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Iglesias-Guevara D, Sánchez-Torres P. Characterization of antifungal properties of avocado leaves and majagua flowers extracts and their potential application to control Alternaria alternata. Int J Food Microbiol 2024; 413:110579. [PMID: 38277871 DOI: 10.1016/j.ijfoodmicro.2024.110579] [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: 10/26/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024]
Abstract
Plant extracts are used as an alternative to a wide range of foods against different types of fungal pathogens. In the present study, the extracts of avocado leaves (Persea americana) and majagua flowers (Talipariti elatum) were tested according to their antifungal activity against different fungi. The most promising extracts were those of majagua flowers that were applied lyophilized and in aqueous extract, being very effective against Alternaria alternata and reaching a 50 % in vitro reduction. Antifungal properties were also evaluated during infection of apples by A. alternata. A decrease in infection progression was confirmed with up to a 30 % reduction in disease incidence and a 20 % reduction in disease severity. Majagua extracts were also tested combined with edible pectin coatings, greatly increasing their effectiveness up 60 % reduction. Thus, extracts of majagua could provide a feasible alternative to control fungal pathogens during postharvest.
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Affiliation(s)
- Dairon Iglesias-Guevara
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain; Faculty of Pharmacy and Food (IFAL), Havana University, Havana, Cuba
| | - Paloma Sánchez-Torres
- Food Biotechnology Department, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Catedrático Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain.
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2
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Schmey T, Tominello-Ramirez CS, Brune C, Stam R. Alternaria diseases on potato and tomato. MOLECULAR PLANT PATHOLOGY 2024; 25:e13435. [PMID: 38476108 DOI: 10.1111/mpp.13435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024]
Abstract
Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by Alternaria solani and brown spot caused by Alternaria alternata are most common, but the disease complex is far more diverse. We first provide an overview of the Alternaria species infecting the two host plants to alleviate some of the confusion that arises from the taxonomic rearrangements in this fungal genus. Highlighting the diversity of Alternaria fungi on both solanaceous hosts, we review studies investigating the genetic diversity and genomes, before we present recent advances from studies elucidating host-pathogen interactions and fungicide resistances. TAXONOMY Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria. BIOLOGY AND HOST RANGE Alternaria spp. adopt diverse lifestyles. We specifically review Alternaria spp. that cause disease in the two solanaceous crops potato (Solanum tuberosum) and tomato (Solanum lycopersicum). They are necrotrophic pathogens with no known sexual stage, despite some signatures of recombination. DISEASE SYMPTOMS Symptoms of the early blight/brown spot disease complex include foliar lesions that first present as brown spots, depending on the species with characteristic concentric rings, which eventually lead to severe defoliation and considerable yield loss. CONTROL Good field hygiene can keep the disease pressure low. Some potato and tomato cultivars show differences in susceptibility, but there are no fully resistant varieties known. Therefore, the main control mechanism is treatment with fungicides.
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Affiliation(s)
- Tamara Schmey
- TUM School of Life Science Weihenstephan, Technical University of Munich, Freising, Germany
| | - Christopher S Tominello-Ramirez
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Christian Albrechts University, Kiel, Germany
| | - Carolin Brune
- TUM School of Life Science Weihenstephan, Technical University of Munich, Freising, Germany
| | - Remco Stam
- Department of Phytopathology and Crop Protection, Institute of Phytopathology, Christian Albrechts University, Kiel, Germany
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3
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Khadiri M, Boubaker H, Laasli SE, Farhaoui A, Ezrari S, Radouane N, Radi M, Askarne L, Barka EA, Lahlali R. Unlocking Nature's Secrets: Molecular Insights into Postharvest Pathogens Impacting Moroccan Apples and Innovations in the Assessment of Storage Conditions. PLANTS (BASEL, SWITZERLAND) 2024; 13:553. [PMID: 38498518 PMCID: PMC10891559 DOI: 10.3390/plants13040553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Apple production holds a prominent position in Morocco's Rosaceae family. However, annual production can fluctuate due to substantial losses caused by fungal diseases affecting stored apples. Our findings emphasize that the pre-storage treatment of apples, disinfection of storage facilities, box type, and fruit sorting are pivotal factors affecting apple losses during storage. Additionally, the adopted preservation technique was significantly correlated with the percentage of damage caused by fungal infections. Blue mold accounts for nearly three-quarters of the diseases detected, followed by gray rot with a relatively significant incidence. This study has revealed several fungal diseases affecting stored apples caused by pathogens such as Penicillium expansum, Botrytis cinerea, Alternaria alternata, Trichothecium roseum, Fusarium avenaceum, Cadophora malorum, and Neofabraea vagabunda. Notably, these last two fungal species have been reported for the first time in Morocco as pathogens of stored apples. These data affirm that the high losses of apples in Morocco, attributed primarily to P. expansum and B. cinerea, pose a significant threat in terms of reduced production and diminished fruit quality. Hence, adopting controlled atmosphere storage chambers and implementing good practices before apple storage is crucial.
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Affiliation(s)
- Mohammed Khadiri
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km10, Rte Haj Kaddour, BP S/40, Meknès 50001, Morocco; (M.K.); (S.-E.L.); (A.F.)
- Laboratoire de Biotechnologies Microbiennes et Protection des Végétaux, Faculté des Sciences, Université Ibn Zhor, BP 8106, Agadir 80000, Morocco; (H.B.); (L.A.)
| | - Hassan Boubaker
- Laboratoire de Biotechnologies Microbiennes et Protection des Végétaux, Faculté des Sciences, Université Ibn Zhor, BP 8106, Agadir 80000, Morocco; (H.B.); (L.A.)
| | - Salah-Eddine Laasli
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km10, Rte Haj Kaddour, BP S/40, Meknès 50001, Morocco; (M.K.); (S.-E.L.); (A.F.)
| | - Abdelaaziz Farhaoui
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km10, Rte Haj Kaddour, BP S/40, Meknès 50001, Morocco; (M.K.); (S.-E.L.); (A.F.)
- Department of Biology, Laboratory of Biotechnology and Valorization of Bio-Resources (BioVaR), Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco
| | - Said Ezrari
- Microbiology Unit, Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Medicine and Pharmacy Oujda, University Mohammed Premier, Oujda 60000, Morocco
| | - Nabil Radouane
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43150, Morocco;
| | - Mohammed Radi
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km10, Rte Haj Kaddour, BP S/40, Meknès 50001, Morocco; (M.K.); (S.-E.L.); (A.F.)
- Laboratory of Environment and Valorization of Microbial and Plant Resources, Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco
| | - Latifa Askarne
- Laboratoire de Biotechnologies Microbiennes et Protection des Végétaux, Faculté des Sciences, Université Ibn Zhor, BP 8106, Agadir 80000, Morocco; (H.B.); (L.A.)
| | - Essaid Ait Barka
- Induced Resistance and Plant Biosection Research Unit-EA 4707-USC INRAE1488, Reims Cham-pagne-Ardenne University, 51687 Reims, France
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km10, Rte Haj Kaddour, BP S/40, Meknès 50001, Morocco; (M.K.); (S.-E.L.); (A.F.)
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4
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Vasundaradevi R, Sarvajith M, Somashekaraiah R, Gunduraj A, Sreenivasa MY. Antagonistic properties of Lactiplantibacillus plantarum MYSVB1 against Alternaria alternata: a putative probiotic strain isolated from the banyan tree fruit. Front Microbiol 2024; 15:1322758. [PMID: 38404595 PMCID: PMC10885809 DOI: 10.3389/fmicb.2024.1322758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024] Open
Abstract
Alternaria alternata, a notorious phytopathogenic fungus, has been documented to infect several plant species, leading to the loss of agricultural commodities and resulting in significant economic losses. Lactic acid bacteria (LAB) hold immense promise as biocontrol candidates. However, the potential of LABs derived from fruits remains largely unexplored. In this study, several LABs were isolated from tropical fruit and assessed for their probiotic and antifungal properties. A total of fifty-five LABs were successfully isolated from seven distinct fruits. Among these, seven isolates showed inhibition to growth of A. alternata. Two strains, isolated from fruits: Ficus benghalensis, and Tinospora cordifolia exhibited promising antifungal properties against A. alternata. Molecular identification confirmed their identities as Lactiplantibacillus plantarum MYSVB1 and MYSVA7, respectively. Both strains showed adaptability to a wide temperature range (10-45°C), and salt concentrations (up to 7%), with optimal growth around 37 °C and high survival rates under simulated gastrointestinal conditions. Among these two strains, Lpb. plantarum MYSVB1 demonstrated significant inhibition (p < 0.01) of the growth of A. alternata. The inhibitory effects of cell-free supernatant (CFS) were strong, with 5% crude CFS sufficient to reduce fungal growth by >70% and complete inhibition by 10% CFS. Moreover, the CFS was inhibitory for both mycelial growth and conidial germination. CFS retained its activity even after long cold storage. The chromatographic analysis identified organic acids in CFS, with succinic acid as the predominant constituent, with lactic acid, and malic acid in descending order. LAB strains isolated from tropical fruits showed promising probiotic and antifungal properties, making them potential candidates for various applications in food and agriculture.
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Affiliation(s)
| | | | | | | | - M. Y. Sreenivasa
- Applied Mycology Laboratory, Department of Studies in Microbiology, University of Mysore, Mysuru, India
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5
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Molnár A, Knapp DG, Lovas M, Tóth G, Boldizsár I, Váczy KZ, Kovács GM. Untargeted metabolomic analyses support the main phylogenetic groups of the common plant-associated Alternaria fungi isolated from grapevine (Vitis vinifera). Sci Rep 2023; 13:19298. [PMID: 37935846 PMCID: PMC10630412 DOI: 10.1038/s41598-023-46020-3] [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: 08/07/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Alternaria, a cosmopolitan fungal genus is a dominant member of the grapevine (Vitis vinifera) microbiome. Several Alternaria species are known to produce a variety of secondary metabolites, which are particularly relevant to plant protection and food safety in field crops. According to previous findings, the majority of Alternaria species inhabiting grapevine belong to Alternaria sect. Alternaria. However, the phylogenetic diversity and secondary metabolite production of the distinct Alternaria species has remained unclear. In this study, our aim was to examine the genetic and metabolic diversity of endophytic Alternaria isolates associated with the above-ground tissues of the grapevine. Altogether, 270 Alternaria isolates were collected from asymptomatic leaves and grape clusters of different grapevine varieties in the Eger wine region of Hungary. After analyses of the nuclear ribosomal DNA internal transcribed spacer (ITS) and RNA polymerase second largest subunit (rpb2) sequences, 170 isolates were chosen for further analyses. Sequences of the Alternaria major allergen gene (Alt a 1), endopolygalacturonase (endoPG), OPA10-2, and KOG1058 were also included in the phylogenetic analyses. Identification of secondary metabolites and metabolite profiling of the isolates were performed using high-performance liquid chromatography (HPLC)-high-resolution tandem mass spectrometry (HR-MS/MS). The multilocus phylogeny results revealed two distinct groups in grapevine, namely A. alternata and the A. arborescens species complex (AASC). Eight main metabolites were identified in all collected Alternaria isolates, regardless of their affiliation to the species and lineages. Multivariate analyses of untargeted metabolites found no clear separations; however, a partial least squares-discriminant analysis model was able to successfully discriminate between the metabolic datasets from isolates belonging to the AASC and A. alternata. By conducting univariate analysis based on the discriminant ability of the metabolites, we also identified several features exhibiting large and significant variation between A. alternata and the AASC. The separation of these groups may suggest functional differences, which may also play a role in the functioning of the plant microbiome.
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Affiliation(s)
- Anna Molnár
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary.
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary.
| | - Dániel G Knapp
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Forestry and Wood Technology, Linnaeus University, Växjö, Sweden
| | - Miklós Lovas
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary
| | - Gergő Tóth
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre U. 9, Budapest, 1092, Hungary
| | - Imre Boldizsár
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Pharmacognosy, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Kálmán Zoltán Váczy
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Budapest, 1525, Hungary
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6
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Cardoni M, Mercado-Blanco J. Confronting stresses affecting olive cultivation from the holobiont perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1261754. [PMID: 38023867 PMCID: PMC10661416 DOI: 10.3389/fpls.2023.1261754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
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Affiliation(s)
- Martina Cardoni
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Khayi S, Armitage AD, Gaboun F, Meftah-kadmiri I, Lahlali R, Fokar M, Mentag R. Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Front Microbiol 2023; 14:1268051. [PMID: 37886058 PMCID: PMC10599148 DOI: 10.3389/fmicb.2023.1268051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Greenwich, United Kingdom
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Issam Meftah-kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Ben Guerir, Morocco
- Plant and Soil Microbiome Sub-Program, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale D’Agriculture de Meknes, Meknès, Morocco
- Plant Pathology Laboratory, AgroBioSciences, College of Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
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Liao YCZ, Cao YJ, Wan Y, Li H, Li DW, Zhu LH. Alternaria arborescens and A. italica Causing Leaf Blotch on Celtis julianae in China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3113. [PMID: 37687359 PMCID: PMC10489861 DOI: 10.3390/plants12173113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Celtis julianae Schneid. is widely planted as a versatile tree species with ecological and economic significance. In September 2022, a leaf blotch disease of C. julianae was observed in Nanjing, Jiangsu, China, with an infection incidence of 63%. The disease led to severe early defoliation, significantly affecting the ornamental and ecological value of the host tree. The accurate identification of pathogens is imperative to conducting further research and advancing disease control. Koch's postulates confirmed that the fungal isolates (B1-B9) were pathogenic to C. julianae. The morphology of the characteristics of the pathogen matched those of Alternaria spp. The internal transcribed spacer region (ITS), large subunit (LSU) and small subunit (SSU) regions of rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Alternaria major allergen gene (Alt a 1), RNA polymerase second largest subunit (RPB2), and portions of translation elongation factor 1-alpha (TEF1-α) genes were sequenced. Based on multi-locus phylogenetic analyses and morphology, the pathogenic fungi were identified as Alternaria arborescens and A. italica. The findings provided useful information for disease management and enhanced the understanding of Alternaria species diversity in China. This is the first report of A. arborescens and A. italica causing leaf blotch of C. julianae in China and worldwide.
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Affiliation(s)
- Yang-Chun-Zi Liao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yi-Jia Cao
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Wan
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Hui Li
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - De-Wei Li
- The Connecticut Agricultural Experiment Station Valley Laboratory, Windsor, CT 06095, USA
| | - Li-Hua Zhu
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China (Y.-J.C.); (Y.W.); (H.L.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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9
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Dettman JR, Eggertson QA, Kim NE. Species diversity and molecular characterization of Alternaria section Alternaria isolates collected mainly from cereal crops in Canada. Front Microbiol 2023; 14:1194911. [PMID: 37303811 PMCID: PMC10249498 DOI: 10.3389/fmicb.2023.1194911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023] Open
Abstract
Alternaria is often one on the most abundant fungal genera recovered from a wide array of plant hosts and environmental substrates. Many species within the sub-generic Alternaria section Alternaria are common plant pathogens that cause pre-harvest losses due to reduced productivity and post-harvest losses due to spoilage and contamination with mycotoxins. As certain species of Alternaria may have distinct mycotoxin profiles, and very broad host ranges, understanding the distribution of species by geography and host is critical for disease prediction, toxicological risk assessment, and guiding regulatory decisions. In two previous reports, we performed phylogenomic analyses to identify highly informative molecular markers for Alternaria section Alternaria, and validated their diagnostic ability. Here, we perform molecular characterization of 558 section Alternaria strains, collected from 64 host genera in 12 countries, using two of these section-specific loci (ASA-10 and ASA-19) along with the RNA polymerase II second largest subunit (rpb2) gene. The majority of strains (57.4%) originated from various cereal crops in Canada, which formed the main focus of our study. Phylogenetic analyses were used to classify strains into section Alternaria species/lineages, demonstrating that the most common species on Canadian cereal crops are Alternaria alternata and A. arborescens. Further population genetic analyses were consistent with A. alternata being a widely distributed species with relatively low levels of geographic isolation (i.e., Canadian isolates did not form distinct clades when compared to other regions). Our expanded sampling of A. arborescens has greatly increased the known diversity of this group, with A. arborescens isolates forming at least three distinct phylogenetic lineages. Proportionally, A. arborescens is more prevalent in Eastern Canada than in Western Canada. Sequence analyses, putative hybrids, and mating-type distributions provided some evidence for recombination events, both within and between species. There was little evidence for associations between hosts and genetic haplotypes of A. alternata or A. arborescens.
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10
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Gao Q, Zhang Y, Gao C, Li H, Cheng Y, Qian X, Zhang L, Liu J, Ogunyemi SO, Guan J. The Microbial Diversity in Relation to Postharvest Quality and Decay: Organic vs. Conventional Pear Fruit. Foods 2023; 12:foods12101980. [PMID: 37238797 DOI: 10.3390/foods12101980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
(1) Background: Organic food produced in environmentally friendly farming systems has become increasingly popular. (2) Methods: We used a DNA metabarcoding approach to investigate the differences in the microbial community between organic and conventional 'Huangguan' pear fruit; and (3) Results: Compared to a conventional orchard, the fruit firmness in the organic orchard had significantly lowered after 30 days of shelf-life storage at 25 °C, and the soluble solids content (SSC), titratable acid (TA), and decay index were higher. There were differences in the microbial diversity between organic and conventional orchards pears. After 30 days of storage, Fusarium and Starmerella became the main epiphytic fungi in organic fruits, while Meyerozyma was dominant in conventional fruits. Gluconobacter, Acetobacter, and Komagataeibacter were dominant epiphytic bacteria on pears from both organic and conventional orchards after a 30-day storage period. Bacteroides, Muribaculaceae, and Nesterenkonia were the main endophytic bacteria throughout storage. There was a negative correlation between fruit firmness and decay index. Moreover, the abundance of Acetobacter and Starmerella were positively correlated with fruit firmness, while Muribaculaceae was negatively correlated, implying that these three microorganisms may be associated with the postharvest decay of organic fruit; (4) Conclusions: The difference in postharvest quality and decay in organic and conventional fruits could potentially be attributed to the variation in the microbial community during storage.
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Affiliation(s)
- Qi Gao
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Yang Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Congcong Gao
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Huimin Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- School of Landscape and Ecological Engineering, Hebei Engineering University, Handan 056021, China
| | - Yudou Cheng
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xun Qian
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Lishu Zhang
- Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou 061001, China
| | - Jinyu Liu
- Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou 061001, China
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310013, China
| | - Junfeng Guan
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050051, China
- Key Laboratory of Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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11
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Nanofungicides with Selenium and Silicon Can Boost the Growth and Yield of Common Bean (Phaseolus vulgaris L.) and Control Alternaria Leaf Spot Disease. Microorganisms 2023; 11:microorganisms11030728. [PMID: 36985301 PMCID: PMC10051325 DOI: 10.3390/microorganisms11030728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
There is an urgent need to reduce the intensive use of chemical fungicides due to their potential damage to human health and the environment. The current study investigated whether nano-selenium (nano-Se) and nano-silica (nano-SiO2) could be used against the leaf spot disease caused by Alternaria alternata in a common bean (Phaseolus vulgaris L.). The engineered Se and SiO2 nanoparticles were compared to a traditional fungicide and a negative control with no treatment, and experiments were repeated during two successive seasons in fields and in vitro. The in vitro study showed that 100 ppm nano-Se had an efficacy rate of 85.1% on A. alternata mycelial growth, followed by the combined applications (Se + SiO2 at half doses) with an efficacy rate of 77.8%. The field study showed that nano-Se and the combined application of nano-Se and nano-SiO2 significantly decreased the disease severity of A. alternata. There were no significant differences among nano-Se, the combined application, and the fungicide treatment (positive control). As compared to the negative control (no treatment), leaf weight increased by 38.3%, the number of leaves per plant by 25.7%, chlorophyll A by 24%, chlorophyll B by 17.5%, and total dry seed yield by 30%. In addition, nano-Se significantly increased the enzymatic capacity (i.e., CAT, POX, PPO) and antioxidant activity in the leaves. Our current study is the first to report that the selected nano-minerals are real alternatives to chemical fungicides for controlling A. alternata in common beans. This work suggests the potential of nanoparticles as alternatives to fungicides. Further studies are needed to better understand the mechanisms and how different nano-materials could be used against phytopathogens.
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12
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Phylogenetic Analysis and Toxigenic Profile of Alternaria Species Isolated from Chickpeas (Cicer arietinum) in Argentina. DIVERSITY 2022. [DOI: 10.3390/d14110924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chickpeas are a very important legume due to their nutritional richness and high protein content and they are used as food for humans and as fodder for livestock. However, they are susceptible to fungal infections and mycotoxin contamination. The Alternaria genus was among the main fungi isolated from chickpea samples in Argentina. The species within this genus are able to produce several mycotoxins such as alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TA). So, the objectives of this study were to identify the Alternaria spp. found in the chickpea samples and to determine their toxigenic potential in vitro. A phylogenetic analysis of 32 Alternaria strains was carried out based on the combined sequences of the tef1, gpd, and Alt a1 genes. All Alternaria strains clustered into the section Alternaria and were identified as A. alternata and A. arborescens. Further, the toxigenic profile of each strain was determined in a ground rice–corn steep liquor medium and analysed by HPLC. Most strains were able to co-produce AOH, AME, and TA. These results indicate a potential risk for human health when consuming chickpeas since this legume could be contaminated with Alternaria and its mycotoxins, which are not yet regulated in food.
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13
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Luo X, Wang H, Wang M. Genomic Sequence Data of Alternaria alternata hznu325 Causing Black Leaf Spot on Chrysanthemum morifolium. PLANT DISEASE 2022; 106:2506-2510. [PMID: 35895327 DOI: 10.1094/pdis-11-21-2517-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Xiujun Luo
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Huizhong Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
| | - Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China
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14
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Li J, Phookamsak R, Jiang H, Bhat DJ, Camporesi E, Lumyong S, Kumla J, Hongsanan S, Mortimer PE, Xu J, Suwannarach N. Additions to the Inventory of the Genus Alternaria Section Alternaria (Pleosporaceae, Pleosporales) in Italy. J Fungi (Basel) 2022; 8:jof8090898. [PMID: 36135624 PMCID: PMC9501253 DOI: 10.3390/jof8090898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Alternaria is comprised of well-known plant pathogens causing various important diseases in plants, as well as being common allergens in animals and humans. Species of Alternaria can be found as saprobes associated with various dead plant materials. This research aims to enhance the taxonomy of saprobic species in the genus Alternaria found on grasses and herbaceous plants from Italy, based on multi-locus phylogenetic analyses of a concatenated ITS, LSU, SSU, tef1-α, rpb2, gapdh and Alt-a1 DNA sequence dataset combined with morphological characteristics. Multi-locus phylogenetic analyses demonstrated six novel species belonging to the genus Alternaria sect. Alternaria as: A. muriformispora sp. nov., A. obpyriconidia sp. nov., A. ovoidea sp. nov., A. pseudoinfectoria sp. nov., A. rostroconidia sp. nov. and A. torilis sp. nov. Detailed morphological descriptions, illustrations and an updated phylogenetic relationship of taxa in the genus Alternaria sect. Alternaria are provided herein.
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Affiliation(s)
- Junfu Li
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China
| | - Rungtiwa Phookamsak
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Hongbo Jiang
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China
| | | | - Erio Camporesi
- Società per gli Studi Naturalistici della Romagna, C.P. 143, 48012 Bagnacavallo, RA, Italy
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sinang Hongsanan
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Peter E. Mortimer
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China
| | - Jianchu Xu
- Honghe Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe 654400, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- East and Central Asia Regional Office, World Agroforestry Centre (ICRAF), Kunming 650201, China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming 650201, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +66-86-512-7518
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15
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Zhang L, Wu R, Mur LAJ, Guo C, Zhao X, Meng H, Yan D, Zhang X, Guan H, Han G, Guo B, Yue F, Wei Y, Zhao P, He W. Assembly of high-quality genomes of the locoweed Oxytropis ochrocephala and its endophyte Alternaria oxytropis provides new evidence for their symbiotic relationship and swainsonine biosynthesis. Mol Ecol Resour 2022; 23:253-272. [PMID: 35932461 DOI: 10.1111/1755-0998.13695] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022]
Abstract
Locoweeds are perennial forbs poisonous to livestock and cause extreme losses to animal husbandry. Locoweed toxicity is attributed to the symbiotic endophytes in Alternaria sect. Undifilum, which produce a mycotoxin swainsonine (SW). We performed a de novo whole genome sequencing of the most common locoweed in China, Oxytropis ochrocephala (2n = 16), and assembled a high-quality, chromosome-level reference genome. Its genome size is 958.83 Mb with 930.94 Mb (97.09 %) anchored and oriented onto 8 chromosomes, and 31,700 protein-coding genes were annotated. Phylogenetic and collinearity analysis showed it is closely related to Medicago truncatula with a pair of large interchromosomal rearrangements, and both species underwent a whole-genome duplication event. We also derived the genome of A. oxytropis at 74.48 Mb with a contig N50 of 8.87 Mb and 10,657 protein-coding genes, and refined the genes of SW biosynthesis. Multiple Alternaria species containing the swnK gene were grouped into a single clade, but in other genera, swnK's homologues are diverse. Resequencing of 41 A. oxytropis strains revealed one SNP in the SWN cluster causing changes in SW concentration. Comparing the transcriptomes of symbiotic and non-symbiotic interactions identified differentially expressed genes (DEG) linked to defense and secondary metabolism in the host. Within the endophyte DEGs were linked to cell wall degradation, fatty acids and nitrogen metabolism. Symbiosis induced the up-regulation of most of the SW biosynthetic genes. These two genomes and relevant sequencing data should provide valuable genetic resources for the study of the evolution, interaction, and SW biosynthesis in the symbiont.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Ruolin Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Luis A J Mur
- Institute of Biology, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Chenchen Guo
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Xuan Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Huizhen Meng
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Di Yan
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Xiuhong Zhang
- Bureau of Natural Resources, Haiyuan, Ningxia, China
| | - Huirui Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Guodong Han
- Key Laboratory of Grassland Resources of Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Bin Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Fangzheng Yue
- Biological Disaster Control and Prevention Centre, National Forestry and Grassland Administration, Shenyang, Liaoning, China
| | - Yahui Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Wei He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China.,Key Laboratory of Grassland Resources of Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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16
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Gao K, Qin Y, Wang L, Li X, Liu S, Xing R, Yu H, Chen X, Li P. Design, Synthesis, and Antifungal Activities of Hymexazol Glycosides Based on a Biomimetic Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9520-9535. [PMID: 35877994 DOI: 10.1021/acs.jafc.2c02507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hymexazol (HYM) is irreplaceable for treating soil-borne diseases due to its high efficiency and low cost, as a broad-spectrum fungicide. However, when HYM is absorbed by plants, it is rapidly converted into two glycoside metabolites, and the antifungal activities of these glycosides are inferior to that of HYM. Therefore, in this study, to maintain strong antifungal activity in vitro and in vivo, HYM was glycosylated with amino sugars that have diverse biological activities to simulate plant glycosylation. The antifungal experiment proved that glycoside 15 has the highest antifungal activity, and N-acetyl glucosamine and HYM had obvious synergistic effects. According to the structure-activity relationship studies, glycoside 15 had greater numbers of active electron-rich regions and front-line orbital electrons due to the introduction of N-acetyl glucosamine. Moreover, glycoside 15 can significantly promote plant growth and induce an increase in plant defense enzyme activity. Additionally, compared to HYM, the results of electron microscopy and proteomics revealed that glycoside 15 has a unique antifungal mechanism. The promising antifungal activity and interactions with plants mean that glycoside 15 is a potential green fungicide candidate. Furthermore, this research conducted an interesting exploration of the agricultural applications of amino sugars.
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Affiliation(s)
- Kun Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Yukun Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Linsong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Xin Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - HuaHua Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Xiaolin Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
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17
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Peel Diffusion and Antifungal Efficacy of Different Fungicides in Pear Fruit: Structure-Diffusion-Activity Relationships. J Fungi (Basel) 2022; 8:jof8050547. [PMID: 35628802 PMCID: PMC9144380 DOI: 10.3390/jof8050547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 01/12/2023] Open
Abstract
Fungal pathogens can invade not only the fruit peel but also the outer part of the fruit mesocarp, limiting the efficacy of fungicides. In this study, the relationships between fungicide structure, diffusion capacity and in vivo efficacy were evaluated for the first time. The diffusion capacity from pear peel to mesocarp of 11 antifungal compounds, including p-aminobenzoic acid, carbendazim, difenoconazole, dipicolinic acid, flusilazole, gentamicin, kojic acid, prochloraz, quinolinic acid, thiophanate methyl and thiram was screened. The obtained results indicated that size and especially polarity were negatively correlated with the diffusion capacity. Although some antifungal compounds, such as prochloraz and carbendazim, were completely degraded after a few days in peel and mesocarp, other compounds, such as p-aminobenzoic acid and kojic acid, showed high stability. When applying the antifungal compounds at the EC50 concentrations, it was observed that the compounds with high diffusion capacity showed higher in vivo antifungal activity against Alternaria alternata than compounds with low diffusion capacity. In contrast, there was no relationship between stability and in vivo efficacy. Collectively, the obtained results indicated that the diffusion capacity plays an important role in the efficacy of fungicides for the control of pear fruit diseases.
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18
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Abstract
Alternaria alternata is a common species of fungus frequently isolated from plants as both an endophyte and a pathogen. Although the current definition of A. alternata rests on a foundation of morphological, genetic and genomic analyses, doubts persist regarding the scope of A. alternata within the genus due to the varied symbiotic interactions and wide host range observed in these fungi. These doubts may be due in large part to the history of unstable taxonomy in Alternaria, based on limited morphological characters for species delimitation and host specificity associated with toxins encoded by genes carried on conditionally dispensable chromosomes. This review explores the history of Alternaria taxonomy, focusing in particular on the use of nutritional mode and host associations in species delimitation, with the goal of evaluating A. alternata as it currently stands based on taxonomic best practice. Given the recombination detected among isolates of A. alternata, different symbiotic associations in this species should not be considered phylogenetically informative.
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Affiliation(s)
- Mara DeMers
- Plant and Microbial Biology Department, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- *Correspondence: Mara DeMers,
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19
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Fungal Allergen and Mold Allergy Diagnosis: Role and Relevance of Alternaria alternata Alt a 1 Protein Family. J Fungi (Basel) 2022; 8:jof8030277. [PMID: 35330279 PMCID: PMC8954643 DOI: 10.3390/jof8030277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Alternaria is a genus of worldwide fungi found in different habitats such as soil, the atmosphere, plants or indoor environments. Alternaria species are saprobic—largely involved in the decomposition of organic material—but they can also act as animal pathogens, causing disease in humans and animals, developing infections, toxicosis and allergic diseases. A. alternata is considered one of the most important sources of fungal allergens worldwide and it is associated with severe asthma and respiratory status. Among the A. alternata allergens, Alt a 1 is the main sensitizing allergen and its usefulness in diagnosis and immunotherapy has been demonstrated. Alt a 1 seems to define a protein family that can be used to identify related pathogenic fungi in plants and fruits, and to establish taxonomic relationships between the different fungal divisions.
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20
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Qiu C, Wang W, Liu Z. Genome Resource of American Ginseng Black Spot Pathogen Alternaria panax. PLANT DISEASE 2022; 106:1020-1022. [PMID: 35259299 DOI: 10.1094/pdis-05-21-0895-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Chaodong Qiu
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Weiquan Wang
- Professional Committee of Planting & Breeding of Chinese Herbal Medicines, China Association of Traditional Chinese Medicine, Beijing, 100000, China
| | - Zhenyu Liu
- School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, Hefei, 230036, China
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21
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Oettl S, Bosello M, Marschall K, Gallmetzer A, Reyes-Domínguez Y, Kreutz C, Tollinger M, Robatscher P, Oberhuber M. (3ξ,4ξ,5ξ,6ξ,7ξ,11ξ)-3,6-Dihydroxy-8-oxo-9-eremophilene-12-oic Acid, a New Phytotoxin of Alternaria alternata ssp. tenuissima Isolates Associated with Fruit Spots on Apple ( Malus × domestica Borkh.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14445-14458. [PMID: 34808059 DOI: 10.1021/acs.jafc.1c02847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Alternaria sp. infections on apple (Malus × domestica Borkh.) lead to impaired fruit quality and yield losses by leaf blotches and fruit spots, caused by host-specific toxins (HSTs) of the Alternaria apple pathotype like AM-toxins. Fungal isolates were obtained during severe outbreaks on cv. Gala, Golden Delicious, and Cripps Pink(cov)/Rosy Glow(cov) in South Tyrol and other regions in northern Italy. The isolates were tested for pathogenicity using in vitro assays with detached apple leaves. Conidial suspensions of pathogenic isolates were shown to provoke necrotic lesions also in apple seedlings and on fruits. Detached-leaf assay-guided fractionation of the isolates' culture supernatant and a high-resolution liquid chromatography-mass spectrometry (LC-MS) analysis tentatively identified 27 known Alternaria phytotoxins and a new putative toxin, (3ξ,4ξ,5ξ,6ξ,7ξ,11ξ)-3,6-dihydroxy-8-oxo-9-eremophilene-12-oic acid (1). The constitution and the relative configuration of the ring stereocenters of 1 were elucidated by NMR spectroscopy, revealing unique structural features among Alternaria phytotoxins. Indeed, molecular analysis revealed the lack of the toxin-related genes AMT1, AMT4, and AMT14 in all isolates from the region, suggesting that Alternaria apple blotch in the area was associated with another metabolite (1).
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Affiliation(s)
- Sabine Oettl
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
| | - Mattia Bosello
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
| | - Klaus Marschall
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
| | - Andreas Gallmetzer
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
| | | | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Martin Tollinger
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Peter Robatscher
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
| | - Michael Oberhuber
- Laimburg Research Centre, Laimburg 6─Pfatten (Vadena), Auer (Ora) 39040, Italy
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22
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Fontaine K, Fourrier-Jeandel C, Armitage AD, Boutigny AL, Crépet M, Caffier V, Gnide DC, Shiller J, Le Cam B, Giraud M, Ioos R, Aguayo J. Identification and pathogenicity of Alternaria species associated with leaf blotch disease and premature defoliation in French apple orchards. PeerJ 2021; 9:e12496. [PMID: 34917421 PMCID: PMC8643104 DOI: 10.7717/peerj.12496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 11/20/2022] Open
Abstract
Leaf blotch caused by Alternaria spp. is a common disease in apple-producing regions. The disease is usually associated with one phylogenetic species and one species complex, Alternaria alternata and the Alternaria arborescens species complex (A. arborescens SC), respectively. Both taxa may include the Alternaria apple pathotype, a quarantine or regulated pathogen in several countries. The apple pathotype is characterized by the production of a host-selective toxin (HST) which is involved in pathogenicity towards the apple. A cluster of genes located on conditionally dispensable chromosomes (CDCs) is involved in the production of this HST (namely AMT in the case of the apple pathotype). Since 2016, leaf blotch and premature tree defoliation attributed to Alternaria spp. have been observed in apple-producing regions of central and south-eastern France. Our study aimed to identify the Alternaria species involved in apple tree defoliation and assess the presence of the apple pathotype in French orchards. From 2016 to 2018, 166 isolates were collected and identified by multi-locus sequence typing (MLST). This analysis revealed that all these French isolates belonged to either the A. arborescens SC or A. alternata. Specific PCR detection targeting three genes located on the CDC did not indicate the presence of the apple pathotype in France. Pathogenicity was assessed under laboratory conditions on detached leaves of Golden Delicious and Gala apple cultivars for a representative subset of 28 Alternaria isolates. All the tested isolates were pathogenic on detached leaves of cultivars Golden Delicious and Gala, but no differences were observed between the pathogenicity levels of A. arborescens SC and A. alternata. However, the results of our pathogenicity test suggest that cultivar Golden Delicious is more susceptible than Gala to Alternaria leaf blotch. Implications in the detection of the Alternaria apple pathotype and the taxonomic assignment of Alternaria isolates involved in Alternaria leaf blotch are discussed.
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Affiliation(s)
- Kévin Fontaine
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Céline Fourrier-Jeandel
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Anne-Laure Boutigny
- ANSES, Laboratoire de la Santé des Végétaux, Unité Bactériologie, Virologie et OGM, Angers, France
| | | | - Valérie Caffier
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Dossi Carine Gnide
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Jason Shiller
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Bruno Le Cam
- Université d’Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Michel Giraud
- Centre opérationnel de Lanxade, CTIFL, Prigonrieux, France
| | - Renaud Ioos
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
| | - Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux, Unité de Mycologie, USC INRAE, Malzéville, France
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23
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Gai Y, Li L, Liu B, Ma H, Chen Y, Zheng F, Sun X, Wang M, Jiao C, Li H. Distinct and essential roles of bZIP transcription factors in the stress response and pathogenesis in Alternaria alternata. Microbiol Res 2021; 256:126915. [PMID: 34953292 DOI: 10.1016/j.micres.2021.126915] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/05/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022]
Abstract
The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata under metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We investigated the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A.alternata by analyzing targeted gene disrupted mutants. Morphological analysis provides evidence that the bZIP transcription factors (Gcn4, MeaB, Atf1, the ER stress regulator Hac1, and the all development altered-1 gene Ada1) are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover,the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings reveal that bZIP transcription factors function as key regulators of fungal morphogenesis, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.
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Affiliation(s)
- Yunpeng Gai
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China; School of Grassland Science, Beijing Forestry University, Beijing, 100083, China.
| | - Lei Li
- Department of Plant Pathology, South China Agricultural University, Guangzhou 510640, China
| | - Bing Liu
- Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Haijie Ma
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Yanan Chen
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fang Zheng
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xuepeng Sun
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Mingshuang Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chen Jiao
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hongye Li
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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24
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Dettman JR, Eggertson Q. Phylogenomic analyses of Alternaria section Alternaria: A high-resolution, genome-wide study of lineage sorting and gene tree discordance. Mycologia 2021; 113:1218-1232. [PMID: 34637684 DOI: 10.1080/00275514.2021.1950456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The genus Alternaria contains a diversity of saprobic and pathogenic species that can be found in a wide range of environments. Alternaria is currently divided into 26 subgeneric sections, and the "small-spored" Alternaria section Alternaria includes many species that are economically important agricultural pathogens. Recognizing that a stable framework for systematics and species identification is essential for management and regulation purposes, this section has experienced much taxonomic debate and systematic revision in recent years. Molecular phylogenetic studies have challenged the reliability of using morphological characteristics to differentiate Alternaria species but have also suggested that commonly used molecular markers for fungal phylogenetics may not be sufficiently informative at this taxonomic level. To allow the assessment of molecular variation and evolutionary history at a genome-wide scale, we present an overview and analysis of phylogenomic resources for Alternaria section Alternaria. We review the currently available genomic resources and report five newly sequenced genomes. We then perform multiple comparative genomic analyses, including macrosynteny assessment and inference of phylogenetic relationships using a variety of data sets and analysis methods. Fine-scale, genome-wide phylogenetic reconstruction revealed incomplete lineage sorting and the genomic distribution of gene/species tree discordance. Based on these patterns, we propose a list of candidate genes that may be developed into informative markers that are diagnostic for the main lineages. This overview identifies gaps in knowledge and can guide future genome sequencing efforts for this important group of plant pathogenic fungi.
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Affiliation(s)
- Jeremy R Dettman
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Quinn Eggertson
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
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25
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Huang K, Tang J, Zou Y, Sun X, Lan J, Wang W, Xu P, Wu X, Ma R, Wang Q, Wang Z, Liu J. Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. Front Microbiol 2021; 12:713462. [PMID: 34616379 PMCID: PMC8488381 DOI: 10.3389/fmicb.2021.713462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/16/2021] [Indexed: 02/05/2023] Open
Abstract
Alternaria alternata is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of A. alternata (Y784-BC03) was isolated and identified from “Hongyang” kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. The assembled genome is composed of 33,869,130bp (32.30Mb) comprising 10 chromosomes and 11,954 genes. A total of 2,180 virulence factors were predicted to be present in the obtained genome sequence. The virulence factors comprised genes encoding secondary metabolites, including non-host-specific toxins, cell wall-degrading enzymes, and major transcriptional regulators. The predicted gene clusters encoding genes for the biosynthesis and export of secondary metabolites in the genome of Y784-BC03 were associated with non-host-specific toxins, including cercosporin, dothistromin, and versicolorin B. Major transcriptional regulators of different mycotoxin biosynthesis pathways were identified, including the transcriptional regulators, polyketide synthase, P450 monooxygenase, and major facilitator superfamily transporters.
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Affiliation(s)
- Ke Huang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China.,Institute of Microbial Ecology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Jianming Tang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Yong Zou
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Xiangcheng Sun
- College of Life Sciences, Northwest A&F University, Yangling, China.,West China Biopharm Research Institute, West China Hospital, Sichuan University, Chengdu, China
| | - Jianbin Lan
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Wei Wang
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China.,Institute of Microbial Ecology, Chongqing University of Arts and Sciences, Chongqing, China
| | - Panpan Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | | | - Rui Ma
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia Liu
- College of Landscape Architecture and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, China
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26
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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27
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Tsushima A, Narusaka M, Gan P, Kumakura N, Hiroyama R, Kato N, Takahashi S, Takano Y, Narusaka Y, Shirasu K. The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants. Front Microbiol 2021; 12:682155. [PMID: 34539598 PMCID: PMC8446390 DOI: 10.3389/fmicb.2021.682155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/11/2021] [Indexed: 01/25/2023] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that promote infection by manipulating host cells. Members of the phytopathogenic fungal genus Colletotrichum collectively have a broad host range and generally adopt a hemibiotrophic lifestyle that includes an initial biotrophic phase and a later necrotrophic phase. We hypothesized that Colletotrichum fungi use a set of conserved effectors during infection to support the two phases of their hemibiotrophic lifestyle. This study aimed to examine this hypothesis by identifying and characterizing conserved effectors among Colletotrichum fungi. Comparative genomic analyses using genomes of ascomycete fungi with different lifestyles identified seven effector candidates that are conserved across the genus Colletotrichum. Transient expression assays showed that one of these putative conserved effectors, CEC3, induces nuclear expansion and cell death in Nicotiana benthamiana, suggesting that CEC3 is involved in promoting host cell death during infection. Nuclear expansion and cell death induction were commonly observed in CEC3 homologs from four different Colletotrichum species that vary in host specificity. Thus, CEC3 proteins could represent a novel class of core effectors with functional conservation in the genus Colletotrichum.
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Affiliation(s)
- Ayako Tsushima
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Mari Narusaka
- Research Institute for Biological Sciences Okayama, Kaga-gun, Japan
| | - Pamela Gan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | | | - Ryoko Hiroyama
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | - Naoki Kato
- Center for Sustainable Resource Science, RIKEN, Wako, Japan
| | | | | | | | - Ken Shirasu
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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28
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Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes. J Fungi (Basel) 2021; 7:jof7070538. [PMID: 34356917 PMCID: PMC8306250 DOI: 10.3390/jof7070538] [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: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.
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29
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Gai Y, Ma H, Chen Y, Li L, Cao Y, Wang M, Sun X, Jiao C, Riely BK, Li H. Chromosome-Scale Genome Sequence of Alternaria alternata Causing Alternaria Brown Spot of Citrus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:726-732. [PMID: 33689393 DOI: 10.1094/mpmi-10-20-0278-sc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Alternaria brown spot (ABS), caused by Alternaria alternata, is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford Nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of 3.08 Mb. The genome is encompassed 12,067 protein-coding genes, 34 ribosomal RNAs, and 107 transfer RNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes and 2 CDCs, which is consistent with the experimental evidences of pulsed-field gel electrophoresis. To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria spp. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria spp. are available. The citrus-related Alternaria genomes database is open accessible through the Citrus Fungal Disease Database.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yunpeng Gai
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Haijie Ma
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- School of Agriculture and Food Sciences, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China
| | - Yanan Chen
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yingzi Cao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mingshuang Wang
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xuepeng Sun
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A
| | - Chen Jiao
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, U.S.A
| | - Brendan K Riely
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Hongye Li
- Key Lab of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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30
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Witte TE, Villeneuve N, Boddy CN, Overy DP. Accessory Chromosome-Acquired Secondary Metabolism in Plant Pathogenic Fungi: The Evolution of Biotrophs Into Host-Specific Pathogens. Front Microbiol 2021; 12:664276. [PMID: 33968000 PMCID: PMC8102738 DOI: 10.3389/fmicb.2021.664276] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022] Open
Abstract
Accessory chromosomes are strain- or pathotype-specific chromosomes that exist in addition to the core chromosomes of a species and are generally not considered essential to the survival of the organism. Among pathogenic fungal species, accessory chromosomes harbor pathogenicity or virulence factor genes, several of which are known to encode for secondary metabolites that are involved in plant tissue invasion. Accessory chromosomes are of particular interest due to their capacity for horizontal transfer between strains and their dynamic "crosstalk" with core chromosomes. This review focuses exclusively on secondary metabolism (including mycotoxin biosynthesis) associated with accessory chromosomes in filamentous fungi and the role accessory chromosomes play in the evolution of secondary metabolite gene clusters. Untargeted metabolomics profiling in conjunction with genome sequencing provides an effective means of linking secondary metabolite products with their respective biosynthetic gene clusters that reside on accessory chromosomes. While the majority of literature describing accessory chromosome-associated toxin biosynthesis comes from studies of Alternaria pathotypes, the recent discovery of accessory chromosome-associated biosynthetic genes in Fusarium species offer fresh insights into the evolution of biosynthetic enzymes such as non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and regulatory mechanisms governing their expression.
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Affiliation(s)
- Thomas E. Witte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas Villeneuve
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Christopher N. Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - David P. Overy
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
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31
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Liu H, Wu S, Li A, Ruan J. SMARTdenovo: a de novo assembler using long noisy reads. GIGABYTE 2021; 2021:gigabyte15. [PMID: 36824332 PMCID: PMC9632051 DOI: 10.46471/gigabyte.15] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.
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Affiliation(s)
- Hailin Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shigang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Alun Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jue Ruan
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China, Corresponding author. E-mail:
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Stutts LR, Vermerris W. Elucidating Anthracnose Resistance Mechanisms in Sorghum-A Review. PHYTOPATHOLOGY 2020; 110:1863-1876. [PMID: 33100146 DOI: 10.1094/phyto-04-20-0132-rvw] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sorghum (Sorghum bicolor) is the fifth most cultivated cereal crop in the world, traditionally providing food, feed, and fodder, but more recently also fermentable sugars for the production of renewable fuels and chemicals. The hemibiotrophic fungal pathogen Colletotrichum sublineola, the causal agent of anthracnose disease in sorghum, is prevalent in the warm and humid climates where much of the sorghum is cultivated and poses a serious threat to sorghum production. The use of anthracnose-resistant sorghum germplasm is the most environmentally and economically sustainable way to protect sorghum against this pathogen. Even though multiple anthracnose resistance loci have been mapped in diverse sorghum germplasm in recent years, the diversity in C. sublineola pathotypes at the local and regional levels means that these resistance genes are not equally effective in different areas of cultivation. This review summarizes the genetic and cytological data underlying sorghum's defense response and describes recent developments that will enable a better understanding of the interactions between sorghum and C. sublineola at the molecular level. This includes releases of the sorghum genome and the draft genome of C. sublineola, the use of next-generation sequencing technologies to identify gene expression networks activated in response to infection, and improvements in methodologies to validate resistance genes, notably virus-induced and transgenic gene silencing approaches.
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Affiliation(s)
- Lauren R Stutts
- Graduate Program in Plant Molecular & Cellular Biology, University of Florida, Gainesville, FL 32610
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, UF Genetics Institute, and Florida Center for Renewable Fuels and Chemicals, University of Florida, Gainesville, FL 32610
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Matić S, Tabone G, Garibaldi A, Gullino ML. Alternaria Leaf Spot Caused by Alternaria Species: An Emerging Problem on Ornamental Plants in Italy. PLANT DISEASE 2020; 104:2275-2287. [PMID: 32584157 DOI: 10.1094/pdis-02-20-0399-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Serious outbreaks of Alternaria leaf spot and plant decay have recently been recorded on several ornamental plants in the Biella Province (Northern Italy). Twenty-two fungal isolates were obtained from Alternaria infected plant tissues from 13 ornamental hosts. All the isolates were identified morphologically as small-spored Alternaria species. Multilocus sequence typing, carried out by means of ITS, rpb2, tef1, endoPG, Alt a 1, and OPA10-2, assigned 19 isolates as Alternaria alternata, two isolates as belonging to the Alternaria arborescens species complex, and one isolate as an unknown Alternaria sp. Haplotype analyses of ornamental and reference A. alternata isolates from 12 countries identified 14 OPA10-2 and 11 endoPG haplotypes showing a relatively high haplotype diversity. A lack of host specialization or geographic distribution was observed. The host range of the studied A. alternata isolates expanded in cross-pathogenicity assays, and more aggressiveness was frequently observed on the experimental plants than on the host plants from which the fungal isolates were originally isolated. High disease severity, population expansion, intraspecies diversity, and increased range of experimental hosts were seen in the emergence of Alternaria disease on ornamentals. More epidemiological and molecular studies should be performed to better understand these diseases, taking into consideration factors such as seed transmission and ongoing climate changes.
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Affiliation(s)
- Slavica Matić
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, 10095 Grugliasco (TO), Italy
- Dept. Agricultural, Forestry and Food Sciences (DISAFA), Università di Torino, 10095 Grugliasco (TO), Italy
| | - Giulia Tabone
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, 10095 Grugliasco (TO), Italy
| | - Angelo Garibaldi
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, 10095 Grugliasco (TO), Italy
| | - Maria Lodovica Gullino
- AGROINNOVA - Centre of Competence for the Innovation in the Agro-environmental Sector, Università di Torino, 10095 Grugliasco (TO), Italy
- Dept. Agricultural, Forestry and Food Sciences (DISAFA), Università di Torino, 10095 Grugliasco (TO), Italy
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