1
|
Xu J, Yang X, Wu C, Chen Z, Dai T. Recombinase Polymerase Amplification-Lateral Flow Dipstick Assay for Rapid Detection of Fusarium circinatum Based on a Newly Identified Unique Target Gene. PLANT DISEASE 2023; 107:1067-1074. [PMID: 36089688 DOI: 10.1094/pdis-04-22-0864-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Pitch canker caused by the fungus Fusarium circinatum is an important disease affecting pine trees in Europe and South Africa. Several countries, including China, have listed F. circinatum as a quarantine pathogen. Therefore, timely detection of F. circinatum could efficiently prevent its introduction into new areas or facilitate spread management in already infected sites. In this study, a recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) assay was developed for rapid detection of F. circinatum based on a new target gene, Fcir2067, identified from whole-genome sequences. The assay was highly specific to F. circinatum. In fact, it exclusively detected F. circinatum isolates; 53 isolates of fungal and oomycete species and 2 nematodes of Bursaphelenchus xylophilus and B. mucronatus were not detected. By detecting as little as 10 pg of F. circinatum genomic DNA in a 50-µl reaction, the RPA-LFD assay was 10 times more sensitive than conventional PCR assays. F. circinatum was also detected in artificially inoculated pine needles of Cedrus deodara. These results demonstrated that the developed RPA-LFD assay has the potential for rapid detection of F. circinatum in regions at high risk of infection. The RPA-LFD assay might serve as an alternative method for the early detection of F. circinatum.
Collapse
Affiliation(s)
- Jieying Xu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiao Yang
- Plant and Pest Diagnostic Clinic, Department of Plant Industry, Clemson University, Pendleton, SC, U.S.A
| | - Cuiping Wu
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, Jiangsu, China
| | - Zhenpeng Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
2
|
Maphosa MN, Steenkamp ET, Kanzi AM, van Wyk S, De Vos L, Santana QC, Duong TA, Wingfield BD. Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum. J Fungi (Basel) 2022; 8:jof8070657. [PMID: 35887414 PMCID: PMC9316270 DOI: 10.3390/jof8070657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.
Collapse
|
3
|
Vázquez-Rosas-Landa M, Sánchez-Rangel D, Hernández-Domínguez EE, Pérez-Torres CA, López-Buenfil A, de Jesús García-Ávila C, Carrillo-Hernández ED, Castañeda-Casasola CC, Rodríguez-Haas B, Pérez-Lira J, Villafán E, Alonso-Sánchez A, Ibarra-Laclette E. Design of a diagnostic system based on molecular markers derived from the ascomycetes pan-genome analysis: The case of Fusarium dieback disease. PLoS One 2021; 16:e0246079. [PMID: 33507916 PMCID: PMC7843019 DOI: 10.1371/journal.pone.0246079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 01/12/2021] [Indexed: 11/21/2022] Open
Abstract
A key factor to take actions against phytosanitary problems is the accurate and rapid detection of the causal agent. Here, we develop a molecular diagnostics system based on comparative genomics to easily identify fusariosis and specific pathogenic species as the Fusarium kuroshium, the symbiont of the ambrosia beetle Euwallaceae kuroshio Gomez and Hulcr which is responsible for Fusarium dieback disease in San Diego CA, USA. We performed a pan-genome analysis using sixty-three ascomycetes fungi species including phytopathogens and fungi associated with the ambrosia beetles. Pan-genome analysis revealed that 2,631 orthologue genes are only shared by Fusarium spp., and on average 3,941 (SD ± 1,418.6) are species-specific genes. These genes were used for PCR primer design and tested on DNA isolated from i) different strains of ascomycete species, ii) artificially infected avocado stems and iii) plant tissue of field-collected samples presumably infected. Our results let us propose a useful set of primers to either identify any species from Fusarium genus or, in a specific manner, species such as F. kuroshium, F. oxysporum, and F. graminearum. The results suggest that the molecular strategy employed in this study can be expanded to design primers against different types of pathogens responsible for provoking critical plant diseases.
Collapse
Affiliation(s)
- Mirna Vázquez-Rosas-Landa
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
| | - Diana Sánchez-Rangel
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
- Catedrático CONACYT en el INECOL, Xalapa, Veracruz, México
| | - Eric E. Hernández-Domínguez
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
- Catedrático CONACYT en el INECOL, Xalapa, Veracruz, México
| | - Claudia-Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
- Catedrático CONACYT en el INECOL, Xalapa, Veracruz, México
| | | | - Clemente de Jesús García-Ávila
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Centro Nacional de Referencia Fitosanitaria (CNRF), Tecámac, Estado de México, México
| | | | - Cynthia-Coccet Castañeda-Casasola
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Centro Nacional de Referencia Fitosanitaria (CNRF), Tecámac, Estado de México, México
| | - Benjamín Rodríguez-Haas
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
| | - Josué Pérez-Lira
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
| | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados (REMAv), Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, México
- * E-mail:
| |
Collapse
|
4
|
Tiwari RK, Kumar R, Sharma S, Sagar V, Aggarwal R, Naga KC, Lal MK, Chourasia KN, Kumar D, Kumar M. Potato dry rot disease: current status, pathogenomics and management. 3 Biotech 2020; 10:503. [PMID: 33163322 DOI: 10.1007/s13205-020-02496-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Potato dry rot disease caused by Fusarium species is a major threat to global potato production. The soil and seed-borne diseases influence the crop stand by inhibiting the development of potato sprouts and cause severe rots in seed tubers, table and processing purpose potatoes in cold stores. The symptoms of the dry rot include sunken and wrinkled brown to black tissue patches on tubers having less dry matter and shriveled flesh. Fungal infection accompanied by toxin development in the rotten tubers raises more concern for consumer health. The widespread dry rot causing fungal species (Fusarium graminearum) is reported to have a hemibiotrophic lifestyle. A cascade of enzymes, toxins and small secreted proteins are involved in the pathogenesis of these hemibiotrophs. With the availability of the genome sequence of the most devastating species Fusarium sambucinum, it is important to identify the potential pathogenicity factors and small secreted proteins that will help in designing management strategies. Limited resistant cultivars and the emergence of fungicide-resistant strains have made it more threatening for potato cultivation and trade. Several novel fungicide molecules (Azoxystrobin, chlorothalonil and fludioxonil), are found very effective as tuber treatment chemicals. Besides, many beneficial bioagents and safer chemicals have shown antibiosis and mycoparasitism against this pathogen. Germplasm screening for dry rot resistance is important to assist the resistance breeding program for the development of resistant cultivars. This review aims to draw attention to the symptomatology, infection process, pathogenomics, the role of toxins and management approaches for potato dry rot disease, which is very much critical in designing better management strategies.
Collapse
Affiliation(s)
- Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Vinay Sagar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Rashmi Aggarwal
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Dharmendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| |
Collapse
|
5
|
Zhu H, Zhu L, Ding N. Genomic Insights into the Aquatic Fusarium spp. QHM and BWC1 and Their Application in Phenol Degradation. Curr Microbiol 2020; 77:2279-2286. [PMID: 32488406 DOI: 10.1007/s00284-020-02050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 05/23/2020] [Indexed: 11/25/2022]
Abstract
Fusarium species are widely distributed in ecosystems with wide pH ranges and play pivotal roles in aquatic communities through xenobiotic degradation. It is necessary to explore genomic insights for the application of Fusarium species. In this study, the aquatic Fusarium strains QHM and BWC1 were isolated from a coal mine and a subterranean river, respectively, cultured under acidic conditions and sequenced genomically. Phylogenetic analysis of the isolates was conducted based on the sequences of internal transcripts and sequences encoding β-microtubulin, translation elongation factors and the second large subunit of the RNA polymerase. Fusarium QHM demonstrates close relationships to the type strains of Fusarium ramigenum and Fusarium napiforme in Fusarium fujikuroi species complex. Fusarium BWC1 is predicted to be Fusarium subglutinans. A total of 479 and 2352 scaffolds, corresponding to 14,814 and 15,295 genes, were obtained for Fusarium spp. QHM and BWC1, respectively. Genomic analyses revealed that they harbored biodegradation pathways for aromatic compounds. Phenol stress experiments indicated that Fusarium spp. QHM and BWC1 exhibited optimal degradation at a density of 300 mg/L to achieve a phenol degradation rate of 39.91-43.65% at pH 3.5-4.0. Fusarium spp. QHM and BWC1 were applied to mock phenol-water, and an average phenol degradation rate of 51.71-65.55% indicated the feasibility of these species. The findings of this study have important implications for Fusarium spp. QHM and BWC1 applied to phenol wastewater in acidic or neutral pH environments.
Collapse
Affiliation(s)
- Hongfei Zhu
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China.
| | - Long Zhu
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China
| | - Ning Ding
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China
| |
Collapse
|
6
|
Sampling and Detection Strategies for the Pine Pitch Canker (PPC) Disease Pathogen Fusarium circinatum in Europe. FORESTS 2019. [DOI: 10.3390/f10090723] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fusarium circinatum Nirenberg & O’Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions—via contaminated seeds, wood material, soil and growing substrates, natural means and human activities—into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the “bridgehead effect”, where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspectives are addressed.
Collapse
|