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Blagojević J, Aleksić G, Vučurović I, Starović M, Ristić D. Exploring the Phylogenetic Diversity of Botryosphaeriaceae and Diaporthe Species Causing Dieback and Shoot Blight of Blueberry in Serbia. PHYTOPATHOLOGY 2024; 114:1333-1345. [PMID: 38015417 DOI: 10.1094/phyto-04-23-0133-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Identifying the precise pathogens responsible for specific plant diseases is imperative for implementing targeted and efficient interventions and mitigating their spread. Dieback and shoot blight significantly diminish the lifespan and productivity of blueberries, yet the causative agents remain largely unidentified. To determine the identity and prevalence of the causal agents of branch dieback and shoot blight, we conducted multiyear and multisite sampling of diseased highbush blueberries (Vaccinium corymbosum cultivar Duke) in Serbia. Sixty-nine monosporic isolates were collected and characterized based on morphological, physiological features and multilocus phylogenetic analysis of internal transcribed spacer, β-tubulin, and translation elongation factor 1-α sequence data. Five species were identified as causal agents: Diaporthe eres (36 isolates), D. foeniculina (3 isolates), Neopestalotiopsis vaccinii (9 isolates), Neopestalotiopsis rosae (6 isolates), and Neofusicoccum parvum (15 isolates). The results of the pathogenicity tests performed with the 23 representative isolates confirmed the role of these species as primary pathogens in causing dieback and shoot blight of blueberry, with Neofusicoccum parvum being the most aggressive and D. eres the least. Our study underscores the diversity of genera and species of ascomycetes capable of causing blueberry dieback and shoot blight. Furthermore, our findings indicate that the agents responsible for the disease in Serbia differ from those identified in other regions worldwide.
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Affiliation(s)
- Jovana Blagojević
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11000 Belgrade, Serbia
| | - Goran Aleksić
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11000 Belgrade, Serbia
| | - Ivan Vučurović
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11000 Belgrade, Serbia
| | - Mira Starović
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11000 Belgrade, Serbia
| | - Danijela Ristić
- Department of Plant Diseases, Institute for Plant Protection and Environment, Teodora Drajzera 9, 11000 Belgrade, Serbia
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Ghosh K, Das S, Sorongpong S, Das N, Pandey P. Emergence of Lasiodiplodia theobromae induced leaf necrosis in tea (Camellia sinensis [L.] O. Kuntze) from India. Arch Microbiol 2024; 206:284. [PMID: 38814366 DOI: 10.1007/s00203-024-04018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
The tea plant, Camellia sinensis [L.] O. Kuntze, is a vital global agricultural commodity, yet faces challenges from fungal infections, which affects its production. To reduce the loss in the tea production, the fungal infections must be removed which is managed with fungicides, which are harmful to the environment. Leaf necrosis, which decreases tea quality and quantity, was investigated across Assam, revealing Lasiodiplodia theobromae as the causative agent. Pathogenicity tests, alongside morphological and molecular analyses, confirmed its role in leaf necrosis. Genome and gene analysis of L. theobromae showed multiple genes related to its pathogenicity. The study also assessed the impact of chemical pesticides on this pathogen. Additionally, the findings in this study highlight the significance of re-assessing management approaches in considering the fungal infection in tea.
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Affiliation(s)
- Kheyali Ghosh
- Assam University Silchar, Cachar, 788011, Assam, India
| | - Sandeep Das
- Assam University Silchar, Cachar, 788011, Assam, India
| | | | - Nandita Das
- Assam University Silchar, Cachar, 788011, Assam, India
| | - Piyush Pandey
- Assam University Silchar, Cachar, 788011, Assam, India.
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Sykes JR, Denby KJ, Franks DW. Computer vision for plant pathology: A review with examples from cocoa agriculture. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11559. [PMID: 38638617 PMCID: PMC11022223 DOI: 10.1002/aps3.11559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 04/20/2024]
Abstract
Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent misapplication of pesticides. Pesticide misapplication is both financially costly and can exacerbate pesticide resistance and pollution. Here, we review the application and development of computer vision and machine learning methods for the detection of plant disease. This review goes beyond the scope of previous works to discuss important technical concepts and considerations when applying computer vision to plant pathology. We present new case studies on adapting standard computer vision methods and review techniques for acquiring training data, the use of diagnostic tools from biology, and the inspection of informative features. In addition to an in-depth discussion of convolutional neural networks (CNNs) and transformers, we also highlight the strengths of methods such as support vector machines and evolved neural networks. We discuss the benefits of carefully curating training data and consider situations where less computationally expensive techniques are advantageous. This includes a comparison of popular model architectures and a guide to their implementation.
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Affiliation(s)
- Jamie R. Sykes
- Department of Computer ScienceUniversity of YorkDeramore Lane, YorkYO10 5GHYorkshireUnited Kingdom
| | - Katherine J. Denby
- Centre for Novel Agricultural Products, Department of BiologyUniversity of YorkWentworth Way, YorkYO10 5DDYorkshireUnited Kingdom
| | - Daniel W. Franks
- Department of Computer ScienceUniversity of YorkDeramore Lane, YorkYO10 5GHYorkshireUnited Kingdom
- Department of BiologyUniversity of YorkWentworth Way, YorkYO10 5DDYorkshireUnited Kingdom
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Leiva AM, Pardo JM, Arinaitwe W, Newby J, Vongphachanh P, Chittarath K, Oeurn S, Thi Hang L, Gil-Ordóñez A, Rodriguez R, Cuellar WJ. Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia. Sci Rep 2023; 13:22500. [PMID: 38110543 PMCID: PMC10728180 DOI: 10.1038/s41598-023-49735-5] [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: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023] Open
Abstract
Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.
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Affiliation(s)
- Ana M Leiva
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Juan M Pardo
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Warren Arinaitwe
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Jonathan Newby
- Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), Cassava Program Asia Office, P.O. Box 783, Vientiane, Lao PDR
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, P.O. Box 811, Vientiane, Lao PDR
| | - Samoul Oeurn
- Plant Protection Sanitary and Phytosanitary Department, General Directorate of Agriculture (GDA), Phnom Penh, 120406, Cambodia
| | - Le Thi Hang
- Plant Protection Research Institute (PPRI), Duc Thang Bac Tu Liem, Hanoi, 100000, Vietnam
| | - Alejandra Gil-Ordóñez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Rafael Rodriguez
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia
| | - Wilmer J Cuellar
- Virology and Crop Protection Laboratory, Cassava Program, International Center for Tropical Agriculture (CIAT), Crops for Nutrition and Health Research Area, The Americas Hub, Km 17 Recta Cali, 763537, Palmira, Colombia.
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Peng J, Li Y, Xing Q, Huang C, Yan J. Dual RNA-Seq Reveals Temperature-Mediated Gene Reprogramming and Molecular Crosstalk between Grapevine and Lasiodiplodia theobromae. J Fungi (Basel) 2023; 9:1197. [PMID: 38132797 PMCID: PMC10745131 DOI: 10.3390/jof9121197] [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: 11/06/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
High temperatures associated with a fluctuating climate profoundly accelerate the occurrence of a myriad of plant diseases around the world. A comprehensive insight into how plants respond to pathogenic microorganisms under high-temperature stress is required for plant disease management, whereas the underlying mechanisms behind temperature-mediated plant immunity and pathogen pathogenicity are still unclear. Here, we evaluated the effect of high temperature on the development of grapevine canker disease and quantified the contribution of temperature variation to the gene transcription reprogramming of grapevine and its pathogenic agent Lasiodiplodia theobromae using a dual RNA-seq approach. The results showed that both grapevine and the pathogen displayed altered transcriptomes under different temperatures, and even the transcription of a plethora of genes from the two organisms responded in different directions and magnitudes. The transcription variability that arose due to temperature oscillation allowed us to identify a total of 26 grapevine gene modules and 17 fungal gene modules that were correlated with more than one gene module of the partner organism, which revealed an extensive web of plant-pathogen gene reprogramming during infection. More importantly, we identified a set of temperature-responsive genes that were transcriptionally orchestrated within the given gene modules. These genes are predicted to be involved in multiple cellular processes including protein folding, stress response regulation, and carbohydrate and peptide metabolisms in grapevine and porphyrin- and pteridine-containing compound metabolisms in L. theobromae, implying that in response to temperature oscillation, a complex web of signaling pathways in two organism cells is activated during infection. This study describes a co-transcription network of grapevine and L. theobromae in the context of considering temperature variation, which provides novel insights into deciphering the molecular mechanisms underlying temperature-modulated disease development.
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Affiliation(s)
| | | | | | | | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China (Q.X.)
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El-Ganainy SM, Ismail AM, Iqbal Z, Elshewy ES, Alhudaib KA, Almaghasla MI, Magistà D. Diversity among Lasiodiplodia Species Causing Dieback, Root Rot and Leaf Spot on Fruit Trees in Egypt, and a Description of Lasiodiplodia newvalleyensis sp. nov. J Fungi (Basel) 2022; 8:jof8111203. [PMID: 36422024 PMCID: PMC9694705 DOI: 10.3390/jof8111203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lasiodiplodia (family Botryosphaeriaceae) is a widely distributed fungal genus that causes a variety of diseases in tropical and subtropical regions. During 2020−2021, a routine survey of fruit tree plants was conducted in five Egyptian Governorates, and fresh samples exhibiting dieback, decline, leaf spot and root rot symptoms were collected. Collection from eight different symptomatic leaves, twigs, branches and roots of fruit trees yielded 18 Lasiodiplodia-like isolates. The sequencing data from the internal transcribed spacer region (ITS), partial translation elongation factor 1-alpha (tef1-a) and β-tubulin (tub2) were used to infer phylogenetic relationships with known Lasiodiplodia species. Two isolates obtained from black necrotic lesions on Phoenix dactylifera leaves were identified as a putative novel species, L. newvalleyensis sp. nov., and were thus subjected to further morphological characterization. The results of isolation and molecular characterization revealed that L. theobromae (n = 9) was the most common species on Mangifera indica, Citrus reticulata, C. sinensis, Ficus carica, Prunus persica, Prunus armeniaca and Pyrus communis trees. Lasiodiplodia pseudotheobromae (n = 5) was isolated from M. indica, Prunus persica and C. sinensis. Lasiodiplodia laeliocattleyae (n = 2) was isolated from C. reticulata. Pathogenicity test results suggested that all Lasiodiplodia species were pathogenic to their hosts. The present study is considered the first to characterize and decipher the diversity of Lasiodiplodia species associated with fruit trees in Egypt, using the multi-locus ITS, tef1-a and tub2 sequence data, along with morphological and pathogenic trials. To our knowledge, this is the first report of L. newvalleyensis on Phoenix dactylifera and L. laeliocattleya on C. reticulata in Egypt and worldwide.
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Affiliation(s)
- Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt
- Correspondence: (S.M.E.-G.); (A.M.I.)
| | - Ahmed Mahmoud Ismail
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt
- Correspondence: (S.M.E.-G.); (A.M.I.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, Riyadh 11451, Saudi Arabia
| | - Eman Said Elshewy
- Vegetable Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza 12619, Egypt
| | - Khalid A. Alhudaib
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
| | - Mustafa I. Almaghasla
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
| | - Donato Magistà
- Department of Soil, Plant and Food Sciences, University of Bari A. Moro, 70126 Bari, Italy
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), 70126 Bari, Italy
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