR1genomic expansion and its role in virulence ofFusariumspecies. Environ Microbiol 2013; 16:1982-2003. [DOI: 10.1111/1462-2920.12331] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Wilfried Jonkers
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Henry Xayamongkhon
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Matthew Haas
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Chantal Olivain
- UMR 1347 Agroécologie; INRA; BP 86510 F-21065 Dijon cedex France
| | - H. Charlotte van der Does
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Karen Broz
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - Martijn Rep
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | | | - Christian Steinberg
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - H. Corby Kistler
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
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Zhao C, Waalwijk C, de Wit PJGM, Tang D, van der Lee T. RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum. BMC Genomics 2013; 14:21. [PMID: 23324402 PMCID: PMC3577648 DOI: 10.1186/1471-2164-14-21] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/29/2012] [Indexed: 11/11/2022] Open
Abstract
Background The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum. Results We identified and revised 655 incorrectly predicted gene models, including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that many of these could be missed genes. Finally, we identified the 5′ UTR and/or 3′ UTR sequences of 7666 genes. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons. Conclusions We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum.
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Affiliation(s)
- Chunzhao Zhao
- Plant Research International, P.O. Box 6708 PB, Wageningen, The Netherlands
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Kazan K, Gardiner DM, Manners JM. On the trail of a cereal killer: recent advances in Fusarium graminearum pathogenomics and host resistance. MOLECULAR PLANT PATHOLOGY 2012; 13:399-413. [PMID: 22098555 PMCID: PMC6638652 DOI: 10.1111/j.1364-3703.2011.00762.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The ascomycete fungal pathogen Fusarium graminearum (sexual stage: Gibberella zeae) causes the devastating head blight or scab disease on wheat and barley, and cob or ear rot disease on maize. Fusarium graminearum infection causes significant crop and quality losses. In addition to roles as virulence factors during pathogenesis, trichothecene mycotoxins (e.g. deoxynivalenol) produced by this pathogen constitute a significant threat to human and animal health if consumed in respective food or feed products. In the last few years, significant progress has been made towards a better understanding of the processes involved in F. graminearum pathogenesis, toxin biosynthesis and host resistance mechanisms through the use of high-throughput genomic and phenomic technologies. In this article, we briefly review these new advances and also discuss how future research can contribute to the development of sustainable plant protection strategies against this important plant pathogen.
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Affiliation(s)
- Kemal Kazan
- CSIRO Plant Industry, Queensland Bioscience Precinct, St Lucia, Brisbane, Qld 4067, Australia.
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