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Su J, Wang J, Tang J, Yu W, Liu J, Dong X, Dong J, Chai X, Ji P, Zhang L. Zinc finger transcription factor ZFP1 is associated with growth, conidiation, osmoregulation, and virulence in the Polygonatum kingianum pathogen Fusarium oxysporum. Sci Rep 2024; 14:16061. [PMID: 38992190 DOI: 10.1038/s41598-024-67040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024] Open
Abstract
Rhizome rot is a destructive soil-borne disease of Polygonatum kingianum and adversely affects the yield and sustenance of the plant. Understanding how the causal fungus Fusarium oxysporum infects P. kingianum may suggest effective control measures against rhizome rot. In germinating conidia of infectious F. oxysporum, expression of the zinc finger transcription factor gene Zfp1, consisting of two C2H2 motifs, was up-regulated. To characterize the critical role of ZFP1, we generated independent deletion mutants (zfp1) and complemented one mutant with a transgenic copy of ZFP1 (zfp1 tZFP1). Mycelial growth and conidial production of zfp1 were slower than those of wild type (ZFP1) and zfp1 tZFP1. Additionally, a reduced inhibition of growth suggested zfp1 was less sensitive to conditions promoting cell wall and osmotic stresses than ZFP1 and zfp1 tZFP1. Furthermore pathogenicity tests suggested a critical role for growth of zfp1 in infected leaves and rhizomes of P. kingianum. Thus ZFP1 is important for mycelial growth, conidiation, osmoregulation, and pathogenicity in P. kingianum.
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Affiliation(s)
- Jianyun Su
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jingyi Wang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jingying Tang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Weimei Yu
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jiajia Liu
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xian Dong
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Jiahong Dong
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xia Chai
- Yunnan Normal University, Kunming, 650500, China.
| | - Pengzhang Ji
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Lei Zhang
- Institute of Medicinal Plant Cultivation, Academy of Southern Medicine, College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Dilla-Ermita CJ, Goldman P, Anchieta A, Feldmann MJ, Pincot DDA, Famula RA, Vachev M, Cole GS, Knapp SJ, Klosterman SJ, Henry PM. Secreted in Xylem 6 ( SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:530-541. [PMID: 38552146 DOI: 10.1094/mpmi-02-24-0012-r] [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: 06/25/2024]
Abstract
Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene (AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 (SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (ΔSIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. ΔSIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Christine Jade Dilla-Ermita
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Polly Goldman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Amy Anchieta
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Mishi Vachev
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Klosterman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Peter M Henry
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
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Logachev A, Kanapin A, Rozhmina T, Stanin V, Bankin M, Samsonova A, Orlova E, Samsonova M. Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini. FRONTIERS IN PLANT SCIENCE 2024; 15:1383914. [PMID: 38872883 PMCID: PMC11169931 DOI: 10.3389/fpls.2024.1383914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.
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Affiliation(s)
- Anton Logachev
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alexander Kanapin
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Rozhmina
- Flax Institute, Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Vladislav Stanin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ekaterina Orlova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
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Kaliapan K, Mazlin SNA, Chua KO, Rejab NA, Mohd-Yusuf Y. Secreted in Xylem (SIX) genes in Fusarium oxysporum f.sp. cubense (Foc) unravels the potential biomarkers for early detection of Fusarium wilt disease. Arch Microbiol 2024; 206:271. [PMID: 38767679 DOI: 10.1007/s00203-024-03996-4] [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: 12/30/2023] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Secreted in Xylem (SIX) are small effector proteins released by Fusarium oxysporum f.sp. cubense (Foc) into the plant's xylem sap disrupting the host's defence responses causing Fusarium wilt disease resulting in a significant decline in banana crop yields and economic losses. Notably, different races of Foc possess unique sets of SIX genes responsible for their virulence, however, these genes remain underutilized, despite their potential as biomarkers for early disease detection. Herein, we identified seven SIX genes i.e. SIX1, SIX2, SIX4, SIX6, SIX8a, SIX9a and SIX13 present in Foc Tropical Race 4 (FocTR4), while only SIX9b in Foc Race 1 (Foc1). Analysis of SIX gene expression in infected banana roots revealed differential patterns during infection providing valuable insights into host-pathogen interactions, virulence level, and early detection time points. Additionally, a comprehensive analysis of virulent Foc1_C2HIR and FocTR4_C1HIR isolates yielded informative genomic insights. Hence, these discoveries contribute to our comprehension of potential disease control targets in these plants, as well as enhancing plant diagnostics and breeding programs.
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Affiliation(s)
- Kausalyaa Kaliapan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Siti Nur Akmar Mazlin
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kah Ooi Chua
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yusmin Mohd-Yusuf
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Glami Lemi Biotechnology Research Centre Universiti Malaya, 71650, Jelebu, Negeri Sembilan, Malaysia.
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Yang J, Han J, Jing Y, Li S, Lan B, Zhang Q, Yin K. Virulent Fusarium isolates with diverse morphologies show similar invasion and colonization strategies in alfalfa. FRONTIERS IN PLANT SCIENCE 2024; 15:1390069. [PMID: 38828216 PMCID: PMC11140090 DOI: 10.3389/fpls.2024.1390069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024]
Abstract
Root rot is a major disease that causes decline of alfalfa production, and Fusarium is a major pathogen associated with root rot. In this study, 13 Fusarium isolates were obtained from alfalfa with root rot in Gansu Province, the major alfalfa production region in China. The isolates were characterized by molecular genotyping (ITS, TEF 1-α and RPB2 fragments) and identified as six species, which included the F. acuminatum, F. incarnatum, F. oxysporum, F. proliferatum, F. redolens, and F. solani. We found that their morphology varied significantly at both the macro- and micro-levels, even for those from the same species. We developed a low cost and fast pathogenicity test and revealed that all isolates were pathogenic to alfalfa with typical root rot symptoms such as leaf yellowing and brown lesions on the root and stem. However, the virulence of the isolates differed. We also found that the conidia of all isolates germinated as early as 24 hours post inoculation (hpi), while hyphae colonized the root extensively and invaded the xylem vessel by 48 hpi. Together our results reveal that different virulent Fusarium isolates use a similar invasion strategy in alfalfa. This natural plant-fungus pathosystem is intriguing and warrants further examination, particularly with regard to efforts aimed at mitigating the impact of multiple similar vascular pathogens on infected alfalfa plants.
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Affiliation(s)
- Jian Yang
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Jing Han
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Yuqing Jing
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Siyang Li
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Bo Lan
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Qian Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Science, Lanzhou, China
| | - Kangquan Yin
- School of Grassland Science, Beijing Forestry University, Beijing, China
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Vetrova S, Alyokhina K, Engalycheva I, Kozar E, Mukhina K, Sletova M, Krivenkov L, Tikhonova T, Kameneva A, Frolova S, Chizhik V, Martynov V. Identification and Pathogenicity of Fusarium Species Associated with Onion Basal Rot in the Moscow Region of Russian Federation. J Fungi (Basel) 2024; 10:331. [PMID: 38786686 PMCID: PMC11121879 DOI: 10.3390/jof10050331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Fusarium basal rot of onions causes large losses during storage of commercial production of onion bulbs, which in turn adversely affects the food market situation in the off-season period. There are no data on the composition of Fusarium spp., which causes onion basal rot in the Russian Federation. Therefore, our research was aimed at Fusarium spp. causing onion basal rot in the Moscow Region of the Russian Federation and studying the pathogenicity of these species for the host plant. We studied 20 isolates of Fusarium spp. collected from affected mature bulbs and seed bulbs. Species identification of the isolates was carried out using analysis of the nucleotide sequences of the three genetic loci ITS, tef1 and rpb2, as well as was based on the macro- and micromorphological characteristics of these isolates. As a result, the species F. annulatum (F. fujikuroi species complex), F. oxysporum (F. oxysporum species complex), F. acuminatum (F. tricinctum species complex) and F. solani (F. solani species complex) were identified to involve in the pathogenesis of Fusarium basal rot. We have shown for the first time that the species F. annulatum and F. acuminatum are highly aggressive and capable of causing onion basal rot. The predominant species were F. annulatum and F. oxysporum. The proportion of these species in the total number of analyzed isolates was 60% and 25%, respectively. The largest proportion (33%) of highly aggressive on mature bulbs isolates was found in the species F. annulatum. The data obtained provide practical insights for developing strategies to manage Fusarium fungi responsible for onion basal rot Moscow Region of the Russian Federation. In addition, data about species composition and aggressive isolates may be used in onion breeding for resistance to Fusarium basal rot.
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Affiliation(s)
- Svetlana Vetrova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Ksenia Alyokhina
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Irina Engalycheva
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Elena Kozar
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Kseniya Mukhina
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Maria Sletova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Leonid Krivenkov
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Tatyana Tikhonova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Alina Kameneva
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Svetlana Frolova
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
| | - Vera Chizhik
- Federal State Budgetary Scientific Institution Federal Scientific Vegetable Center, 143072 Moscow, Russia; (K.A.); (I.E.); (E.K.); (K.M.); (M.S.); (L.K.); (T.T.); (A.K.); (S.F.); (V.C.)
- Federal State Budgetary Scientific Institution All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Viktor Martynov
- Federal State Budgetary Scientific Institution All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
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Nishmitha K, Bashyal BM, Dubey SC, Kamil D. Molecular characterization of Indian races of Fusarium oxysporum f. sp. lentis (Fol) based on secreted in Xylem (SIX) effector genes and development of a SIX11 gene-based molecular marker for specific detection of Fol. Arch Microbiol 2024; 206:200. [PMID: 38564016 DOI: 10.1007/s00203-024-03945-1] [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: 12/27/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Fusarium wilt of lentil caused by Fusarium oxysporum f. sp. lentis (Fol) is a destructive pathogen limiting lentil production in India. In the present study, Secreted in Xylem (SIX) effectors genes were explored in Indian races of Fol and also a diagnostic tool for reliable detection of the disease was developed. Four SIX effectors genes, SIX11, SIX13, SIX6 and SIX2 were identified in 12 isolates of Fol belonging to seven races. SIX11 was present in all the races while SIX 13 was absent in race 6 and SIX6 was present only in race 4. The phylogenetic analysis revealed the conserved nature of the SIX genes within the forma specialis and showed sequence homology with F. oxysporum f. sp. pisi. The presence of three effectors, SIX11, SIX13 and SIX6 in race 4 correlates with high disease incidence in lentil germplasms. The in-silico characterization revealed the presence of signal peptide and localization of the effectors. Further SIX11 effector gene present in all the isolates was used to develop Fol-specific molecular marker for accurate detection. The marker developed could differentiate F. oxysporum f. sp. lycopersici, F. solani, F. oxysporum, Rhizoctonia solani and Sclerotium rolfsii and had a detection limit of 0.01ng μL- 1. The effector-based marker detection helps in the unambiguous detection of the pathogen under field conditions.
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Affiliation(s)
- K Nishmitha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S C Dubey
- Birsa Agricultural University, Jharkhand, 834006, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Wesoly M, Daulton E, Jenkins S, van Amsterdam S, Clarkson J, Covington JA. Early Detection of Fusarium Basal Rot Infection in Onions and Shallots Based on VOC Profiles Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3664-3672. [PMID: 38320984 PMCID: PMC10885136 DOI: 10.1021/acs.jafc.3c06569] [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: 02/08/2024]
Abstract
Gas chromatography ion-mobility spectrometry (GC-IMS) technology is drawing increasing attention due to its high sensitivity, low drift, and capability for the identification of compounds. The noninvasive detection of plant pests and pathogens is an application area well suited to this technology. In this work, we employed GC-IMS technology for early detection of Fusarium basal rot in brown onion, red onion, and shallot bulbs and for tracking disease progression during storage. The volatile profiles of the infected and healthy control bulbs were characterized using GC-IMS and gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS). GC-IMS data combined with principal component analysis and supervised methods provided discrimination between infected and healthy control bulbs as early as 1 day after incubation with the pathogen, classification regarding the proportion of infected to healthy bulbs in a sample, and prediction of the infection's duration with an average R2 = 0.92. Furthermore, GC-TOF-MS revealed several compounds, mostly sulfides and disulfides, that could be uniquely related to Fusarium basal rot infection.
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Affiliation(s)
- Malgorzata Wesoly
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, Warsaw 00-664, Poland
| | - Emma Daulton
- School of Engineering, University of Warwick, Coventry Cv4 7AL, U.K
| | - Sascha Jenkins
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne CV35 9EF, U.K
| | | | - John Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne CV35 9EF, U.K
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Sakane K, Akiyama M, Jogaiah S, Ito SI, Sasaki K. Pathogenicity chromosome of Fusarium oxysporum f. sp. cepae. Fungal Genet Biol 2024; 170:103860. [PMID: 38114016 DOI: 10.1016/j.fgb.2023.103860] [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: 06/13/2023] [Revised: 11/10/2023] [Accepted: 12/16/2023] [Indexed: 12/21/2023]
Abstract
Fusarium oxysporum f. sp. cepae (Foc) is the causative agent of Fusarium basal rot disease in onions, which leads to catastrophic global crop production losses. Therefore, the interaction of Foc with its host has been actively investigated, and the pathogen-specific (PS) regions of the British strain Foc_FUS2 have been identified. However, it has not been experimentally determined whether the identified PS region plays a role in pathogenicity. To identify the pathogenicity chromosome in the Japanese strain Foc_TA, we initially screened effector candidates, defined as small proteins with a signal peptide that contain two or more cysteines, from genome sequence data. Twenty-one candidate effectors were identified, five of which were expressed during infection. Of the expressed effector candidates, four were located on the 4-Mb-sized chromosome in Foc_TA. To clarify the relationship between pathogenicity and the 4-Mb-sized chromosome in Foc_TA, nine putative 4-Mb-sized chromosome loss strains were generated by treatment with benomyl (a mitotic inhibitor drug). A pathogenicity test with putative 4-Mb-sized chromosome loss strains showed that these strains were impaired in their pathogenicity toward onions. Genome analysis of three putative 4-Mb-sized chromosome loss strains revealed that two strains lost a 4-Mb-sized chromosome in common, and another strain maintained a 0.9-Mb region of the 4-Mb-sized chromosome. Our findings show that the 4-Mb-sized chromosome is the pathogenicity chromosome in Foc_TA, and the 3.1-Mb region within the 4-Mb-sized chromosome is required for full pathogenicity toward onion.
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Affiliation(s)
- Kosei Sakane
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | - Mitsunori Akiyama
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Sudisha Jogaiah
- Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Kasaragod 671316, India
| | - Shin-Ichi Ito
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kazunori Sasaki
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan.
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Yağmur A, Demir S, Canpolat S, Rezaee Danesh Y, Farda B, Djebaili R, Pace L, Pellegrini M. Onion Fusarium Basal Rot Disease Control by Arbuscular Mycorrhizal Fungi and Trichoderma harzianum. PLANTS (BASEL, SWITZERLAND) 2024; 13:386. [PMID: 38337919 PMCID: PMC10857072 DOI: 10.3390/plants13030386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Soilborne pathogens reduce 60% of the yield of onion crops. A common fungal pathogen causing wilt disease and severe losses is Fusarium basal rot (FBR). In this study, the combination of Arbuscular Mycorrhizal Fungi (AMF) with Trichoderma harzianum was investigated against FBR. Onion samples were collected from the Ankara-Polatlı region. Among the isolates, isolate S6 was identified as F. oxysporum f. sp. cepae (FOC) using morphological and molecular methods and pathogenicity tests. Different combinations of AMF (Funneliformis mosseae pure strain and the commercial AMF) and T. harzianum were inoculated on susceptible onion cultivars (Seç, Gence, and Şampiyon). The effects of the treatments on FOC biocontrol were studied under growth chamber conditions. The results showed that Şampiyon was the most resistant, while Gence was the most susceptible to basal rot disease. Different colonization rates (8.91-24%), spore densities (16.4-50.4 spore/10 g soil), and the extent to which a plant needs mycorrhizal conditions to grow to its maximum potential (i.e., mycorrhizal dependencies-18.3-51.9%) were recorded by treatment. Both single and combined applications of AMF and Trichoderma applications suppressed FOC. Suppressive effects were more pronounced when the F. mosseae pure strain was used alone (when F. mosseae was used, disease severity decreased from 90 to 68%, p < 0.05). The F. mosseae pure strain also showed the best plant growth promotion and phosphorus content release. The results indicate an interesting potential use of F. mosseae and the combination of AMF with T. harzianum in the management of FOC in onions.
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Affiliation(s)
- Abdulaziz Yağmur
- Directorate of Plant Protection Central Research Institute, Ministry of Agriculture and Forestry, 06172 Ankara, Turkey; (A.Y.); (S.C.)
| | - Semra Demir
- Department of Plant Protection, Faculty of Agriculture, Van Yuzuncu Yil University, 65090 Van, Turkey;
| | - Sirel Canpolat
- Directorate of Plant Protection Central Research Institute, Ministry of Agriculture and Forestry, 06172 Ankara, Turkey; (A.Y.); (S.C.)
| | - Younes Rezaee Danesh
- Department of Plant Protection, Faculty of Agriculture, Van Yuzuncu Yil University, 65090 Van, Turkey;
- Department of Plant Protection, Faculty of Agriculture, Urmia University, Urmia 5756151818, Iran
| | - Beatrice Farda
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (B.F.); (L.P.); (M.P.)
| | - Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (B.F.); (L.P.); (M.P.)
| | - Loretta Pace
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (B.F.); (L.P.); (M.P.)
| | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (B.F.); (L.P.); (M.P.)
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11
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Manikandan K, Shanmugam V, Kavi Sidharthan V, Saha P, Saharan MS, Singh D. Characterization of field isolates of Fusarium spp. from eggplant in India for species complexity and virulence. Microb Pathog 2024; 186:106472. [PMID: 38048836 DOI: 10.1016/j.micpath.2023.106472] [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: 09/30/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
Abstract
Eggplant wilt, despite emerging as a severe disease in India, the etiology must be better studied for its species' complexity and variability. The identity of fungal isolates associated with eggplants of India was established morphologically followed by sequencing and phylogenetic analysis. Three species, Fusarium falciforme, Fusarium incarnatum and Fusarium proliferatum, were observed for the first time in India. The isolates were tested for pathogenicity. Though all of them were pathogenic, the isolates displayed varying degrees of virulence. In further studies, the genetic relatedness of the isolates for virulence was assessed with candidate avirulent (SIX effectors), virulent (Fow1 and Fow2) and SSR markers. The SIX effector genes could not delineate the virulent isolates and were expressed in some non-F. oxysporum isolates for the first time. Likewise, the virulent genes, Fow1 for expression across the isolates and Fow2 for random expression across the isolates, were unsuitable markers for identifying the virulent groups. Hence, the F. oxysporum and F. solani isolates were genotyped with SSR markers. Though the clustering did not correlate with their virulence levels, the dendrogram grouping revealed variability among the F. oxysporum and F. solani isolates. This study concludes that although multiple species of Fusarium are associated with eggplant wilt in India, only F. oxysporum and F. solani are widespread in the surveyed areas. Though the three markers could not delineate the race specificity of the isolates, only the SSR makers could identify the genetic variability and hence, would help screen eggplant germplasm for fusarium wilt resistance.
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Affiliation(s)
- Karuppiah Manikandan
- Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Veerubommu Shanmugam
- Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India.
| | | | - Partha Saha
- ICAR-Central Tobacco Research Institute, Rajahmundry, Andhra Pradesh, 533105, India
| | - Mahender Singh Saharan
- Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Dinesh Singh
- Division of Plant Pathology, ICAR- Indian Agricultural Research Institute, New Delhi, 110 012, India
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12
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Wang H, Yao L, Chen J, Ding Z, Ou X, Zhang C, Zhao J, Han Y. Antifungal Peptide P852 Effectively Controls Fusarium oxysporum, a Wilt-Causing Fungus, by Affecting the Glucose Metabolism and Amino Acid Metabolism as well as Damaging Mitochondrial Function. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19638-19651. [PMID: 38015891 DOI: 10.1021/acs.jafc.3c07953] [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: 11/30/2023]
Abstract
Fusarium oxysporum causes wilt disease, which causes huge economic losses to a wide range of agricultural cash crops. Antifungal peptide P852 is an effective biocide. However, the mechanism of direct inhibition of pathogenic fungus needs to be explored. The proteomics and transcriptomics results showed that P852 mainly affected intracellular pathways such as glucose metabolism, amino acid metabolism, and oxidoreductase activity in F. oxysporum. P852 disrupts the intracellular oxidative equilibrium in F. oxysporum, and transmission electron microscopy observed mitochondrial swelling, disruption of membrane structure, and leakage of contents. Decreased mitochondrial membrane potential, mitochondrial cytochrome c leakage, and reduced ATP production were also detected. These results suggest that P852 is able to simultaneously inhibit intracellular metabolism and disrupt the mitochondrial function of F. oxysporum, exerting its inhibitory effects in multiple pathways together. The present study provides some insights into the multitargeted mechanism of fungus inhibition of antifungal lipopeptide substances produced by Bacillus spp.
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Affiliation(s)
- Hongji Wang
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Lan Yao
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Jie Chen
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Zeran Ding
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Xuan Ou
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Chaowen Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Jianjun Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
| | - Yuzhu Han
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China
- Immunology Research Center, Institute of Medicine, Southwest University, Chongqing 402460, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing 402460, China
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13
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Shin JH, Lee HK, Lee SC, Han YK. Biological Control of Fusarium oxysporum, the Causal Agent of Fusarium Basal Rot in Onion by Bacillus spp. THE PLANT PATHOLOGY JOURNAL 2023; 39:600-613. [PMID: 38081320 PMCID: PMC10721391 DOI: 10.5423/ppj.oa.08.2023.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/20/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Fusarium oxysporum is the main pathogen causing Fusarium basal rot in onion (Allium cepa L.), which incurs significant yield losses before and after harvest. Among management strategies, biological control is an environmentally safe and sustainable alternative to chemical control. In this study, we isolated and screened bacteria for antifungal activity against the basal rot pathogen F. oxysporum. Isolates 23-045, 23-046, 23-052, 23-055, and 23-056 significantly inhibited F. oxysporum mycelial growth and conidial germination. Isolates 23-045, 23-046, 23-052, and 23-056 suppressed the development of Fusarium basal rot in both onion seedlings and bulbs in pot and spray inoculation assays. Isolate 23-055 was effective in onion seedlings but exhibited weak inhibitory effect on onion bulbs. Based on analyses of the 16S rRNA and rpoB gene sequences together with morphological analysis, isolates 23-045, 23-046, 23-052, and 23-055 were identified as Bacillus thuringiensis, and isolate 23-056 as Bacillus toyonensis. All five bacterial isolates exhibited cellulolytic, proteolytic, and phosphate-solubilizing activity, which may contribute to their antagonistic activity against onion basal rot disease. Taken together B. thuringiensis 23-045, 23-046, 23-052, and 23-055 and B. toyonensis 23-056 have potential for the biological control of Fusarium basal rot in onion.
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Affiliation(s)
- Jong-Hwan Shin
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - Ha-Kyoung Lee
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - Seong-Chan Lee
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea
| | - You-Kyoung Han
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea
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14
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Sakane K, Kunimoto M, Furumoto K, Shigyo M, Sasaki K, Ito SI. The SIX5 Protein in Fusarium oxysporum f. sp. cepae Acts as an Avirulence Effector toward Shallot ( Allium cepa L. Aggregatum Group). Microorganisms 2023; 11:2861. [PMID: 38138005 PMCID: PMC10745378 DOI: 10.3390/microorganisms11122861] [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: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
Fusarium oxysporum f. sp. cepae (Foc) causes basal rot disease in Allium species, including onions (Allium cepa L.) and shallots (A. cepa L. Aggregatum group). Among Allium species, shallots can be crossbred with onions and are relatively more resistant to Foc than onions. Thus, shallots are considered a potential disease-resistant resource for onions. However, the mechanisms underlying the molecular interactions between shallots and Foc remain unclear. This study demonstrated that SIX5, an effector derived from Foc (FocSIX5), acts as an avirulence effector in shallots. We achieved this by generating a FocSIX5 gene knockout mutant in Foc, for which experiments which revealed that it caused more severe wilt symptoms in Foc-resistant shallots than the wild-type Foc and FocSIX5 gene complementation mutants. Moreover, we demonstrated that a single amino acid substitution (R67K) in FocSIX5 was insufficient to overcome shallot resistance to Foc.
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Affiliation(s)
- Kosei Sakane
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan;
| | - Masaaki Kunimoto
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (M.K.); (K.F.); (M.S.)
| | - Kazuki Furumoto
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (M.K.); (K.F.); (M.S.)
| | - Masayoshi Shigyo
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (M.K.); (K.F.); (M.S.)
| | - Kazunori Sasaki
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (M.K.); (K.F.); (M.S.)
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Shin-ichi Ito
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan; (M.K.); (K.F.); (M.S.)
- Research Center for Thermotolerant Microbial Resources (RCTMR), Yamaguchi University, Yamaguchi 753-8515, Japan
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15
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Shin JH, Lee HK, Back CG, Kang SH, Han JW, Lee SC, Han YK. Identification of Fusarium Basal Rot Pathogens of Onion and Evaluation of Fungicides against the Pathogens. MYCOBIOLOGY 2023; 51:264-272. [PMID: 37711982 PMCID: PMC10498799 DOI: 10.1080/12298093.2023.2243759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 09/16/2023]
Abstract
Onion (Allium cepa L.) is an economically important vegetable crop worldwide. However, various fungal diseases, including Fusarium basal rot (FBR), neck rot, and white rot, reduce onion production or bulb storage life. FBR caused by Fusarium species is among the most destructive onion diseases. In this study, we identified Fusarium species associated with FBR in Jeolla and Gyeongsang Provinces in South Korea and evaluated fungicides against the pathogens. Our morphological and molecular analyses showed that FBR in onions is associated with Fusarium commune, Fusarium oxysporum, and Fusarium proliferatum. We selected seven fungicides (fludioxonil, hexaconazole, mandestrobin, penthiopyrad, prochloraz-manganese, pydiflumetofen, and tebuconazole) and evaluated their inhibitory effects on mycelial growth of the pathogens at three different concentrations (0.01, 0.1, and 1 mg/mL). We found that prochloraz-manganese was highly effective, inhibiting 100% of the mycelial growth of the pathogens at all concentrations, followed by tebuconazole. Fludioxonil showed < 50% inhibition at 1 mg/mL for the tested isolates.
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Affiliation(s)
- Jong-Hwan Shin
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Ha-Kyoung Lee
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Gi Back
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Soo-hyun Kang
- Allium Vegetables Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Muan, Republic of Korea
| | - Ji-won Han
- Allium Vegetables Research Institute, National Institute of Horticultural & Herbal Science, Rural Development Administration, Muan, Republic of Korea
| | - Seong-Chan Lee
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - You-Kyoung Han
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
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16
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Ma LJ, Zhang Y, Li C, Liu S, Liu C, Mostert D, Yu H, Haridas S, Webster K, Li M, Grigoriev I, Viljoen A, Yi G. Accessory genes in tropical race 4 contributed to the recent resurgence of the devastating disease of Fusarium wilt of banana. RESEARCH SQUARE 2023:rs.3.rs-3197485. [PMID: 37609348 PMCID: PMC10441461 DOI: 10.21203/rs.3.rs-3197485/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most damaging plant diseases recorded. Foc race 1 (R1) decimated the Gros Michel-based banana trade. Currently, tropical race 4 (TR4) is threatening the global production of its replacement cultivar, Cavendish banana. Population genomics and phylogenetics revealed that all Cavendish banana-infecting race 4 strains shared an evolutionary origin that is distinct from R1 strains. The TR4 genome lacks accessory or pathogenicity chromosomes, reported in other F. oxysporum genomes. Accessory genes-enriched for virulence and mitochondrial-related functions-are attached to ends of some core chromosomes. Meta-transcriptomics revealed the unique induction of the entire mitochondria-localized nitric oxide (NO) biosynthesis pathway upon TR4 infection. Empirically, we confirmed the unique induction of NO burst in TR4,suggesting the involvement of nitrosative pressure in its virulence. Targeted mutagenesis demonstrated the functional importance of accessory genes SIX1 and SIX4 as virulent factors.
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Affiliation(s)
| | | | | | | | | | - Diane Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | | | | | | | | | - Igor Grigoriev
- US DOE Joint Genome Institute/ Lawrence Berkeley National Lab/ University of California Berkeley
| | - Altus Viljoen
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
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Gálvez L, Brizuela AM, Garcés I, Cainarca JS, Palmero D. First Report of Fusarium oxysporum f. sp. lactucae Race 4 Causing Lettuce Wilt in Spain. PLANT DISEASE 2023; 107:2549. [PMID: 36774562 DOI: 10.1094/pdis-12-22-2819-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Spain is the fourth largest lettuce-producing country in the world and the leading European producer. Much of the production, mainly grow in open field, is dedicated to export with a value of 887 million U.S. dollars per year. In summer 2021 wilting symptoms were observed in a commercial field crop on butterhead lettuce 'Amible' in Albacete (Castilla-La Mancha, Spain). Approximately 15% of plants were affected, but losses were even more severe on subsequent crops. Vascular tissue of affected plants showed a brown to red discoloration. Sections of infected vascular tissue (3 to 5 mm long) were surface sterilized in 70% ethanol for 30 s, washed three times with sterile water, and plated on potato dextrose agar (PDA) amended with streptomycin sulfate (100 mg/liter). From 5-day-old cultures typical pale cream to purplish mycelia with microconidia, macroconidia, and chlamydospores of Fusarium oxysporum were observed. Microconidia were abundant on carnation leaf agar and measured 6.1 to 9.2 μm (mean 7.1 ± 0.7 μm; n=50)). Macroconidia were sparse, three-septate, straight to slightly curved, 23.3 to 34.8 × 4 to 5.2 µm (mean 31.5 ± 2.8 × 4.2 ± 0.3 µm; n=50). Chlamydospores were terminal and intercalary, rough walled, and measured 7.2 to 10.1 μm (mean 9.5 ± 0.6 μm; n=50) µm. DNA was extracted from three single-spore isolates using the protocol of Querol et al. (1992) and the translation elongation factor 1-α gene (TEF) was sequenced with exTEF-F/FUexTEF-R primers as described by Taylor et al. (2016). All TEF sequences (GenBank accession no. OP903519) were identical. In BLAST analyses, the isolates showed 100% identity to the corresponding region of Fusarium oxysporum f. sp. lactucae (FOL) race 4 (MK059958). All Spanish isolates were identified as FOL race 4 using a race-specific polymerase chain reaction (PCR) with the primers FPUF/FPUR (Gilardi et al. 2017), and a previously identified FOL race 4 isolate Fus 1.01 as a positive control. Pathogenicity tests were conducted to confirm the positive result of the race 4-specific PCR and to complete Koch's postulates. Three differential lettuce cultivars ('Costa Rica No. 4', 'Banchu Red Fire', and 'Romana Romabella 30 CN') provided by Rijk Zwaan (The Netherlands) were inoculated with three Spanish isolates (Al1A1, Al1D, Al2B) and the Fus 1.01 isolate used as FOL race 4 positive control (Claerbout et al., 2018). Roots of 3-week-old plants (five replicates per treatment) were dipped in a spore suspension (1 × 106 conidia/ml) for 10 min before transplanting into 250-ml pots with sterile substrate. Non-inoculated control plants were dipped in sterile water for 10 min. The experiment was carried out twice. Inoculated lettuce seedlings were planted and maintained in a growth chamber (25°C day, 18°C night). Plants were slightly watered every other day. After 21 days, wilting was observed in the cultivars 'Costa Rica No. 4' and 'Romana Romabella 30 CN'. Moreover, taproots were cut longitudinally, and vascular browning was observed in the taproot. No discoloration could be observed in the taproot of 'Banchu Red Fire' plants, coinciding with the result of isolate Fus 1.01 used as FOL race 4 positive control. Non-inoculated control plants remained healthy and vascular browning was not observed. In both experiments, F. oxysporum f.sp. lactucae was consistently reisolated using PDA medium. These results confirmed that the isolates Al1A1, Al1D and Al2B were FOL race 4. This race has recently been identified in The Netherlands (Gilardi et al. 2017), Belgium (Claerbout et al. 2018), United Kingdom, Ireland (Taylor et al. 2019) and Italy (Gilardi et al. 2019) and could become a serious threat to Spain lettuce production.
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Affiliation(s)
- Laura Gálvez
- Universidad Politécnica de Madrid, 16771, Producción Agraria, Madrid, Comunidad de Madrid, Spain;
| | | | - Irene Garcés
- Universidad Politécnica de Madrid, ETSIAAB, Madrid, Spain;
| | | | - Daniel Palmero
- Universidad Politécnica de Madrid, Agricultural Production- ETSIAAB, Madrid, Spain;
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Fusarium oxysporum and Colletotrichum musae Associated with Wilt Disease of Coffea arabica in Coffee Gardens in Saudi Arabia. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:3050495. [PMID: 36132979 PMCID: PMC9484884 DOI: 10.1155/2022/3050495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
Abstract
This study aimed to identify if Fusarium and Colletotrichum species are linked to coffee leaf wilt symptoms (Coffea arabica L.) gardens in Jazan region, Kingdom Saudi Arabia. The symptomatic wilted leaves and shoots were collected from Jazan Mountain Region Development Authority (JMRDA) farm in jabal Fifa. Samples of roots and leaves tissues were plated on Dox' Agar medium and incubated for one week at 24oC. Two morphologically different fungus colonies grew on the medium. A PCR-based method was used for the molecular amplification and characterization of the fungi using a 18SrRNA specific primer. 1323 and 1501 bp PCR products were obtained by using the 1% agarose gel electrophoresis. The sequence analysis and genbank homology revealed that the present fungi were Fusarium oxysporum and Colletotrichum musae with 99 and 98% similarity, respectively. Both fungi sequences were submitted to the genebank under accession numbers OP010081 and OP010082, respectively. This is the first report of these two genera of fungi infecting the roots and leaves of coffee trees in Jazan Region of Saudi Arabia and suggests that other fungus species may play a significant role as diseases in other coffee-producing areas.
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Cai H, Yu N, Liu Y, Wei X, Guo C. Meta-analysis of fungal plant pathogen Fusarium oxysporum infection-related gene profiles using transcriptome datasets. Front Microbiol 2022; 13:970477. [PMID: 36090060 PMCID: PMC9449528 DOI: 10.3389/fmicb.2022.970477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Fusarium oxysporum is a serious soil-borne fungal pathogen that affects the production of many economically important crops worldwide. Recent reports suggest that this fungus is becoming the dominant species in soil and could become the main infectious fungus in the future. However, the infection mechanisms employed by F. oxysporum are poorly understood. In the present study, using a network meta-analysis technique and public transcriptome datasets for different F. oxysporum and plant interactions, we aimed to explore the common molecular infection strategy used by this fungus and to identify vital genes involved in this process. Principle component analysis showed that all the fungal culture samples from different datasets were clustered together, and were clearly separated from the infection samples, suggesting the feasibility of an integrated analysis of heterogeneous datasets. A total of 335 common differentially expressed genes (DEGs) were identified among these samples, of which 262 were upregulated and 73 were downregulated significantly across the datasets. The most enriched functional categories of the common DEGs were carbohydrate metabolism, amino acid metabolism, and lipid metabolism. Nine co-expression modules were identified, and two modules, the turquoise module and the blue module, correlated positively and negatively with all the infection processes, respectively. Co-expression networks were constructed for these two modules and hub genes were identified and validated. Our results comprise a cross fungal-host interaction resource, highlighting the use of a network biology approach to gain molecular insights.
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Affiliation(s)
| | | | | | | | - Changhong Guo
- Key Laboratory of Molecular and Cytogenetics, Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, China
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20
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Labanska M, van Amsterdam S, Jenkins S, Clarkson JP, Covington JA. Preliminary Studies on Detection of Fusarium Basal Rot Infection in Onions and Shallots Using Electronic Nose. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22145453. [PMID: 35891126 PMCID: PMC9315870 DOI: 10.3390/s22145453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 06/01/2023]
Abstract
The evaluation of crop health status and early disease detection are critical for implementing a fast response to a pathogen attack, managing crop infection, and minimizing the risk of disease spreading. Fusarium oxysporum f. sp. cepae, which causes fusarium basal rot disease, is considered one of the most harmful pathogens of onion and accounts for considerable crop losses annually. In this work, the capability of the PEN 3 electronic nose system to detect onion and shallot bulbs infected with F. oxysporum f. sp. cepae, to track the progression of fungal infection, and to discriminate between the varying proportions of infected onion bulbs was evaluated. To the best of our knowledge, this is a first report on successful application of an electronic nose to detect fungal infections in post-harvest onion and shallot bulbs. Sensor array responses combined with PCA provided a clear discrimination between non-infected and infected onion and shallot bulbs as well as differentiation between samples with varying proportions of infected bulbs. Classification models based on LDA, SVM, and k-NN algorithms successfully differentiate among various rates of infected bulbs in the samples with accuracy up to 96.9%. Therefore, the electronic nose was proved to be a potentially useful tool for rapid, non-destructive monitoring of the post-harvest crops.
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Affiliation(s)
- Malgorzata Labanska
- The Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, 05-870 Blonie, Poland
| | - Sarah van Amsterdam
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK; (S.v.A.); (S.J.); (J.P.C.)
| | - Sascha Jenkins
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK; (S.v.A.); (S.J.); (J.P.C.)
| | - John P. Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK; (S.v.A.); (S.J.); (J.P.C.)
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Kamali-Sarvestani S, Mostowfizadeh-Ghalamfarsa R, Salmaninezhad F, Cacciola SO. Fusarium and Neocosmospora Species Associated with Rot of Cactaceae and Other Succulent Plants. J Fungi (Basel) 2022; 8:jof8040364. [PMID: 35448595 PMCID: PMC9024871 DOI: 10.3390/jof8040364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/21/2022] [Accepted: 03/26/2022] [Indexed: 01/31/2023] Open
Abstract
Infections by Fusarium and Fusarium-like species on cacti and other succulent plants cause the syndrome known as Fusarium dry rot and soft rot. There are only few records of Fusarium species as pathogens of cacti and other succulent plants from Iran. The objective of this study was the identification and characterization of fusarioid species recovered from ornamental succulents in Shiraz County, Iran. Three fusarioid species, including F. oxysporum, F. proliferatum, and Neocosmospora falciformis (formerly F. falciforme), were recovered from 29 diverse species of cacti and other succulents with symptoms of Fusarium dry rot and soft rot. The three fungal species were identified on the basis of morphological characters and the phylogenetic analysis of the translation elongation factor1-α (tef1) nuclear gene. The F. oxysporum isolates were identified as F. oxysporum f. sp. opuntiarum. The pathogenicity of the three fusarioid species was tested on a range of economically important ornamental succulents, mostly in the Cactaceae family. The three species showed a broad host spectrum and induced different types of symptoms on inoculated plants, including soft and dry rot, chlorosis, necrotic spots, wilt, drying, root and crown rot. This is the first report of N. falciformis as a pathogen of succulent plants worldwide.
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Affiliation(s)
- Sahar Kamali-Sarvestani
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.K.-S.); (F.S.)
| | - Reza Mostowfizadeh-Ghalamfarsa
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.K.-S.); (F.S.)
- Correspondence: (R.M.-G.); (S.O.C.); Tel.: +39-0957147371 (S.O.C.)
| | - Fatemeh Salmaninezhad
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 7144165186, Iran; (S.K.-S.); (F.S.)
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
- Correspondence: (R.M.-G.); (S.O.C.); Tel.: +39-0957147371 (S.O.C.)
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22
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Kotera S, Hishiike M, Saito H, Komatsu K, Arie T. Differentiation of the Pea Wilt Pathogen Fusarium oxysporum f. sp. pisi from Other Isolates of Fusarium Species by PCR. Microbes Environ 2022; 37:ME21061. [PMID: 34980803 PMCID: PMC8958301 DOI: 10.1264/jsme2.me21061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/05/2021] [Indexed: 12/02/2022] Open
Abstract
Pea wilt disease, caused by the soilborne and seedborne fungal pathogen Fusarium oxysporum f. sp. pisi (Fop), first appeared in Japan in 2002. We herein investigated the molecular characteristics of 16 Fop isolates sampled from multiple locations and at different times in Japan. The 16 isolates were divided into three clades in molecular phylogenic ana-lyses based on both the TEF1α gene and the rDNA-IGS region. All of the Fop isolates harbored a PDA1 gene, which encodes the cytochrome P450 pisatin demethylase (Pda1), and also carried one or both of the SIX6 and SIX13 genes, which encode secreted in xylem (Six) proteins. Other forms of F. oxysporum and other species of Fusarium did not carry these sets of genes. Based on these results, a PCR method was developed to identify Fop and differentiate it from other forms and non-pathogenic isolates of Fusarium spp. We also demonstrated that the PCR method effectively detected Fop in infected pea plants and infested soils.
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Affiliation(s)
- Shunsuke Kotera
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
| | - Masashi Hishiike
- Wakayama Agricultural Experiment Station, Takao, Kishigawacho, Kinokawa, Wakayama, 640–0423, Japan
| | - Hiroki Saito
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), 3–5–8 Saiwaicho, Fuchu, Tokyo, 183–8509, Japan
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Antagonistic activity and characterization of indigenous soil isolates of bacteria and fungi against onion wilt incited by Fusarium sp. Arch Microbiol 2021; 204:68. [PMID: 34950974 DOI: 10.1007/s00203-021-02663-2] [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: 02/17/2021] [Revised: 10/10/2021] [Accepted: 10/14/2021] [Indexed: 02/04/2023]
Abstract
Tuber rot disease due to phytopathogen Fusarium oxysporum f. sp. cepae (Foc) infection is one of the main factors causing the decreasing global onions production. This study aims to find bacteria and fungi candidates with Foc antagonistic activity through in vitro tests using dual culture techniques. A total of three bacterial isolates and three fungal isolates isolated from the rhizosphere of healthy onion plants showed the ability to inhibit Fusarium oxysporum growth. LC648364 isolate had an average inhibitory capability of 65.93%. At the same time, LC648367 and LC648368 fungal isolates can inhibit the growth of F. oxysporum by as much as 74.82% and 67.76%, respectively. Molecular analysis based on 16S rRNA markers showed three isolates belonging to the Bacillus. The LC648364 isolates are closely related to species Bacillus sp. strain LLB-17, LC648365 is closely related to B. subtilis strain S11 and LC648366 is closely related to B. cereus strain EM6. For the fungi, based on internal transcribed spacer (ITS) gene markers, there are three isolates. The LC648367 isolate is closely related to Aspergillus tubingensis, LC648368 is closely related to Trichoderma asperellum and LC648369 is closely related to Issatchenkia orientalis. This study can be used to develop indigenous microbial consortiums as biological control agents for phytopathogenic fungi Fusarium tuber rot on onion.
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Huo YY, Li TT, Yang J, Huang HY, Chen CJ, Xu FR, Dong X. Chemical Constituents of the Essential oil from Cuminum cyminum L. and Its Antifungal Activity against Panax notoginseng Pathogens. Chem Biodivers 2021; 18:e2100638. [PMID: 34788487 DOI: 10.1002/cbdv.202100638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/21/2021] [Indexed: 11/06/2022]
Abstract
Cuminum cyminum L. (Cumin) is a flavoring agent that is commonly used worldwide, and is rich in essential oil. Essential oils (Eos) have been intensively investigated in regard to their potential for disease control in plants, which is provided a chance for the blossom of green pesticides. The chemical components of Cumin essential oil (CEO) were revealed by GC/MS, such as cuminaldehyde (44.53 %), p-cymene (12.14 %), (-)-β-pinene (10.47 %) and γ-terpinene (8.40 %), and found they can inhibit the growth of P. notoginseng-associated pathogenic fungi in vitro and the inhibitory effect of cuminaldehyde was similar to that of hymexazol. SEM and TEM images demonstrated that cuminaldehyde and CEO increased cell permeability and disrupted membrane integrity. The expression of disease-related genes of Fusarium oxysporum showed that CEO induced the expression of most genes, which disrupted biosynthesis, metabolism and signaling pathways. These studies verified the potential of CEO as a plant fungicide that is environmentally friendly and provided ideas for developing new products for controlling root diseases that affect P. notoginseng.
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Affiliation(s)
- Ying-Ying Huo
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Tian-Tian Li
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Jing Yang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Heng-Yu Huang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Chuan-Jiao Chen
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Fu-Rong Xu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
| | - Xian Dong
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650500, P. R. China
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Perincherry L, Urbaniak M, Pawłowicz I, Kotowska K, Waśkiewicz A, Stępień Ł. Dynamics of Fusarium Mycotoxins and Lytic Enzymes during Pea Plants' Infection. Int J Mol Sci 2021; 22:9888. [PMID: 34576051 PMCID: PMC8467997 DOI: 10.3390/ijms22189888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/01/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Fusarium species are common plant pathogens that cause several important diseases. They produce a wide range of secondary metabolites, among which mycotoxins and extracellular cell wall-degrading enzymes (CWDEs) contribute to weakening and invading the host plant successfully. Two species of Fusarium isolated from peas were monitored for their expression profile of three cell wall-degrading enzyme coding genes upon culturing with extracts from resistant (Sokolik) and susceptible (Santana) pea cultivars. The extracts from Santana induced a sudden increase in the gene expression, whereas Sokolik elicited a reduced expression. The coherent observation was that the biochemical profile of the host plant plays a major role in regulating the fungal gene expression. In order to uncover the fungal characteristics in planta, both pea cultivars were infected with two strains each of F. proliferatum and F. oxysporum on the 30th day of growth. The enzyme activity assays from both roots and rhizosphere indicated that more enzymes were used for degrading the cell wall of the resistant host compared to the susceptible host. The most commonly produced enzymes were cellulase, β-glucosidase, xylanase, pectinase and lipase, where the pathogen selectively degraded the components of both the primary and secondary cell walls. The levels of beauvericin accumulated in the infected roots of both cultivars were also monitored. There was a difference between the levels of beauvericin accumulated in both the cultivars, where the susceptible cultivar had more beauvericin than the resistant one, showing that the plants susceptible to the pathogen were also susceptible to the toxin accumulation.
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Affiliation(s)
- Lakshmipriya Perincherry
- Department of Plant-Pathogen Interaction, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.U.); (K.K.)
| | - Monika Urbaniak
- Department of Plant-Pathogen Interaction, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.U.); (K.K.)
| | - Izabela Pawłowicz
- Department of Plant Physiology, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland;
| | - Karolina Kotowska
- Department of Plant-Pathogen Interaction, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.U.); (K.K.)
| | - Agnieszka Waśkiewicz
- Department of Chemistry, Poznań University of Life Sciences, 60-625 Poznań, Poland;
| | - Łukasz Stępień
- Department of Plant-Pathogen Interaction, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland; (M.U.); (K.K.)
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26
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Raman T, Edwin Raj E, Muthukathan G, Loganathan M, Periyasamy P, Natesh M, Manivasakan P, Kotteeswaran S, Rajendran S, Subbaraya U. Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen ( Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms. J Fungi (Basel) 2021; 7:jof7090717. [PMID: 34575755 PMCID: PMC8469521 DOI: 10.3390/jof7090717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 02/05/2023] Open
Abstract
Fusarium wilt is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc) and is the most serious disease affecting bananas (Musa spp.). The fungus is classified into Foc race 1 (R1), Foc race 2, and Foc race 4 based on host specificity. As the rate of spread and the ranges of the devastation of the Foc races exceed the centre of the banana’s origin, even in non-targeted cultivars, there is a possibility of variation in virulence-associated genes. Therefore, the present study investigates the genome assembly of Foc races that infect the Cavendish (AAA) banana group in India, specifically those of the vegetative compatibility group (VCG) 0124 (race 1), 0120 (subtropical race 4), and 01213/16 (tropical race 4). While comparing the general features of the genome sequences (e.g., RNAs, GO, SNPs, and InDels), the study also looked at transposable elements, phylogenetic relationships, and virulence-associated effector genes, and sought insights into race-specific molecular mechanisms of infection based on the presence of unique genes. The results of the analyses revealed variations in the organisation of genome assembly and virulence-associated genes, specifically secreted in xylem (SIX) genes, when compared to their respective reference genomes. The findings contributed to a better understanding of Indian Foc genomes, which will aid in the development of effective Fusarium wilt management techniques for various Foc VCGs in India and beyond.
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Affiliation(s)
- Thangavelu Raman
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
- Correspondence:
| | - Esack Edwin Raj
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
- Research and Development Division, MIRO Forestry SL Ltd., Mile 91, Tonkolili District, Northern Provenance P.O. Box GP20200, Sierra Leone
| | - Gopi Muthukathan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Murugan Loganathan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Pushpakanth Periyasamy
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Marimuthu Natesh
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Prabaharan Manivasakan
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Sharmila Kotteeswaran
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Sasikala Rajendran
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
| | - Uma Subbaraya
- Plant Pathology Division, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu 620102, India; (E.E.R.); (G.M.); (M.L.); (P.P.); (M.N.); (P.M.); (S.K.); (S.R.); (U.S.)
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Nephalela-Mavhunga M, Kwinda GT, Summerell BA, Venter E, Jacobs A. Genetic Diversity of the Fusarium oxysporum Complex Isolated from the Grassland Biome of South Africa. PHYTOPATHOLOGY 2021; 111:1459-1469. [PMID: 33225833 DOI: 10.1094/phyto-09-20-0377-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The genetic diversity of pathogenic members of the Fusarium oxysporum species complex (FOSC) has been intensively studied worldwide, yet strains occurring in native soils with low anthropogenic disturbance remain poorly understood. This study focused on 355 F. oxysporum isolates from soils with low anthropogenic activity obtained from the grassland biome of South Africa. Analysis of the translation elongation factor 1-alpha (tef-1α) gene revealed high levels of sequence type diversity within the soil population in comparison with the global dataset. Phylogenetic relationships of the South African isolates revealed that four nested within FOSC clade 1. This is the first report of members of the basal clade recovered from ecosystems with low anthropogenic disturbance from Sub-Saharan Africa. The remaining strains nested within clades 2 to 5. This study contributes significantly to our understanding of the distribution of the FOSC in natural systems as we show that FOSC populations in the South African grassland biome are genetically diverse. This fills in our knowledge gap because previous studies reported only on the occurrence and diversity of the FOSC isolated from plant debris in South Africa. This is the first comprehensive survey of fusaria from grassland soils with low anthropogenic disturbance in South Africa.
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Affiliation(s)
- Mudzuli Nephalela-Mavhunga
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Grace T Kwinda
- Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria 0001, South Africa
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens and Domain Trust, Sydney NSW 2000, Australia
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Adriaana Jacobs
- Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria 0001, South Africa
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Nellist CF, Armitage AD, Bates HJ, Sobczyk MK, Luberti M, Lewis LA, Harrison RJ. Comparative Analysis of Host-Associated Variation in Phytophthora cactorum. Front Microbiol 2021; 12:679936. [PMID: 34276614 PMCID: PMC8285097 DOI: 10.3389/fmicb.2021.679936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/30/2022] Open
Abstract
Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.
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Affiliation(s)
| | - Andrew D. Armitage
- NIAB EMR, East Malling, United Kingdom
- National Resources Institute, University of Greenwich, Chatham, United Kingdom
| | - Helen J. Bates
- NIAB EMR, East Malling, United Kingdom
- NIAB, Cambridge, United Kingdom
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Le D, Ameye M, De Boevre M, De Saeger S, Audenaert K, Haesaert G. Population, Virulence, and Mycotoxin Profile of Fusarium spp. Associated With Basal Rot of Allium spp. in Vietnam. PLANT DISEASE 2021; 105:1942-1950. [PMID: 33306427 DOI: 10.1094/pdis-08-20-1850-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium basal rot (FBR) is particularly problematic to Allium producers worldwide. In Vietnam, information on the profile of FBR is scarce, even though the presence of Fusarium spp. in Allium plants has long been recorded. In this study, a total of 180 isolates of Fusarium spp. were recovered from Allium bulbs/plants showing symptoms of FBR in 34 commercial Allium fields around Da Lat, Lam Dong, Vietnam. These isolates were identified to the species level by sequencing the internal transcribed spacer region and the translation elongation factor 1α gene. F. oxysporum was most prevalent (81%) in samples from all locations and Allium varieties, followed by F. solani (15%) and F. proliferatum (4%), which were only found in onion (Allium cepa L.). Pathogenicity tests on onion seedlings (56 isolates) and mini bulbs (10 isolates) indicated that onion can be infected by all of these species but virulence varied greatly between isolates. Moreover, isolates that were virulent on seedlings were sometimes not virulent on bulbs and vice versa, which points to a specialization of isolates for the host phenology. Mycotoxin analyses showed that the highest amounts of beauvericin were detected in seedlings and bulbs infected by F. oxysporum, whereas F. proliferatum was mainly responsible for the presence of fumonisin B1 in bulbs, suggesting a natural occurrence of beauvericin and fumonisin B1 in onions infected by these pathogens.
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Affiliation(s)
- Dung Le
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, BE-9000 Ghent, Belgium
- Faculty of Agriculture and Forestry, Dalat University, Lamdong, Dalat 66000, Vietnam
| | - Maarten Ameye
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, BE-9000 Ghent, Belgium
| | - Marthe De Boevre
- Faculty of Pharmaceutical Sciences, Department of Bioanalysis, Ghent University, BE-9000 Ghent, Belgium
| | - Sarah De Saeger
- Faculty of Pharmaceutical Sciences, Department of Bioanalysis, Ghent University, BE-9000 Ghent, Belgium
| | - Kris Audenaert
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, BE-9000 Ghent, Belgium
| | - Geert Haesaert
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, BE-9000 Ghent, Belgium
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Dvorianinova EM, Pushkova EN, Novakovskiy RO, Povkhova LV, Bolsheva NL, Kudryavtseva LP, Rozhmina TA, Melnikova NV, Dmitriev AA. Nanopore and Illumina Genome Sequencing of Fusarium oxysporum f. sp. lini Strains of Different Virulence. Front Genet 2021; 12:662928. [PMID: 34220940 PMCID: PMC8248858 DOI: 10.3389/fgene.2021.662928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Jenkins S, Taylor A, Jackson AC, Armitage AD, Bates HJ, Mead A, Harrison RJ, Clarkson JP. Identification and Expression of Secreted In Xylem Pathogenicity Genes in Fusarium oxysporum f. sp. pisi. Front Microbiol 2021; 12:593140. [PMID: 33897626 PMCID: PMC8062729 DOI: 10.3389/fmicb.2021.593140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Fusarium oxysporum is a soilborne fungal plant pathogen responsible for causing disease in many economically important crops with “special forms” (formae speciales) adapted to infect specific plant hosts. F. oxysporum f. sp. pisi (FOP) is the causal agent of Fusarium wilt disease of pea. It has been reported in every country where peas are grown commercially. Disease is generally controlled using resistant cultivars possessing single major gene resistance and therefore there is a constant risk of breakdown. The main aim of this work was to characterise F. oxysporum isolates collected from diseased peas in the United Kingdom as well as FOP isolates obtained from other researchers representing different races through sequencing of a housekeeping gene and the presence of Secreted In Xylem (SIX) genes, which have previously been associated with pathogenicity in other F. oxysporum f. spp. F. oxysporum isolates from diseased United Kingdom pea plants possessed none or just one or two known SIX genes with no consistent pattern of presence/absence, leading to the conclusion that they were foot-rot causing isolates rather than FOP. In contrast, FOP isolates had different complements of SIX genes with all those identified as race 1 containing SIX1, SIX6, SIX7, SIX9, SIX10, SIX11, SIX12, and SIX14. FOP isolates that were identified as belonging to race 2 through testing on differential pea cultivars, contained either SIX1, SIX6, SIX9, SIX13, SIX14 or SIX1, SIX6, SIX13. Significant upregulation of SIX genes was also observed in planta over the early stages of infection by different FOP races in pea roots. Race specific SIX gene profiling may therefore provide potential targets for molecular identification of FOP races but further research is needed to determine whether variation in complement of SIX genes in FOP race 2 isolates results in differences in virulence across a broader set of pea differential cultivars.
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Affiliation(s)
- Sascha Jenkins
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, United Kingdom
| | - Andrew Taylor
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, United Kingdom
| | - Alison C Jackson
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, United Kingdom
| | - Andrew D Armitage
- NIAB-EMR, East Malling Research, Kent, United Kingdom.,Natural Resources Institute, University of Greenwich, Kent, United Kingdom
| | - Helen J Bates
- NIAB-EMR, East Malling Research, Kent, United Kingdom
| | - Andrew Mead
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | | | - John P Clarkson
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne Campus, Warwick, United Kingdom
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Jangir P, Mehra N, Sharma K, Singh N, Rani M, Kapoor R. Secreted in Xylem Genes: Drivers of Host Adaptation in Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:628611. [PMID: 33968096 PMCID: PMC8101498 DOI: 10.3389/fpls.2021.628611] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/01/2021] [Indexed: 05/17/2023]
Abstract
Fusarium oxysporum (Fo) is a notorious pathogen that significantly contributes to yield losses in crops of high economic status. It is responsible for vascular wilt characterized by the browning of conductive tissue, wilting, and plant death. Individual strains of Fo are host specific (formae speciales), and approximately, 150 forms have been documented so far. The pathogen secretes small effector proteins in the xylem, termed as Secreted in Xylem (Six), that contribute to its virulence. Most of these proteins contain cysteine residues in even numbers. These proteins are encoded by SIX genes that reside on mobile pathogenicity chromosomes. So far, 14 proteins have been reported. However, formae speciales vary in SIX protein profile and their respective gene sequence. Thus, SIX genes have been employed as ideal markers for pathogen identification. Acquisition of SIX-encoding mobile pathogenicity chromosomes by non-pathogenic lines, through horizontal transfer, results in the evolution of new virulent lines. Recently, some SIX genes present on these pathogenicity chromosomes have been shown to be involved in defining variation in host specificity among formae speciales. Along these lines, the review entails the variability (formae speciales, races, and vegetative compatibility groups) and evolutionary relationships among members of F. oxysporum species complex (FOSC). It provides updated information on the diversity, structure, regulation, and (a)virulence functions of SIX genes. The improved understanding of roles of SIX in variability and virulence of Fo has significant implication in establishment of molecular framework and techniques for disease management. Finally, the review identifies the gaps in current knowledge and provides insights into potential research landscapes that can be explored to strengthen the understanding of functions of SIX genes.
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Affiliation(s)
| | | | | | | | | | - Rupam Kapoor
- Department of Botany, University of Delhi, New Delhi, India
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Tang T, Wang F, Jie G, Guo X, Duan Y, You J. Duohua huangjing (Polygonatum cyrtonema Hua) seedling basal rot caused by Fusarium redolens in China. PLANT DISEASE 2021; 105:2717. [PMID: 33858188 DOI: 10.1094/pdis-03-21-0597-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Duohua huangjing (Polygonatum cyrtonema Hua) seedling basal stem rot caused by Fusarium redolens in China Tao Tang1, Fanfan Wang1, Jie Guo1, Xiaoliang Guo1, Yuanyuan Duan1,Jingmao You1* 1 Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, 445000, China. Duohua huangjing (Polygonatum cyrtonema Hua), a herbal medicine, that is mostly planted in several provinces in China. In April 2020, severe diseases with about 40% seedling losse was found in the Huangjing seedling base in Shiyan city, Hubei province. The symptoms included softening and decay of the roots and stem bases, a progressive yellowing and wilting of leaves, and finally being completely rotted. Small pieces of symptomatic stems (0.5 cm in length) and leaves (0.5 × 0.5 cm in size) were surface sterilized with 75% ethanol for 30 s, followed by 0.1% HgCl2 for 1 min, rinsed three times with sterile water, and then dried with sterilized absorbent paper. The sections were placed on potato dextrose agar (PDA) medium containing 10 µg/ml of ampicillin and incubated at 25°C in the dark. After 3 days incubation, eight isolates with the same colony morphology were sub-cultured and purified by hyphal tip isolation. Macroconidia were sickle-shaped, 15.8 - 32.3 × 3.1 - 5.6 μm (n = 25), and three to five septate. Microconidia were oval or kidney-shaped, 5.2 - 11.4 × 2.0 - 3.2 μm (n = 25), and zero to one septate. To confirm the identity of the pathogen, molecular identification was performed with strain HJCD1. Following DNA extraction, PCR was performed using the TSINGKE 2×T5 Direct PCR Mix kit. Target areas of amplification were the internal transcribed spacer (ITS) and translation elongation factor 1α (TEF-1α) using ITS1/4 (White et al. 1990) , EF1/EF2 (Taylor et al. 2016), respectively. Following BLAST searches and phylogenetic reconstruction, the ITS region (GenBank MW485770.1) showed 99% identity with those of Fusarium redolens in GenBank (KU350713.1) and the TEF-1α (GenBank MW503930.1) showed 100% identity with F. redolens GenBank (MK922537.1). Pathogenicity tests were performed to fulfill Koch's postulates. Huangjing seedlings were rinsed with sterile water, wiped clean with sterile absorbent paper, and transferred to a tray covered with wet filter paper to maintain high humidity. The mycelial piugs of F. redolens HJCD1 were inoculated onto the surface of leaves and basal stems. Controls were inoculated with sterile PDA plugs. The inoculated seedlings were sealed with plastic wrap, and then cultivated in a 25 ℃ growth chamber with 16 h of light per day. The pathogen-inoculated plants exhibited etiolation and typical wilt symptoms after 4 days, whereas no symptoms were observed in the control plants. F. redolens was reisolated from the infected tissues, and colony morphology and ITS sequence of re-isolates were same as that of HJCD1. The pathogen has been reported previously in american ginseng in China (Fan et al. 2021), lentil in Pakistan (Rafique et al. 2020), and wild rocket in United Kingdom (Taylor et al. 2019). However, to the best of our knowledge, this is the first report of F. redolens causing seelding basal rot on Duohua huangjing in China. References: White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. Taylor, A., et al. 2016. Mol. Plant Pathol. 17:1032. https://doi.org/10.1111/mpp.12346 Fan, S. H., et al. 2021. Plant Dis. https://doi.org/10.1094/PDIS-11-19-2519-PDN Rafique, K., et al. 2020. Plant Dis. 9:104. https://doi.org/10.1094/PDIS-11-19-2519-PDN Taylor, A., et al. 2019. Plant Dis.6:103. https://doi.org/10.1094/PDIS-12-18-2143-PDN Funding: Science Funds for Young Scholar of Hubei Academy of Agricultural Science (grant no. 2020NKYJJ20), National Modern Agricultural Industrial Technology System (grant no. CARS-21), Technology R&D Program of Enshi (grant no. D20190015), Science Funds for Young Scholar of Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences (grant no. 2019ZYCJJ03), Key Laboratory of Integrated Management of Crops of Central China, Ministry of Agriculture, P. R. China / Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control (grant no.2020ZTSJJ6).
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Affiliation(s)
- Tao Tang
- Hubei Academy of Agricultural Sciences, Institute of Chinese Herbal Medicines , Enshi, Hubei , China;
| | - Fanfan Wang
- Hubei Academy of Agricultural Sciences, Institute of Chinese Herbal Medicines, Enshi, China;
| | | | - Xiaoliang Guo
- Hubei Academy of Agricultural Sciences, Institute of Chinese Herbal Medicines, Enshi, HuBei, China;
| | - Yuanyuan Duan
- Hubei Academy of Agricultural Sciences, Institute of Chinese Herbal Medicines, Enshi, China;
| | - Jingmao You
- Hubei Academy of Agricultural Sciences, Institute of Chinese Herbal Medicines , NO.253,College Road, Enshi, HuBei, China, 445000;
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Gamboa-Becerra R, López-Lima D, Villain L, Breitler JC, Carrión G, Desgarennes D. Molecular and Environmental Triggering Factors of Pathogenicity of Fusarium oxysporum and F. solani Isolates Involved in the Coffee Corky-Root Disease. J Fungi (Basel) 2021; 7:jof7040253. [PMID: 33801572 PMCID: PMC8067267 DOI: 10.3390/jof7040253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 12/27/2022] Open
Abstract
Coffee corky-root disease causes serious damages to coffee crop and is linked to combined infection of Fusarium spp. and root-knot nematodes Meloidogyne spp. In this study, 70 Fusarium isolates were collected from both roots of healthy coffee plants and with corky-root disease symptoms. A phylogenetic analysis, and the detection of pathogenicity SIX genes and toxigenicity Fum genes was performed for 59 F. oxysporum and 11 F. solani isolates. Based on the molecular characterization, seven F. oxysporum and three F. solani isolates were assessed for their pathogenicity on coffee seedlings under optimal watering and water stress miming root-knot nematode effect on plants. Our results revealed that a drastic increment of plant colonization capacity and pathogenicity on coffee plants of some Fusarium isolates was caused by water stress. The pathogenicity on coffee of F. solani linked to coffee corky-root disease and the presence of SIX genes in this species were demonstrated for the first time. Our study provides evidence for understanding the pathogenic basis of F. oxysporum and F. solani isolates on coffee and revealed the presence of SIX and Fum genes as one of their pathogenicity-related mechanisms. We also highlight the relevance of chlorophyll, a fluorescence as an early and high-throughput phenotyping tool in Fusarium pathogenicity studies on coffee.
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Affiliation(s)
- Roberto Gamboa-Becerra
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
| | - Daniel López-Lima
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
| | - Luc Villain
- CIRAD, UMR DIADE, F-34394 Montpellier, France; (L.V.); (J.-C.B.)
| | | | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
- Correspondence: (G.C.); (D.D.); Tel.: +52-228-842-1800 (D.D.)
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología A.C. Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico; (R.G.-B.); (D.L.-L.)
- Correspondence: (G.C.); (D.D.); Tel.: +52-228-842-1800 (D.D.)
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Czislowski E, Zeil-Rolfe I, Aitken EAB. Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana ( Musa sp.) Hosts. Int J Mol Sci 2021; 22:ijms22052508. [PMID: 33801529 PMCID: PMC7975973 DOI: 10.3390/ijms22052508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC.
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Simbaqueba J, Rodríguez EA, Burbano-David D, González C, Caro-Quintero A. Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali ( Foph) That Infects Cape Gooseberry Plants. Front Microbiol 2021; 11:593915. [PMID: 33537009 PMCID: PMC7847934 DOI: 10.3389/fmicb.2020.593915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/28/2020] [Indexed: 02/02/2023] Open
Abstract
The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A transcriptomic analysis of a highly virulent strain of F. oxysporum in cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other formae speciales (ff. spp.) of F. oxysporum. This pathogenic strain was classified as a new f. sp. named Foph, due to its specificity for cape gooseberry hosts. Here, we sequenced and assembled the genome of five strains of F. oxysporum from a fungal collection associated to the cape gooseberry crop (including Foph), focusing on the validation of the presence of SIX homologous and on the identification of putative effectors unique to Foph. By comparative and phylogenomic analyses based on single-copy orthologous, we found that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol that contain effector genes and identified six new putative effector genes, specific to Foph pathogenic strains. We also conducted a molecular characterization using this set of putative novel effectors in a panel of 36 additional stains of F. oxysporum including two of the four sequenced strains, from the fungal collection mentioned above. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified in this genomic analysis, represent new sources involved in the interaction between Foph and cape gooseberry, that could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.
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Affiliation(s)
- Jaime Simbaqueba
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Edwin A Rodríguez
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Diana Burbano-David
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Carolina González
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
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Batson AM, Fokkens L, Rep M, du Toit LJ. Putative Effector Genes Distinguish Two Pathogenicity Groups of Fusarium oxysporum f. sp. spinaciae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:141-156. [PMID: 33103963 DOI: 10.1094/mpmi-06-20-0145-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in F. oxysporum f. sp. spinaciae genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographically diverse F. oxysporum isolates was tested for pathogenicity on each of three spinach inbreds. Thirty-nine isolates identified as F. oxysporum f. sp. spinaciae caused quantitative differences in disease severity among the inbreds that revealed two distinct pathogenicity groups of F. oxysporum f. sp. spinaciae. Putative effector gene profiles, predicted from whole-genome sequences generated for nine F. oxysporum f. sp. spinaciae isolates and five nonpathogenic, spinach-associated F. oxysporum (NPS) isolates, distinguished the F. oxysporum f. sp. spinaciae isolates from the NPS isolates, and separated the F. oxysporum f. sp. spinaciae isolates into two groups. Five of the putative effector genes appeared to be unique to F. oxysporum f. sp. spinaciae, as they were not found in 222 other publicly available genome assemblies of F. oxysporum, implicating potential involvement of these genes in pathogenicity to spinach. In addition, two combinations of the 14 known Secreted in Xylem (SIX) genes that have been affiliated with host pathogenicity in other formae speciales of F. oxysporum were identified in genome assemblies of the nine F. oxysporum f. sp. spinaciae isolates, either SIX8 and SIX9 or SIX4, SIX8, and SIX14. Characterization of these putative effector genes should aid in understanding mechanisms of pathogenicity in F. oxysporum f. sp. spinaciae, developing molecular tools for rapid detection and quantification of F. oxysporum f. sp. spinaciae, and breeding for resistance to Fusarium wilt in spinach.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Alexander M Batson
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands
| | - Lindsey J du Toit
- Washington State University Northwestern Washington Research and Extension Center Mount Vernon, Mount Vernon, WA 98273, U.S.A
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Hudson O, Waliullah S, Fulton JC, Ji P, Dufault NS, Keinath A, Ali ME. Marker Development for Differentiation of Fusarium Oxysporum f. sp. Niveum Race 3 from Races 1 and 2. Int J Mol Sci 2021; 22:E822. [PMID: 33467563 PMCID: PMC7830397 DOI: 10.3390/ijms22020822] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/30/2022] Open
Abstract
Fusarium wilt of watermelon, caused by Fusarium oxysporum f. sp. niveum (FON), is pathogenic only to watermelon and has become one of the main limiting factors in watermelon production internationally. Detection methods for this pathogen are limited, with few published molecular assays available to differentiate FON from other formae speciales of F. oxysporum. FON has four known races that vary in virulence but are difficult and costly to differentiate using traditional inoculation methods and only race 2 can be differentiated molecularly. In this study, genomic and chromosomal comparisons facilitated the development of a conventional polymerase chain reaction (PCR) assay that could differentiate race 3 from races 1 and 2, and by using two other published PCR markers in unison with the new marker, the three races could be differentiated. The new PCR marker, FNR3-F/FNR3-R, amplified a 511 bp region on the "pathogenicity chromosome" of the FON genome that is absent in race 3. FNR3-F/FNR3-R detected genomic DNA down to 2.0 pg/µL. This marker, along with two previously published FON markers, was successfully applied to test over 160 pathogenic FON isolates from Florida, Georgia, and South Carolina. Together, these three FON primer sets worked well for differentiating races 1, 2, and 3 of FON. For each marker, a greater proportion (60 to 90%) of molecular results agreed with the traditional bioassay method of race differentiation compared to those that did not. The new PCR marker should be useful to differentiate FON races and improve Fusarium wilt research.
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Affiliation(s)
- Owen Hudson
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (S.W.); (P.J.)
| | - Sumyya Waliullah
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (S.W.); (P.J.)
| | - James C. Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.C.F.); (N.S.D.)
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (S.W.); (P.J.)
| | - Nicholas S. Dufault
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.C.F.); (N.S.D.)
| | - Anthony Keinath
- Department of Plant and Environmental Sciences, Clemson University, Charleston, SC 29414, USA;
| | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (O.H.); (S.W.); (P.J.)
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Constantin ME, Fokkens L, de Sain M, Takken FLW, Rep M. Number of Candidate Effector Genes in Accessory Genomes Differentiates Pathogenic From Endophytic Fusarium oxysporum Strains. FRONTIERS IN PLANT SCIENCE 2021; 12:761740. [PMID: 34912358 PMCID: PMC8666634 DOI: 10.3389/fpls.2021.761740] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/08/2021] [Indexed: 05/21/2023]
Abstract
The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investigated at the molecular level, and the genetic basis that underlies endophytic versus pathogenic behavior is unknown. To investigate this, 44 Fo strains from non-cultivated Australian soils, grass roots from Spain, and tomato stems from United States were characterized genotypically by whole genome sequencing, and phenotypically by examining their ability to symptomlessly colonize tomato plants and to confer resistance against Fusarium Wilt. Comparison of the genomes of the validated endophytic Fo strains with those of 102 pathogenic strains revealed that both groups have similar genomes sizes, with similar amount of accessory DNA. However, although endophytic strains can harbor homologs of known effector genes, they have typically fewer effector gene candidates and associated non-autonomous transposons (mimps) than pathogenic strains. A pathogenic 'lifestyle' is associated with extended effector gene catalogs and a set of "host specific" effectors. No candidate effector genes unique to endophytic strains isolated from the same plant species were found, implying little or no host-specific adaptation. As plant-beneficial interactions were observed to be common for the tested Fo isolates, the propensity for endophytism and the ability to confer biocontrol appears to be a predominant feature of this organism. These findings allow prediction of the lifestyle of a Fo strain based on its genome sequence as a potential pathogen or as a harmless or even beneficial endophyte by determining its effectorome and mimp number.
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Dobbs JT, Kim MS, Dudley NS, Klopfenstein NB, Yeh A, Hauff RD, Jones TC, Dumroese RK, Cannon PG, Stewart JE. Whole genome analysis of the koa wilt pathogen (Fusarium oxysporum f. sp. koae) and the development of molecular tools for early detection and monitoring. BMC Genomics 2020; 21:764. [PMID: 33148175 PMCID: PMC7640661 DOI: 10.1186/s12864-020-07156-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. RESULTS This study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa. CONCLUSIONS These results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.
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Affiliation(s)
- John T. Dobbs
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331 USA
| | - Nicklos S. Dudley
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Ned B. Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Aileen Yeh
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - Robert D. Hauff
- Division of Forestry and Wildlife, Department of Land and Natural Resources, 1151 Punchbowl Street, Room 325, Honolulu, HI 96813 USA
| | - Tyler C. Jones
- Hawai‘i Agriculture Research Center, Maunawili Research Station, Oahu, HI USA
| | - R. Kasten Dumroese
- USDA Forest Service, Rocky Mountain Research Station, 1221 South Main Street, Moscow, ID 83843 USA
| | - Philip G. Cannon
- USDA Forest Service, Forest Health Protection, 1323 Club Drive, Vallejo, CA 94592 USA
| | - Jane E. Stewart
- Colorado State University, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, CO 80523 USA
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Henry P, Kaur S, Pham QAT, Barakat R, Brinker S, Haensel H, Daugovish O, Epstein L. Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii. BMC Genomics 2020; 21:730. [PMID: 33081696 PMCID: PMC7576743 DOI: 10.1186/s12864-020-07141-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3. RESULTS A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other. CONCLUSIONS There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible. Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.
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Affiliation(s)
- Peter Henry
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,USDA-ARS, 1636 East Alisal St., Salinas, CA, 93905, USA
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Quyen Anh Tran Pham
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Current address: Janssen Biopharma, Inc., 260 E Grand Ave., South San Francisco, CA, 94080, USA
| | - Radwan Barakat
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.,Department of Plant Production & Protection, College of Agriculture, Hebron University, Hebron, Palestine
| | - Samuel Brinker
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Hannah Haensel
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA
| | - Oleg Daugovish
- University of California Cooperative Extension, 669 County Square Drive, Suite 100, Ventura, CA, 93003, USA
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California, 95616-8680, USA.
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Li J, Gao M, Gabriel DW, Liang W, Song L. Secretome-Wide Analysis of Lysine Acetylation in Fusarium oxysporum f. sp. lycopersici Provides Novel Insights Into Infection-Related Proteins. Front Microbiol 2020; 11:559440. [PMID: 33013791 PMCID: PMC7506082 DOI: 10.3389/fmicb.2020.559440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 01/13/2023] Open
Abstract
Fusarium oxysporum f. sp. lycopersici (Fol) is the causal agent of Fusarium wilt disease in tomato. Proteins secreted by this pathogen during initial host colonization largely determine the outcome of pathogen-host interactions. Lysine acetylation (Kac) plays a vital role in the functions of many proteins, but little is known about Kac in Fol secreted proteins. In this study, we analyzed lysine acetylation of the entire Fol secretome. Using high affinity enrichment of Kac peptides and LC-MS/MS analysis, 50 potentially secreted Fol proteins were identified and acetylation sites determined. Bioinformatics analysis revealed 32 proteins with canonical N-terminal signal peptide leaders, and most of them were predicted to be enzymes involved in a variety of biological processes and metabolic pathways. Remarkably, all 32 predicted secreted proteins were novel and encoded on the core chromosomes rather than on the previously identified LS pathogenicity chromosomes. Homolog scanning of the secreted proteins among 40 different species revealed 4 proteins that were species specific, 3 proteins that were class-specific in the Ascomycota phylum, and 25 proteins that were more widely conserved genes. These secreted proteins provide a starting resource for investigating putative novel pathogenic genes, with 26 up-regulated genes encoding Kac proteins that may play an important role during initial symptomless infection stages.
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Affiliation(s)
- Jingtao Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Mingming Gao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Dean W Gabriel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Wenxing Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Limin Song
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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Adhikari TB, Gao A, Ingram T, Louws FJ. Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems. Front Microbiol 2020; 11:1995. [PMID: 32973719 PMCID: PMC7482420 DOI: 10.3389/fmicb.2020.01995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/28/2020] [Indexed: 01/19/2023] Open
Abstract
In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar 'Happy Root' (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.
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Affiliation(s)
- Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Anne Gao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Thomas Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.,Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
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44
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Duan Y, Qu W, Chang S, Li C, Xu F, Ju M, Zhao R, Wang H, Zhang H, Miao H. Identification of Pathogenicity Groups and Pathogenic Molecular Characterization of Fusarium oxysporum f. sp. sesami in China. PHYTOPATHOLOGY 2020; 110:1093-1104. [PMID: 32065037 DOI: 10.1094/phyto-09-19-0366-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fusarium oxysporum f. sp. sesami is an extremely destructive pathogen, causing sesame Fusarium wilt disease worldwide. To clarify the pathogenicity and the genetic characters of F. oxysporum f. sp. sesami, we systematically investigated 69 F. oxysporum isolates collected from major sesame-growing areas in China. Among these isolates, 54 isolates were pathogenic and 15 were nonpathogenic according to pathogenicity testing on sesame seedlings. For the pathogenic isolates, three F. oxysporum f. sp. sesami pathogenicity groups were defined based on the three differential sesame hosts for the first time. A translation elongation factor 1α gene tree was constructed to determine the genetic diversity of the F. oxysporum isolates but could not separate F. oxysporum f. sp. sesami isolates from the nonpathogenic isolates and other F. oxysporum formae speciales. Ten secreted-in-xylem (SIX) genes (one family of effectors) were identified in F. oxysporum f. sp. sesami isolates by a search with the genome data, and were subsequently screened in the 69 F. oxysporum isolates. Compared with the SIX gene profiles in other F. oxysporum formae speciales, the presence and sequence variations of the SIX gene homologs directly correlated with the specific pathogenicity of F. oxysporum f. sp. sesami toward sesame. Furthermore, eight of these F. oxysporum f. sp. sesami SIX genes were significantly expressed in sesame plants as infection of the F. oxysporum f. sp. sesami isolate. These findings have important significance for understanding the pathogenic basis of F. oxysporum f. sp. sesami isolates, and will contribute to improve the diagnostics to effectively control Fusarium wilt disease in sesame.
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Affiliation(s)
- Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Wenwen Qu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Shuxian Chang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Fangfang Xu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, P. R. China
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45
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Pathogenomics and Management of Fusarium Diseases in Plants. Pathogens 2020; 9:pathogens9050340. [PMID: 32369942 PMCID: PMC7281180 DOI: 10.3390/pathogens9050340] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
There is an urgency to supplant the heavy reliance on chemical control of Fusarium diseases in different economically important, staple food crops due to development of resistance in the pathogen population, the high cost of production to the risk-averse grower, and the concomitant environmental impacts. Pathogenomics has enabled (i) the creation of genetic inventories which identify those putative genes, regulators, and effectors that are associated with virulence, pathogenicity, and primary and secondary metabolism; (ii) comparison of such genes among related pathogens; (iii) identification of potential genetic targets for chemical control; and (iv) better characterization of the complex dynamics of host–microbe interactions that lead to disease. This type of genomic data serves to inform host-induced gene silencing (HIGS) technology for targeted disruption of transcription of select genes for the control of Fusarium diseases. This review discusses the various repositories and browser access points for comparison of genomic data, the strategies for identification and selection of pathogenicity- and virulence-associated genes and effectors in different Fusarium species, HIGS and successful Fusarium disease control trials with a consideration of loss of RNAi, off-target effects, and future challenges in applying HIGS for management of Fusarium diseases.
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46
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Adams TM, Armitage AD, Sobczyk MK, Bates HJ, Tabima JF, Kronmiller BA, Tyler BM, Grünwald NJ, Dunwell JM, Nellist CF, Harrison RJ. Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races. Front Microbiol 2020; 11:490. [PMID: 32351458 PMCID: PMC7174552 DOI: 10.3389/fmicb.2020.00490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, "red core". The host-pathogen interaction has a well described gene-for-gene resistance relationship, but to date neither candidate avirulence nor resistance genes have been identified. We sequenced a set of American, Canadian, and United Kingdom isolates of known race type, along with three representatives of the closely related pathogen of the raspberry (Rubus idaeus), P. rubi, and found a clear population structure, with a high degree of nucleotide divergence seen between some race types and abundant private variation associated with race types 4 and 5. In contrast, between isolates defined as United Kingdom races 1, 2, and 3 (UK1-2-3) there was no evidence of gene loss or gain; or the presence of insertions/deletions (INDELs) or Single Nucleotide Polymorphisms (SNPs) within or in proximity to putative pathogenicity genes could be found associated with race variation. Transcriptomic analysis of representative UK1-2-3 isolates revealed abundant expression variation in key effector family genes associated with pathogen race; however, further long read sequencing did not reveal any long range polymorphisms to be associated with avirulence to race UK2 or UK3 resistance, suggesting either control in trans or other stable forms of epigenetic modification modulating gene expression. This work reveals the combined power of population resequencing to uncover race structure in pathosystems and in planta transcriptomic analysis to identify candidate avirulence genes. This work has implications for the identification of putative avirulence genes in the absence of associated expression data and points toward the need for detailed molecular characterisation of mechanisms of effector regulation and silencing in oomycete plant pathogens.
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Affiliation(s)
- Thomas M. Adams
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Andrew D. Armitage
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Maria K. Sobczyk
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Helen J. Bates
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
| | - Javier F. Tabima
- Department of Botany and Plant Pathology, Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Brent A. Kronmiller
- Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Brett M. Tyler
- Department of Botany and Plant Pathology, Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
- Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J. Grünwald
- Horticultural Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Richard J. Harrison
- Department of Genetics, Genomics and Breeding, NIAB EMR, Kent, United Kingdom
- NIAB Cambridge Crop Research, NIAB, Cambridge, United Kingdom
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Brevibacillus fortis NRS-1210 produces edeines that inhibit the in vitro growth of conidia and chlamydospores of the onion pathogen Fusarium oxysporum f. sp. cepae. Antonie van Leeuwenhoek 2020; 113:973-987. [PMID: 32279200 DOI: 10.1007/s10482-020-01404-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/11/2020] [Indexed: 12/20/2022]
Abstract
Onions can be damaged by Fusarium basal rot caused by the soilborne fungus Fusarium oxysporum f. sp. cepae (FOC). Control of this pathogen is challenging since there is limited genetic resistance in onion. The identification of molecules that inhibit this pathogen is needed. Antagonism screening showed Brevibacillus fortis NRS-1210 secreted antifungal compounds into growth medium. The spent growth medium, diluted 1:1, inhibited growth of FOC conidia after seven hours and killed 67-91% of conidia after 11 h. The spent medium also inhibited growth of propagules from F. graminearum, F. proliferatum, F. verticillioides and Galactomyces citri-aurantii. Full strength spent growth medium did not effectively kill FOC conidia and chlamydospores inoculated into a sand cornmeal mixture. In silico analysis of the B. fortis NRS-1210 genome indicated the biosynthetic clusters of several antibiotics. Fractionation of spent medium followed by reverse-phase liquid chromatography with tandem mass spectrometry analysis found that fractions with the most antifungal activity contained a combination of edeines A, B and F and no other recognized antibiotics. 1H NMR signals of the active fraction corresponded to edeine, a pentapeptide with broad spectrum antimicrobial activity which blocks translation in both prokaryotes and eukaryotes. Comparative genomics of Brevibacillus genomes shows edeine producers form a clade which consists of: Brevibacillus brevis, Brevibacillus formosus, 'Brevibacillus antibioticus', Brevibacillus schisleri, Brevibacillus fortis, and Brevibacillus porteri. This observation suggests edeine played an important role in the evolution and speciation of the Brevibacillus genus.
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48
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Isolation and Identification of Fusarium spp., the Causal Agents of Onion ( Allium cepa) Basal Rot in Northeastern Israel. BIOLOGY 2020; 9:biology9040069. [PMID: 32252245 PMCID: PMC7236657 DOI: 10.3390/biology9040069] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 11/16/2022]
Abstract
Over the past decade, there have been accumulating reports from farmers and field extension personnel on the increasing incidence and spread of onion (Allium cepa) bulb basal rot in northern Israel. The disease is caused mainly by Fusarium species. Rotting onion bulbs were sampled from fields in the Golan Heights in northeastern Israel during the summers of 2017 and 2018. Tissue from the sampled onion bulbs was used for the isolation and identification of the infecting fungal species using colony and microscopic morphology characterization. Final confirmation of the pathogens was performed with PCR amplification and sequencing using fungi-specific and Fusarium species-specific primers. Four Fusarium spp. isolates were identified in onion bulbs samples collected from the contaminated field: F. proliferatum, F. oxysporum f. sp. cepae, and two species less familiar as causative agents of this disease, F. acutatum and F. anthophilium. Phylogenetic analysis revealed that these species subdivided into two populations, a northern group isolated from white (Riverside cv.) onion bulbs, and a southern group isolated from red (565/505 cv.) bulbs. Pathogenicity tests conducted with seedlings and bulbs under moist conditions proved that all species could cause the disease symptoms, but with different degrees of virulence. Inoculating seeds with spore suspensions of the four species, in vitro, significantly reduced seedlings’ germination rate, hypocotyl elongation, and fresh biomass. Mature onion bulbs infected with the fungal isolates produced typical rot symptoms 14 days post-inoculation, and the fungus from each infected bulb was re-isolated and identified to satisfy Koch’s postulates. The onion bulb assay also reflected the degree of sensitivity of different onion cultivars to the disease. This work is the first confirmed report of the direct and primary cause of Fusarium onion basal rot disease in northeastern Israel. These findings are a necessary step towards uncovering the mycoflora of the diseased onion plants and developing a preventive program that would reduce the disease damage.
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49
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Latvala S, Haapalainen M, Kivijärvi P, Suojala-Ahlfors T, Iivonen S, Hannukkala A. Sampling and PCR method for detecting pathogenic Fusarium oxysporum strains in onion harvest. Lett Appl Microbiol 2020; 70:210-220. [PMID: 31838746 DOI: 10.1111/lam.13264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 12/09/2019] [Indexed: 01/09/2023]
Abstract
Fusarium basal rot is a worldwide disease problem in onions, and causes substantial losses in onion production, both during the growing season and in the storage. To minimize the post-harvest losses, a protocol for screening of latent infections with pathogenic Fusarium oxysporum strains from harvested onions was developed. This protocol is based on a dual PCR test with primers specific for the fungal species and new SIX3 primers specific for the onion-pathogenic F. oxysporum strains. A pooled sample containing pieces from 50 harvested symptomless onions was prepared for the dual PCR using microwave disruption of the filamentous Fusarium fungi and Whatman FTATM filter paper matrix technology, or as a reference protocol, by extracting DNA with a commercial kit. The two sample preparation protocols gave consistent results with the tested onion samples. Detection limit of the dual PCR protocol was 100 pg of F. oxysporum DNA, in a mixture with onion DNA, when the FTA card was applied. The new protocol reported here is simple and sensitive enough for routine testing, enabling the detection of latent infections in harvest lots even at the infection levels under 10%. SIGNIFICANCE AND IMPACT OF THE STUDY: Fusarium basal rot causes serious problems in onion production. To minimize post-harvest losses, a simple protocol based on FTATM technology and a dual PCR test with Fusarium oxysporum species-specific and pathogenicity-specific primers was developed. By testing pooled onion samples using this method, latent infections with F. oxysporum can be screened from a representative sample of the harvest. This screening method could be a useful tool to manage the post-harvest losses caused by latent infections with F. oxysporum and, with modification of the PCR protocol, with other Fusarium species pathogenic to onion.
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Affiliation(s)
- S Latvala
- Natural Resources Institute Finland (Luke), Natural Resources, Jokioinen, Finland
| | - M Haapalainen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - P Kivijärvi
- Natural Resources Institute Finland (Luke), Production Systems, Mikkeli, Finland
| | - T Suojala-Ahlfors
- Natural Resources Institute Finland (Luke), Production Systems, Turku, Finland
| | - S Iivonen
- Natural Resources Institute Finland (Luke), Finnish Organic Research Institute, Mikkeli, Finland
| | - A Hannukkala
- Natural Resources Institute Finland (Luke), Natural Resources, Jokioinen, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Taylor A, Armitage AD, Handy C, Jackson AC, Hulin MT, Harrison RJ, Clarkson JP. Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi. Front Microbiol 2019; 10:2905. [PMID: 31921077 PMCID: PMC6930931 DOI: 10.3389/fmicb.2019.02905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.
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Affiliation(s)
- Andrew Taylor
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | - Claire Handy
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Alison C Jackson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | | | | | - John P Clarkson
- Warwick Crop Centre, School of Life Sciences, University of Warwick, Warwick, United Kingdom
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