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Lu H, Wilson B, Zhang H, Woruba SB, Feng B, Johnson AC, Komolong B, Kuniata L, Yang G, Gurr GM. Detection and identification of Bogia coconut syndrome phytoplasma from seed-associated tissues and seedlings of coconut (Cocos nucifera) and betel nut (Areca catechu). Sci Rep 2024; 14:11542. [PMID: 38773154 PMCID: PMC11109132 DOI: 10.1038/s41598-024-61916-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
Evidence for seed transmission of phytoplasmas has grown in several pathosystems including coconut (Cocos nucifera). Bogia coconut syndrome (BCS) is a disease associated with the lethal yellowing syndrome associated with the presence of 'Candidatus Phytoplasma noviguineense' that affects coconut, betel nut (Areca catechu) and bananas (Musa spp.) in Papua New Guinea. Coconut and betel nut drupes were sampled from BCS-infected areas in Papua New Guinea, dissected, the extracted nucleic acid was used in polymerase chain reaction (PCR), and loop mediated isothermal amplification (LAMP) used to check for presence of phytoplasma DNA. In a second study, drupes of both plant species were collected from multiple field sites and grown in insect-proof cages. Leaf samples taken at 6 months were also tested with PCR and LAMP. The studies of dissected coconut drupes detected phytoplasma DNA in several tissues including the embryo. Drupes from betel nut tested negative. Among the seedlings, evidence of possible seed transmission was found in both plant species. The results demonstrate the presence of 'Ca. P. noviguineense' in coconut drupes and seedlings, and in seedlings of betel nut; factors that need to be considered in ongoing management and containment efforts.
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Affiliation(s)
- Hengyu Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
- Key Laboratory of Green Control of Insect Pests (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China
- Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bree Wilson
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Hanfang Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
- Key Laboratory of Green Control of Insect Pests (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China
- Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sharon B Woruba
- Kokonas Indastri Koporesen, Madang, Madang Province, Papua New Guinea
| | - Bowen Feng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
- Key Laboratory of Green Control of Insect Pests (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China
- Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Anne C Johnson
- Gulbali Institute, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Birte Komolong
- National Agricultural Research Institute, P.O. Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Lastus Kuniata
- New Britain Palm Oil, Ramu Agri Industries Ltd, Gusap Downs, PO Box 2183, Lae, Morobe Province, Papua New Guinea
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
- Key Laboratory of Green Control of Insect Pests (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China.
- Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Geoff M Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
- Key Laboratory of Green Control of Insect Pests (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 350002, China.
- Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Gulbali Institute, Charles Sturt University, Orange, NSW, 2800, Australia.
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Kirdat K, Tiwarekar B, Sathe S, Yadav A. From sequences to species: Charting the phytoplasma classification and taxonomy in the era of taxogenomics. Front Microbiol 2023; 14:1123783. [PMID: 36970684 PMCID: PMC10033645 DOI: 10.3389/fmicb.2023.1123783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Phytoplasma taxonomy has been a topic of discussion for the last two and half decades. Since the Japanese scientists discovered the phytoplasma bodies in 1967, the phytoplasma taxonomy was limited to disease symptomology for a long time. The advances in DNA-based markers and sequencing improved phytoplasma classification. In 2004, the International Research Programme on Comparative Mycoplasmology (IRPCM)- Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group provided the description of the provisional genus ‘Candidatus Phytoplasma’ with guidelines to describe the new provisional phytoplasma species. The unintentional consequences of these guidelines led to the description of many phytoplasma species where species characterization was restricted to a partial sequence of the 16S rRNA gene alone. Additionally, the lack of a complete set of housekeeping gene sequences or genome sequences, as well as the heterogeneity among closely related phytoplasmas limited the development of a comprehensive Multi-Locus Sequence Typing (MLST) system. To address these issues, researchers tried deducing the definition of phytoplasma species using phytoplasmas genome sequences and the average nucleotide identity (ANI). In another attempts, a new phytoplasma species were described based on the Overall Genome relatedness Values (OGRI) values fetched from the genome sequences. These studies align with the attempts to standardize the classification and nomenclature of ‘Candidatus’ bacteria. With a brief historical account of phytoplasma taxonomy and recent developments, this review highlights the current issues and provides recommendations for a comprehensive system for phytoplasma taxonomy until phytoplasma retains ‘Candidatus’ status.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Bhavesh Tiwarekar
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Amit Yadav
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- *Correspondence: Amit Yadav, ,
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Wei W, Zhao Y. Phytoplasma Taxonomy: Nomenclature, Classification, and Identification. BIOLOGY 2022; 11:biology11081119. [PMID: 35892975 PMCID: PMC9394401 DOI: 10.3390/biology11081119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary Phytoplasmas are vector-borne and graft-transmissible bacteria that cause various plant diseases, leading to severe economic losses. Since phytoplasmas cannot be cultured in cell-free media, their identification and taxonomy rely on molecular techniques and gene sequences. In this article, we summarize the recent advances in phytoplasma taxonomy from three different aspects, including (i) nomenclature (naming Candidatus Phytoplasma species); (ii) classification (group and subgroup assignment based on 16S rRNA gene sequences); and (iii) identification (fine differentiation of phytoplasma strains). In addition, some important issues, especially those related to recognizing new ‘Candidatus Phytoplasma’ species, are discussed. This information will be helpful for rapid diagnosis of phytoplasma diseases and accurate taxonomic identification of both emerging and known phytoplasma strains. Abstract Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of ‘Candidatus phytoplasma’ species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for ‘Candidatus Phytoplasma’ species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined.
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Affiliation(s)
- Wei Wei
- Correspondence: ; Tel.: +1-301-504-0786
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Bertaccini A. Plants and Phytoplasmas: When Bacteria Modify Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111425. [PMID: 35684198 PMCID: PMC9182842 DOI: 10.3390/plants11111425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 05/14/2023]
Abstract
Plant pathogen presence is very dangerous for agricultural ecosystems and causes huge economic losses. Phytoplasmas are insect-transmitted wall-less bacteria living in plants, only in the phloem tissues and in the emolymph of their insect vectors. They are able to manipulate several metabolic pathways of their hosts, very often without impairing their life. The molecular diversity described (49 'Candidatus Phytoplasma' species and about 300 ribosomal subgroups) is only in some cases related to their associated symptomatology. As for the other plant pathogens, it is necessary to verify their identity and recognize the symptoms associated with their presence to appropriately manage the diseases. However, the never-ending mechanism of patho-adaptation and the copresence of other pathogens makes this management difficult. Reducing the huge impact of phytoplasma-associated diseases in all the main crops and wild species is, however, relevant, in order to reduce their effects that are jeopardizing plant biodiversity.
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Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, 40127 Bologna, Italy
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Bertaccini A, Arocha-Rosete Y, Contaldo N, Duduk B, Fiore N, Montano HG, Kube M, Kuo CH, Martini M, Oshima K, Quaglino F, Schneider B, Wei W, Zamorano A. Revision of the ' Candidatus Phytoplasma' species description guidelines. Int J Syst Evol Microbiol 2022; 72. [PMID: 35471141 DOI: 10.1099/ijsem.0.005353] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus 'Candidatus Phytoplasma' was proposed to accommodate cell wall-less bacteria that are molecularly and biochemically incompletely characterized, and colonize plant phloem and insect vector tissues. This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the genus 'Ca. Phytoplasma', the proposed guidelines were revised and clarified to accommodate those 'Ca. Phytoplasma' species strains sharing >98.65 % sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least twofold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65 % sequence identity with the reference strain but >98.65 % with other strain(s) within the same 'Ca. Phytoplasma' species should be considered related strains to that 'Ca. Phytoplasma' species. The guidelines herein, keep the original published reference strains. However, to improve 'Ca. Phytoplasma' species assignment, complementary strains are suggested as an alternative to the reference strains. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of 'Ca. Phytoplasma' species and alternative reference strains described are reported. For new 'Ca. Phytoplasma' species that will be assigned with identity ≥98.65 % of their 16S rRNA gene sequences, a threshold of 95 % genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. There are 49 officially published 'Candidatus Phytoplasma' species, including 'Ca. P. cocostanzaniae' and 'Ca. P. palmae' described in this manuscript.
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Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | | | - Nicoletta Contaldo
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Nicola Fiore
- Faculty of Agricultural Sciences, Department of Plant Protection, University of Chile, Santiago, Chile
| | - Helena Guglielmi Montano
- Department of Entomology and Plant Pathology, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Marta Martini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Kenro Oshima
- Faculty of Bioscience and Applied Chemistry, Department of Clinical Plant Science, Hosei University, Japan
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Bernd Schneider
- Julius Kuehn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | - Wei Wei
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD, USA
| | - Alan Zamorano
- Faculty of Agricultural Sciences, Department of Plant Protection, University of Chile, Santiago, Chile
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Davis RI, Jones LM, Pease B, Perkins SL, Vala HR, Kokoa P, Apa M, Dale CJ. Plant Virus and Virus-like Disease Threats to Australia's North Targeted by the Northern Australia Quarantine Strategy. PLANTS 2021; 10:plants10102175. [PMID: 34685987 PMCID: PMC8537380 DOI: 10.3390/plants10102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
Abstract
The Northern Australia Quarantine Strategy (NAQS) is a biosecurity initiative operated by the Australian federal government’s Department of Agriculture, Water and the Environment (DAWE). It is unique worldwide because it deals specifically with the potential arrival via unregulated pathways of exotic threats from overseas in a vast and sparsely populated region. It aims to protect the nation’s animal- and plant-based production industries, as well as the environment, from incursions of organisms from countries that lie immediately to the north. These are diseases, pests, and weeds present in these countries that are currently either absent from, or under active containment in, Australia and may arrive by natural or human-assisted means. This review article focuses on the plant viruses and virus-like diseases that are most highly targeted by the NAQS program. It presents eight pathogen species/group entries in the NAQS A list of target pathogens, providing an overview of the historical and current situation, and collates some new data obtained from surveillance activities conducted in northern Australia and collaborative work overseas.
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Affiliation(s)
- Richard I. Davis
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
- Correspondence:
| | - Lynne M. Jones
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Bradley Pease
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Sandy L. Perkins
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Harshitsinh R. Vala
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Pere Kokoa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Marilyn Apa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Christopher J. Dale
- International Plant Health Surveillance Program, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia;
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Ajithkumar K, Savitha AS, Mahadevakumar S, Sreenivasa MY, Naik MK, Rajanna B, Sathyanarayana R, Singh PK. A new host record for Candidatus Phytoplasma cynodontis (16Sr XIV-A) associated with phyllody and fasciation of linseed (Linum usitatissimum) from India. Lett Appl Microbiol 2021; 73:672-681. [PMID: 34545601 DOI: 10.1111/lam.13561] [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: 08/15/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/27/2022]
Abstract
Linseed commonly called as flaxseed (Linum usitatissimum Linn.) is an important oilseed crop cultivated widely in Northern parts of Karnataka. During, 2019 (January-February), a characteristic disease was noticed with symptoms that resembled phytoplasma or like disease symptoms. The incidence was ranged from 6·5 to 16·5% in the experimental station of Raichur Agricultural University. The typical symptoms observed were virescence of floral parts, fasciation of the inflorescence axis, phyllody, stunted and flattened stem with reduced leaves. Symptomatic and healthy samples were collected and processed for molecular detection of phytoplasma. Total DNA was isolated from four infected plants and two healthy plants. The 16S rDNA region was amplified using P1/P7 followed by R16F2n/R16R2 primer pair which showed the amplification of expected amplicon size from all four infected samples. Furthermore, the SecA gene was amplified using SecA1/SecA3 primers. The PCR amplified products were subjected for direct sequencing from both directions and the consensus sequences were obtained and nBLAST search analysis revealed that the 16Sr RNA and SecA sequences were sharing maximum similarity (100%) with the reference sequence of Ca. P. cynodontis. The sequences were analysed phylogenetically by constructing a Phylogram independently by NJ method along with reference sequence of 16S rRNA region and SecA region retrieved from GenBank database showed that the phytoplasma sequence from linseed phyllody of the present study placed in a distinct clade along with reference sequence of "Ca. P. cynodontis" thus confirming the identity phylogenetically. Furthermore, iPhyClassifier and virtual RFLP proved that the phytoplasma belonged to 16SrXIV (subgroup A) phytoplasma. Previously linseed is known to be associated with 16SrII-D phytoplasma but the association of the 16SrXIV-A group of phytoplasma is not reported so far. Therefore, this is the new host record for Ca. P. cynodontis (16SrXIV-A) phytoplasma associated with linseed stem fasciation, phyllody from India.
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Affiliation(s)
- K Ajithkumar
- AICRP on Linseed, Main Agricultural Research Station, University of Agricultural Sciences, Raichur, India
| | - A S Savitha
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, Raichur, India
| | - S Mahadevakumar
- Applied Phytopathology Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, India
| | - M Y Sreenivasa
- Phytopathology Laboratory, Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, India
| | - M K Naik
- University of Agricultural and Horticultural Sciences, Shivamogga, India
| | - B Rajanna
- AICRP on Linseed, Main Agricultural Research Station, University of Agricultural Sciences, Raichur, India
| | | | - P K Singh
- CSA University of Agriculture & Technology, Kanpur, Uttar Pradesh, India
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Jones LM, Pease B, Perkins SL, Constable FE, Kinoti WM, Warmington D, Allgood B, Powell S, Taylor P, Pearce C, Davis RI. 'Candidatus Phytoplasma dypsidis', a novel taxon associated with a lethal wilt disease of palms in Australia. Int J Syst Evol Microbiol 2021; 71. [PMID: 34003739 DOI: 10.1099/ijsem.0.004818] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phytoplasma was initially detected in Dypsis poivriana by nested and real-time PCR from the botanical gardens in Cairns, Queensland, Australia in 2017. Further surveys in the Cairns region identified phytoplasma infections in eight additional dying ornamental palm species (Euterpe precatoria, Cocos nucifera, Verschaffeltia splendida, Brassiophoenix drymophloeodes, Burretiokentia hapala, Cyrtostachys renda, Reinhardtia gracilis, Carpoxylon macrospermum), a Phoenix species, a Euterpe species and two native palms (Archontophoenix alexandrae). Analysis of 16S rRNA gene sequences showed that this phytoplasma is distinct as it shared less than 97.5 % similarity with all other 'Candidatus Phytoplasma' species. At 96.3 % similarity, the most closely related formally described member of the provisional 'Ca. Phytoplasma' genus was 'Ca. Phytoplasma noviguineense', a novel taxon from the island of New Guinea found in monocotyledonous plants. It was slightly more closely related (96.6-96.8 %) to four palm-infecting strains from the Americas, which belong to strain group 16SrIV and which have not been assigned to a formal 'Candidatus Phytoplasma' species taxon. Phylogenetic analysis of the 16S rRNA gene and ribosomal protein genes of the phytoplasma isolate from a dying coconut palm revealed that the phytoplasma represented a distinct lineage within the phytoplasma clade. As the nucleotide identity with other phytoplasmas is less than 97.5 % and the phylogenetic analyses show that it is distinct, a novel taxon 'Candidatus Phytoplasma dypsidis' is proposed for the phytoplasma found in Australia. Strain RID7692 (GenBank accession no. MT536195) is the reference strain. The impact and preliminary aspects of the epidemiology of the disease outbreak associated with this novel taxon are described.
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Affiliation(s)
- Lynne M Jones
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, 114 Catalina Crescent, Cairns International Airport, Qld 4870, Australia
| | - Bradley Pease
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, 114 Catalina Crescent, Cairns International Airport, Qld 4870, Australia
| | - Sandy L Perkins
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, 114 Catalina Crescent, Cairns International Airport, Qld 4870, Australia
| | - Fiona E Constable
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - Wycliff M Kinoti
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBioscience, Bundoora, Victoria 3083, Australia
| | - David Warmington
- Botanic Reserves Parks and Leisure, Cairns Regional Council, Cairns Queensland 4870, Australia
| | - Ben Allgood
- Botanic Reserves Parks and Leisure, Cairns Regional Council, Cairns Queensland 4870, Australia
| | - Sonya Powell
- Botanic Reserves Parks and Leisure, Cairns Regional Council, Cairns Queensland 4870, Australia
| | - Pieter Taylor
- Infrastructure Services, Cairns Regional Council, Cairns Queensland 4870, Australia
| | - Ceri Pearce
- Biosecurity Queensland, Queensland Department of Agriculture and Fisheries, Centre for Wet Tropics Agriculture, South Johnstone QLD 4859, Australia
| | - Richard I Davis
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, 114 Catalina Crescent, Cairns International Airport, Qld 4870, Australia
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9
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Zhao Y, Wei W, Davis RE, Lee IM, Bottner-Parker KD. The agent associated with blue dwarf disease in wheat represents a new phytoplasma taxon, ' Candidatus Phytoplasma tritici'. Int J Syst Evol Microbiol 2021; 71. [PMID: 33464199 DOI: 10.1099/ijsem.0.004604] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wheat blue dwarf (WBD) is one of the most economically damaging cereal crop diseases in northwestern PR China. The agent associated with the WBD disease is a phytoplasma affiliated with the aster yellows (AY) group, subgroup C (16SrI-C). Since phytoplasma strains within the AY group are ecologically and genetically diverse, it has been conceived that the AY phytoplasma group may consist of more than one species. This communication presents evidence to demonstrate that, while each of the two 16 rRNA genes of the WBD phytoplasma shares >97.5 % sequence similarity with that of the 'Candidatus Phytoplasma asteris' reference strain, the WBD phytoplasma clearly represents an ecologically separated lineage: the WBD phytoplasma not only has its unique transmitting vector (Psammotettix striatus) but also elicits a distinctive symptom in its predominant plant host (wheat). In addition, the WBD phytoplasma possesses molecular characteristics that further manifest its significant divergence from 'Ca. P. asteris'. Such molecular characteristics include lineage-specific antigenic membrane proteins and a lower than 95 % genome-wide average nucleotide identity score with 'Ca. P. asteris'. These ecological, molecular and genomic evidences justify the recognition of the WBD phytoplasma as a novel taxon, 'Candidatus Phytoplasma tritici'.
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Affiliation(s)
- Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Wei Wei
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Robert E Davis
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ing-Ming Lee
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Kristi D Bottner-Parker
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
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Ramos Hernández E, Lesher Gordillo JM, Oropeza Salín C, Ortiz García CF, Magaña Alejandro MA, Sánchez Soto S, García Estrada Y. Detection and Identification of Phytoplasmas in the 16SrIV-A, -B, and -D Subgroups in Palms in Tabasco, Mexico. PLANT DISEASE 2020; 104:2606-2612. [PMID: 32813613 DOI: 10.1094/pdis-09-18-1488-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The 16SrIV-A phytoplasmas are associated with the devastating disease lethal yellowing (LY) of palms. In Tabasco (Mexico), the death of Cocos nucifera, Adonidia merrillii, and Attalea butyracea palms have been suspected to be associated with LY based on symptomatology. Samples from the trunk of both symptomatic and nonsymptomatic palms were collected in three different environments: two species of palms within a rural zone and the other within an urban zone. DNA was extracted to perform a nested PCR with phytoplasma primers P1/P7-LY16SF/R16R2. A 1,345-bp fragment was amplified from the DNA extracted from each of the 29 LY-symptomatic palms sampled. Phytoplasma identification was achieved by amplicon sequencing and virtual restriction fragment length polymorphism analyses. Three 16SrIV phytoplasma subgroups were detected: 16SrIV-A in C. nucifera, 16SrIV-B in A. merrillii, and 16SrIV-D in C. nucifera, A. merrillii, and A. butyracea. Phylogenetic analysis showed also that the three phytoplasma strains found in the palm species clustered with phytoplasmas reported in the literature in the three subgroups identified. This is the first report of phytoplasmas associated with these palm species in Tabasco.
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Affiliation(s)
- Eder Ramos Hernández
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Huimanguillo, 86400, Huimanguillo, Tabasco, México
| | - Julia M Lesher Gordillo
- Universidad Juárez Autónoma de Tabasco, División Académica de Ciencias Biológicas, 86150, Villahermosa, Tabasco, México
| | - Carlos Oropeza Salín
- Centro de Investigación Científica de Yucatán A.C., 97205, Chuburná de Hidalgo, Mérida, Yucatán, México
| | | | - Miguel A Magaña Alejandro
- Universidad Juárez Autónoma de Tabasco, División Académica de Ciencias Biológicas, 86150, Villahermosa, Tabasco, México
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Muirhead K, Pérez-López E, Bahder BW, Hill JE, Dumonceaux T. The CpnClassiPhyR Is a Resource for cpn60 Universal Target-Based Classification of Phytoplasmas. PLANT DISEASE 2019; 103:2494-2497. [PMID: 31453748 DOI: 10.1094/pdis-03-19-0454-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytoplasmas are plant-pathogenic bacteria that are associated with yield losses in many crop plants worldwide. Phytoplasma strain differentiation is accomplished using in silico restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA-encoding gene sequences, which has resulted in the definition of ribosomal groups and subgroups of phytoplasmas. Due to limitations associated with this approach, a complementary classification scheme was recently developed based on RFLP analysis of the single-copy, protein-encoding gene chaperonin-60 (cpn60). We present the CpnClassiPhyR, software that facilitates phytoplasma strain classification using both RFLP and automated phylogenetic analysis of cpn60 sequences. This software is available through a web interface at http://cpnclassiphyr.ca.
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Affiliation(s)
| | - Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brian W Bahder
- University of Florida Fort Lauderdale Research and Education Center
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tim Dumonceaux
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
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Banerjee A, Pérez-López E, Mossman K. Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies. Front Microbiol 2018; 9:2863. [PMID: 30524418 PMCID: PMC6262150 DOI: 10.3389/fmicb.2018.02863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Arinjay Banerjee
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, Michael DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karen Mossman
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, Michael DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, ON, Canada
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Perez-Lopez E, Vincent C, Moreau D, Hammond C, Town J, Dumonceaux TJ. A novel 'Candidatus Phytoplasma asteris' subgroup 16SrI-(E/AI)AI associated with blueberry stunt disease in eastern Canada. Int J Syst Evol Microbiol 2018; 69:322-332. [PMID: 30431416 DOI: 10.1099/ijsem.0.003100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas ('Candidatus Phytoplasma' species) are phytopathogenic bacteria vectored by insects and are associated with crop diseases that cause severe yield losses by affecting reproductive tissue development. Infection of northern highbush blueberry plants (Vaccinium corymbosum; Ericaceae) with phytoplasma leads to yield losses by altering plant development resulting in stunting and subsequent plant death. Samples collected from symptomatic blueberry plants in two important blueberry-producing areas in Canada, in the provinces of Québec and Nova Scotia, were analysed for the presence of DNA sequences associated with phytoplasma. Analysis of the 16S rRNA gene sequences demonstrated that the plants were infected with a strain of 'Candidatus Phytoplasma asteris', which was previously identified as blueberry stunt phytoplasma (BBS; 16SrI-E). Examination of further bacterial sequences revealed that two distinct 16S rRNA-encoding gene sequences were present in each sample in combination with a single chaperonin-60 (cpn60) sequence and a single rpoperon sequence, suggesting that this strain displays 16S rRNA-encoding gene sequence heterogeneity. Two distinct rrnoperons, rrnE and the newly described rrnAI, were identified in samples analysed from all geographic locations. We propose, based on the sequences obtained, delineating the new subgroup 16SrI-(E/AI)AI, following the nomenclature proposed for heterogeneous subgroups. To our knowledge, this is the first report of a heterogeneous phytoplasma strain affecting blueberry plants and associated with blueberry stunt disease.
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Affiliation(s)
- Edel Perez-Lopez
- 1Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Charles Vincent
- 2Agriculture et Agroalimentaire Canada, Centre de recherche et de développement de Saint-Jean-sur-Richelieu, Québec, Canada
| | - Debra Moreau
- 3Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada
| | - Christine Hammond
- 4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Jennifer Town
- 4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Tim J Dumonceaux
- 5Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,4Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
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