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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Coca-Ruiz V, Suárez I, Aleu J, Cantoral JM, González C, Garrido C, Brito N, Collado IG. Unravelling the Function of the Sesquiterpene Cyclase STC3 in the Lifecycle of Botrytis cinerea. Int J Mol Sci 2024; 25:5125. [PMID: 38791163 PMCID: PMC11120764 DOI: 10.3390/ijms25105125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/25/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The genome sequencing of Botrytis cinerea supplies a general overview of the map of genes involved in secondary metabolite synthesis. B. cinerea genomic data reveals that this phytopathogenic fungus has seven sesquiterpene cyclase (Bcstc) genes that encode proteins involved in the farnesyl diphosphate cyclization. Three sesquiterpene cyclases (BcStc1, BcStc5 and BcStc7) are characterized, related to the biosynthesis of botrydial, abscisic acid and (+)-4-epi-eremophilenol, respectively. However, the role of the other four sesquiterpene cyclases (BcStc2, BcStc3, BcStc4 and BcStc6) remains unknown. BcStc3 is a well-conserved protein with homologues in many fungal species, and here, we undertake its functional characterization in the lifecycle of the fungus. A null mutant ΔBcstc3 and an overexpressed-Bcstc3 transformant (OvBcstc3) are generated, and both strains show the deregulation of those other sesquiterpene cyclase-encoding genes (Bcstc1, Bcstc5 and Bcstc7). These results suggest a co-regulation of the expression of the sesquiterpene cyclase gene family in B. cinerea. The phenotypic characterization of both transformants reveals that BcStc3 is involved in oxidative stress tolerance, the production of reactive oxygen species and virulence. The metabolomic analysis allows the isolation of characteristic polyketides and eremophilenols from the secondary metabolism of B. cinerea, although no sesquiterpenes different from those already described are identified.
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Affiliation(s)
- Víctor Coca-Ruiz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Ivonne Suárez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Jesús M. Cantoral
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
- Instituto de Investigación Vitivinícola y Agroalimentaria (IVAGRO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Celedonio González
- Área de Bioquímica y Biología Molecular, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Tenerife, Spain;
| | - Carlos Garrido
- Laboratorio de Microbiología, Departamento de Biomedicina, Biotecnología y Salud Pública, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (J.M.C.); (C.G.)
- Instituto de Investigación Vitivinícola y Agroalimentaria (IVAGRO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Nélida Brito
- Área de Bioquímica y Biología Molecular, Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Tenerife, Spain;
| | - Isidro G. Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain; (V.C.-R.); (I.S.); (J.A.)
- Instituto de Investigación en Biomoléculas (INBIO), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
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de Oliveira TC, Freyria NJ, Sarmiento-Villamil JL, Porth I, Tanguay P, Bernier L. Unraveling the transcriptional features and gene expression networks of pathogenic and saprotrophic Ophiostoma species during the infection of Ulmus americana. Microbiol Spectr 2024; 12:e0369423. [PMID: 38230934 PMCID: PMC10845970 DOI: 10.1128/spectrum.03694-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
American elm (Ulmus americana), highly prized for its ornamental value, has suffered two successive outbreaks of Dutch elm disease (DED) caused by ascomycete fungi belonging to the genus Ophiostoma. To identify the genes linked to the pathogenicity of different species and lineages of Ophiostoma, we inoculated 2-year-old U. americana saplings with six strains representing three species of DED fungi, and one strain of the saprotroph Ophiostoma quercus. Differential expression analyses were performed following RNA sequencing of fungal transcripts recovered at 3- and 10-days post-infection. Based on a total of 8,640 Ophiostoma genes, we observed a difference in fungal gene expression depending on the strain inoculated and the time of incubation in host tissue. Some genes overexpressed in the more virulent strains of Ophiostoma encode hydrolases that possibly act synergistically. A mutant of Ophiostoma novo-ulmi in which the gene encoding the ogf1 transcription factor had been deleted did not produce transcripts for the gene encoding the hydrophobin cerato-ulmin and was less virulent. Weighted gene correlation network analyses identified several candidate pathogenicity genes distributed among 13 modules of interconnected genes.IMPORTANCEOphiostoma is a genus of cosmopolitan fungi that belongs to the family Ophiostomataceae and includes the pathogens responsible for two devastating pandemics of Dutch elm disease (DED). As the mechanisms of action of DED agents remain unclear, we carried out the first comparative transcriptomic study including representative strains of the three Ophiostoma species causing DED, along with the phylogenetically close saprotrophic species Ophiostoma quercus. Statistical analyses of the fungal transcriptomes recovered at 3 and 10 days following infection of Ulmus americana saplings highlighted several candidate genes associated with virulence and host-pathogen interactions wherein each strain showed a distinct transcriptome. The results of this research underscore the importance of investigating the transcriptional behavior of different fungal taxa to understand their pathogenicity and virulence in relation to the timeline of infection.
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Affiliation(s)
- Thais C. de Oliveira
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
| | - Nastasia J. Freyria
- Department of Natural Resource Sciences, McGill University, St. Anne-de-Bellevue, Quebec, Quebec, Canada
| | - Jorge Luis Sarmiento-Villamil
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
- Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga (IHSM-CSIC-UMA), Estación Experimental “La Mayora”, Málaga, Spain
| | - Ilga Porth
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, Québec, Quebec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
- Centre d’étude de la Forêt, Faculté de foresterie, de géographie et de géomatique, Université Laval, Québec, Quebec, Canada
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Qiu C, Halterman D, Zhang H, Liu Z. Multifunctionality of AsCFEM6 and AsCFEM12 effectors from the potato early blight pathogen Alternaria solani. Int J Biol Macromol 2024; 257:128575. [PMID: 38048930 DOI: 10.1016/j.ijbiomac.2023.128575] [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: 09/26/2023] [Revised: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Plant pathogens secrete fungal-specific common in several fungal extracellular membrane (CFEM) effectors to manipulate host immunity and contribute to their virulence. Little is known about effectors and their functions in Alternaria solani, the necrotrophic fungal pathogen causing potato early blight. To identify candidate CFEM effector genes, we mined A. solani genome databases. This led to the identification of 12 genes encoding CFEM proteins (termed AsCFEM1-AsCFEM12) and 6 of them were confirmed to be putative secreted effectors. In planta expression revealed that AsCFEM6 and AsCFEM12 have elicitor function that triggers plant defense response including cell death in different botanical families. Targeted gene disruption of AsCFEM6 and AsCFEM12 resulted in a change in spore development, significant reduction of virulence on potato and eggplant susceptible cultivars, increased resistance to fungicide stress, variation in iron acquisition and utilization, and the involvement in 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis pathway. Using maximum likelihood method, we found that positive selection likely caused the polymorphism within AsCFEM6 and AsCFEM12 homologs in different Alternaria spp. Site-directed mutagenesis analysis indicated that positive selection sites within their CFEM domains are required for cell death induction in Nicotiana benthamiana and are critical for response to abiotic stress in yeast. These results demonstrate that AsCFEM effectors possess additional functions beyond their roles in host plant immune response and pathogen virulence.
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Affiliation(s)
- Chaodong Qiu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
| | - Huajian Zhang
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
| | - Zhenyu Liu
- Department of Plant Pathology, School of Plant Protection, Anhui Agricultural University, Hefei, China; Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei 230036, China.
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Xie Y, Shi L, Cheng K, Li Y, Yu S. Host Recognition and Specific Infection of Endomelanconiopsis endophytica during Early Infection. J Fungi (Basel) 2023; 9:1040. [PMID: 37888296 PMCID: PMC10607883 DOI: 10.3390/jof9101040] [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: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis.
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Affiliation(s)
- Yan Xie
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liuqing Shi
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Keke Cheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Li
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Chellappan BV, El-Ganainy SM, Alrajeh HS, Al-Sheikh H. In Silico Characterization of the Secretome of the Fungal Pathogen Thielaviopsis punctulata, the Causal Agent of Date Palm Black Scorch Disease. J Fungi (Basel) 2023; 9:jof9030303. [PMID: 36983471 PMCID: PMC10051545 DOI: 10.3390/jof9030303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
The black scorch disease of date palm caused by Thielaviopsis punctulata is a serious threat to the cultivation and productivity of date palm in Arabian Peninsula. The virulence factors that contribute to pathogenicity of T. punctulata have not been identified yet. In the present study, using bioinformatics approach, secretory proteins of T. punctulata were identified and functionally characterized. A total of 197 putative secretory proteins were identified, of which 74 were identified as enzymes for carbohydrate degradation (CAZymes), 25 were proteases, and 47 were predicted as putative effectors. Within the CAZymes, 50 cell wall-degrading enzymes, potentially to degrade cell wall components such as cellulose, hemicellulose, lignin, and pectin, were identified. Of the 47 putative effectors, 34 possessed at least one functional domain. The secretome of T. punctulata was compared to the predicted secretome of five closely related species (T. musarum, T. ethacetica, T. euricoi, T. cerberus, and T. populi) and identified species specific CAZymes and putative effector genes in T. punctulata, providing a valuable resource for the research aimed at understanding the molecular mechanism underlying the pathogenicity of T. punctulata on Date palm.
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Affiliation(s)
- Biju Vadakkemukadiyil Chellappan
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Correspondence:
| | - Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Agricultural Research Center, Plant Pathology Research Institute, Giza 12619, Egypt
| | - Hind Salih Alrajeh
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
| | - Hashem Al-Sheikh
- Department of Biological Sciences, College of Science, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
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