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Yadav SK, Singh D, Prasad L, Jat B, Rao GP, Saharan MS, Kaur V. Utilization of 16Sr RNA and secA genes for molecular discernment of ' Candidatus Phytoplasma australasiaticum' strain associated with linseed germplasm in India. 3 Biotech 2024; 14:201. [PMID: 39149558 PMCID: PMC11322467 DOI: 10.1007/s13205-024-04046-y] [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: 07/08/2024] [Accepted: 08/04/2024] [Indexed: 08/17/2024] Open
Abstract
The growing prevalence of phytoplasma associated symptoms on linseed or flax (Linum usitatissimum L.) germplasm at Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR) fields was noticed during the 2019-22 growing seasons. The characteristic phytoplasma symptoms of phyllody, stem fasciation, stunting, along with floral and capsule malformations were observed in 41 linseed accessions grown at experimental fields of ICAR-NBPGR, Delhi. During 3 years, the presence of phytoplasma in symptomatic linseed accessions was confirmed by nested-PCR assays utilizing 16S rRNA and secA gene-specific primers. The 16S rRNA and secA gene sequences of linseed phytoplasma strains from the representative symptomatic 41 linseed accessions exhibited 100% sequence identity among themselves and 99.93% and 99.82% sequence homology with reference strain, 'Candidatus Phytoplasma australasiaticum' (GenBank Accession: Y10097). Phylogenetic analysis of 16S rRNA and secA gene sequences clustered the linseed isolates with the peanut witches' broom group belonging to 'Ca. P. australasiaticum' strains. The virtual RFLP analysis of 16S rRNA F2nR2 fragment (~1.2 kb) of linseed phytoplasma strains further classified it into 16Sr group II, subgroup D. Our results suggested confirmation of the association of 'Ca. P. australasiaticum' strain (16SrII-D) in the linseed germplasm accessions from North India, which is the first report from India. The phytoplasma infection also reduced the growth and yield parameters of two linseed accessions (IC0498748 and EC0718851).
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Affiliation(s)
- Shashank Kumar Yadav
- Division of Germplasm Evaluation, Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR), Pusa Campus, New Delhi, 110012 India
| | - Devender Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR), Pusa Campus, New Delhi, 110012 India
| | - Lakshman Prasad
- Division of Plant Pathology, Indian Council of Agricultural Research- Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - Balram Jat
- Division of Germplasm Evaluation, Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR), Pusa Campus, New Delhi, 110012 India
| | - Govind Pratap Rao
- Division of Plant Pathology, Indian Council of Agricultural Research- Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - Mahender Singh Saharan
- Division of Plant Pathology, Indian Council of Agricultural Research- Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012 India
| | - Vikender Kaur
- Division of Germplasm Evaluation, Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR), Pusa Campus, New Delhi, 110012 India
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2
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Montano HG, Bertaccini A, Fiore N. Phytoplasma-Associated Diseases in South America: Thirty Years of Research. Microorganisms 2024; 12:1311. [PMID: 39065080 PMCID: PMC11278980 DOI: 10.3390/microorganisms12071311] [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: 05/22/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Phytoplasma-associated diseases are mainly insect-transmitted and are present worldwide. Considering that disease detection is a relevant environmental factor that may elucidate the presence of these diseases, a review reporting the geographic distribution of phytoplasma taxa in geographically consistent areas helps manage diseases appropriately and reduce their spreading. This work summarizes the data available about the identification of the phytoplasma associated with several diverse diseases in South America in the last decades. The insect vectors and putative vectors together with the plant host range of these phytoplasmas are also summarized. Overall, 16 'Candidatus Phytoplasma' species were detected, and those most frequently detected in agricultural-relevant crops such as corn, alfalfa, grapevine, and other horticultural species are 'Ca. P. pruni', 'Ca. P. asteris', and 'Ca. P. fraxini'.
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Affiliation(s)
- Helena Guglielmi Montano
- Department of Entomology and Plant Pathology, Federal Rural University of Rio de Janeiro (UFRRJ), Seropédica 23897-000, Brazil;
| | - Assunta Bertaccini
- Department of Agriculture and Food Science, Alma Mater Studiorum—University of Bologna, 40127 Bologna, Italy
| | - Nicola Fiore
- Department of Plant Health, Faculty of Agricultural Sciences, University of Chile, Santiago 8820808, Chile;
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3
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Singh SK, Ranebennur H, Gupta S, Pandey H, Singh V, Rao GP. Detection and molecular characterization of ' Candidatus Phytoplasma australasiaticum' in Aegle marmelos: a fruit of high medicinal values in India. 3 Biotech 2024; 14:147. [PMID: 38706929 PMCID: PMC11068701 DOI: 10.1007/s13205-024-03995-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024] Open
Abstract
In surveys conducted from 2020 to 2022, five leaf samples each from symptomatic Agele marmelos trees and seedlings, along with five samples from asymptomatic trees and seedlings, were collected in Ayodhya, Uttar Pradesh, India. The DNA extraction from all the samples was subjected to nested PCR assays, using the universal phytoplasma-specific primers set (P1/P7 followed by R16F2n/R16R2). The resulting 1.2 kb amplified products were observed in all the symptomatic samples but not in the asymptomatic samples. Bael phytoplasma strain sequences from the trees and seedlings were found 100% identical within themselves and only two representative sequences (one each from tree and seedling) were deposited in GenBank (NCBI) as PP415872 (AmA-1) and PP415873 (AmA-2). BLASTn searches revealed the maximum (100%) sequence identity with a phytoplasma strain from murraya little leaf strain of Faizabad (GenBank Acc.no. OP984129) and lowest (99.84%) with arecanut crown choking of Shimoga (GenBank Acc. no. OM417502) from Karnataka. Phylogenetic analysis clustered the bael phytoplasma isolates with peanut witches' broom group phytoplasma strains. Virtual RFLP analysis confirmed their identity as 'Ca. P. australasiaticum', a 16SrII-D subgroup strain. This study presents the first identification of a phytoplasma strain in A. marmelos, emphasizing its potential threat to fruit crops and the need for vigilance in nursery practices to prevent further dissemination.
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Affiliation(s)
- Sushil Kumar Singh
- Department of Plant Pathology, Acharya Narendra Dev University of Agriculture & Technology, Kumarganj, Ayodhya, 224229 Uttar Pradesh India
| | - Hemavati Ranebennur
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Shivani Gupta
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Himanshu Pandey
- PG Department of Agriculture, Khalsa College, Amritsar, 143002 Punjab India
| | - Vivek Singh
- Department of Plant Pathology, Acharya Narendra Dev University of Agriculture & Technology, Kumarganj, Ayodhya, 224229 Uttar Pradesh India
| | - Govind Pratap Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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4
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Zhang Y, Qiao Z, Li J, Bertaccini A. Paulownia Witches' Broom Disease: A Comprehensive Review. Microorganisms 2024; 12:885. [PMID: 38792713 PMCID: PMC11123829 DOI: 10.3390/microorganisms12050885] [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: 04/02/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Phytoplasmas are insect-transmitted bacterial pathogens associated with diseases in a wide range of host plants, resulting in significant economic and ecological losses. Perennial deciduous trees in the genus Paulownia are widely planted for wood harvesting and ornamental purposes. Paulownia witches' broom (PaWB) disease, associated with a 16SrI-D subgroup phytoplasma, is a destructive disease of paulownia in East Asia. The PaWB phytoplasmas are mainly transmitted by insect vectors in the Pentatomidae (stink bugs), Miridae (mirid bugs) and Cicadellidae (leafhoppers) families. Diseased trees show typical symptoms, such as branch and shoot proliferation, which together are referred to as witches' broom. The phytoplasma presence affects the physiological and anatomical structures of paulownia. Gene expression in paulownia responding to phytoplasma presence have been studied at the transcriptional, post-transcriptional, translational and post-translational levels by high throughput sequencing techniques. A PaWB pathogenic mechanism frame diagram on molecular level is summarized. Studies on the interactions among the phytoplasma, the insect vectors and the plant host, including the mechanisms underlying how paulownia effectors modify processes of gene expression, will lead to a deeper understanding of the pathogenic mechanisms and to the development of efficient control measures.
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Affiliation(s)
- Yajie Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450000, China; (Y.Z.); (Z.Q.)
- Henan Provincial Institute of Scientific and Technical Information, Zhengzhou 450003, China
| | - Zesen Qiao
- College of Forestry, Henan Agricultural University, Zhengzhou 450000, China; (Y.Z.); (Z.Q.)
| | - Jidong Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450000, China; (Y.Z.); (Z.Q.)
- Department of Agriculture and Food Science, Alma Mater Studiorum—University of Bologna, 40127 Bologna, Italy
| | - Assunta Bertaccini
- Department of Agriculture and Food Science, Alma Mater Studiorum—University of Bologna, 40127 Bologna, Italy
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5
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Carreón-Anguiano KG, Vila-Luna SE, Sáenz-Carbonell L, Canto-Canche B. PhyEffector, the First Algorithm That Identifies Classical and Non-Classical Effectors in Phytoplasmas. Biomimetics (Basel) 2023; 8:550. [PMID: 37999191 PMCID: PMC10669590 DOI: 10.3390/biomimetics8070550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
Phytoplasmas are the causal agents of more than 100 plant diseases in economically important crops. Eleven genomes have been fully sequenced and have allowed us to gain a better understanding of the biology and evolution of phytoplasmas. Effectors are key players in pathogenicity and virulence, and their identification and description are becoming an essential practice in the description of phytoplasma genomes. This is of particular importance because effectors are possible candidates for the development of new strategies for the control of plant diseases. To date, the prediction of effectors in phytoplasmas has been a great challenge; the reliable comparison of effectoromes has been hindered because research teams have used the combination of different programs in their predictions. This is not trivial since significant differences in the results can arise, depending on the predictive pipeline used. Here, we tested different predictive pipelines to create the PhyEffector algorithm; the average value of the F1 score for PhyEffector was 0.9761 when applied to different databases or genomes, demonstrating its robustness as a predictive tool. PhyEffector can recover both classical and non-classical phytoplasma effectors, making it an invaluable tool to accelerate effectoromics in phytoplasmas.
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Affiliation(s)
| | | | | | - Blondy Canto-Canche
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico (S.E.V.-L.); (L.S.-C.)
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6
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Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Al-Sadi AM, Al-Subhi AM, Foissac X, Salar P, Cai H, Yang JY, Davis R, Jones L, Rodoni B, Constable FE. The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486824 DOI: 10.1099/ijsem.0.005977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely 'Candidatus Phytoplasma aurantifolia' and 'Ca. Phytoplasma australasia'. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | | | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | - Abdullah M Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ali M Al-Subhi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Xavier Foissac
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Pascal Salar
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Hong Cai
- The Key Laboratory for Plant Pathology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
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7
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Contaldo N, Zambon Y, Galbacs ZN, Miloro F, Havelda Z, Bertaccini A, Varallyay E. Small RNA Profiling of Aster Yellows Phytoplasma-Infected Catharanthus roseus Plants Showing Different Symptoms. Genes (Basel) 2023; 14:genes14051114. [PMID: 37239473 DOI: 10.3390/genes14051114] [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: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Micropropagated Catharantus roseus plants infected with 'Candidatus Phytoplasma asteris' showed virescence symptoms, witches' broom symptoms, or became asymptomatic after their planting in pots. Nine plants were grouped into three categories according to these symptoms, which were then employed for investigation. The phytoplasma concentration, as determined by qPCR, correlated well with the severity of symptoms. To reveal the changes in the small RNA profiles in these plants, small RNA high-throughput sequencing (HTS) was carried out. The bioinformatics comparison of the micro (mi) RNA and small interfering (si) RNA profiles of the symptomatic and asymptomatic plants showed changes, which could be correlated to some of the observed symptoms. These results complement previous studies on phytoplasmas and serve as a starting point for small RNA-omic studies in phytoplasma research.
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Affiliation(s)
- Nicoletta Contaldo
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), 70126 Bari, Italy
| | - Yuri Zambon
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Zsuszanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary
| | - Fabio Miloro
- Plant Developmental Biology Group, Department of Plant Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary
| | - Zoltan Havelda
- Plant Developmental Biology Group, Department of Plant Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary
| | - Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary
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8
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Stanković M. 10th Anniversary of Plants-Recent Advances and Further Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:1696. [PMID: 37111918 PMCID: PMC10145593 DOI: 10.3390/plants12081696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/08/2023] [Indexed: 06/19/2023]
Abstract
Published for the first time in 2012, Plants will celebrate its 10th anniversary [...].
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Affiliation(s)
- Milan Stanković
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
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9
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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: 7] [Impact Index Per Article: 7.0] [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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10
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Shreenath YS, Nabi SU, Madhu GS, Kumawat KL, Rao GP. Identification and multilocus gene characterization of phytoplasmas associated with sweet cherry in India. 3 Biotech 2022; 12:291. [PMID: 36276469 PMCID: PMC9509515 DOI: 10.1007/s13205-022-03357-2] [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: 01/13/2022] [Accepted: 09/09/2022] [Indexed: 11/01/2022] Open
Abstract
Symptoms of leaf roll, swollen nodes, flat branch and witches' broom were observed in five cultivars of sweet cherry from Srinagar, Jammu and Kashmir province, India, during 2019-2021. Phytoplasmas association were confirmed by amplifying 16S rRNA, secA, rp, tuf and secY genes with phytoplasma-specific primers in all symptomatic sweet cherry cultivars in nested PCR assays. Pairwise sequence comparison, phylogeny and virtual RFLP (16S rRNA gene) analyses confirmed the presence of 'Candidatus Phytoplasma asteris' and 'Ca. P. trifolii' strains in the sweet cherry samples. The incidence of flat branch and witches' broom symptoms associated with 'Ca. P. trifolii' varied from 5.8 to 25% in cultivars Bigarreau Nepoleon (Double), Bigarreau Noir Grossa and CITH-Cherry-9. However, incidence of leaf rolling, swollen nodes and bud proliferation associated with 'Ca. P. asteris' was recorded 7.5% in cultivar Stella and 10% in Sunburst, respectively, in the surveyed area. The multigene characterization of sweet cherry phytoplasma strains confirmed the validity of these molecular markers for identification of phytoplasmas enclosed in 16SrI and 16SrVI groups. The presence of phytoplasmas in sweet cherry is the first report from India.
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Affiliation(s)
- Y. S. Shreenath
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K 191132 India
| | - G. S. Madhu
- ICAR-Central Institute of Temperate Horticulture, Srinagar, J&K 191132 India
| | - Kishan Lal Kumawat
- ICAR-Central Institute of Arid Horticulture, Bikaner, Rajasthan 334006 India
| | - Govind P. Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012 India
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11
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Pusz-Bochenska K, Perez-Lopez E, Wist TJ, Bennypaul H, Sanderson D, Green M, Dumonceaux TJ. Multilocus sequence typing of diverse phytoplasmas using hybridization probe-based sequence capture provides high resolution strain differentiation. Front Microbiol 2022; 13:959562. [PMID: 36246242 PMCID: PMC9556853 DOI: 10.3389/fmicb.2022.959562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
Phytoplasmas are insect-vectored, difficult-to-culture bacterial pathogens that infect a wide variety of crop and non-crop plants, and are associated with diseases that can lead to significant yield losses in agricultural production worldwide. Phytoplasmas are currently grouped in the provisional genus ‘Candidatus Phytoplasma’, which includes 49 ‘Candidatus’ species. Further differentiation of phytoplasmas into ribosomal groups is based on the restriction fragment length polymorphism (RFLP) pattern of the 16S rRNA-encoding operon, with more than 36 ribosomal groups (16Sr) and over 100 subgroups reported. Since disease symptoms on plants are not associated with phytoplasma identity, accurate diagnostics is of critical importance to manage disease associated with these microorganisms. Phytoplasmas are typically detected from plant and insect tissue using PCR-based methods targeting universal taxonomic markers. Although these methods are relatively sensitive, specific and are widely used, they have limitations, since they provide limited resolution of phytoplasma strains, thus necessitating further assessment of biological properties and delaying implementation of mitigation measures. Moreover, the design of PCR primers that can target multiple loci from phytoplasmas that differ at the sequence level can be a significant challenge. To overcome these limitations, a PCR-independent, multilocus sequence typing (MLST) assay to characterize an array of phytoplasmas was developed. Hybridization probe s targeting cpn60, tuf, secA, secY, and nusA genes, as well as 16S and rp operons, were designed and used to enrich DNA extracts from phytoplasma-infected samples for DNA fragments corresponding to these markers prior to Illumina sequencing. This method was tested using different phytoplasmas including ‘Ca. P. asteris’ (16SrI-B), ‘Ca. P. pruni’ (16SrIII-A),‘Ca. P. prunorum’ (16SrX-B), ‘Ca. P. pyri’ (16SrX-C), ‘Ca. P. mali’ (16SrX-A), and ‘Ca. P. solani’ (16SrXII-A). Thousands of reads were obtained for each gene with multiple overlapping fragments, which were assembled to generate full-length (typically >2 kb), high-quality sequences. Phytoplasma groups and subgroups were accurately determined based on 16S ribosomal RNA and cpn60 gene sequences. Hybridization-based MLST facilitates the enrichment of target genes of phytoplasmas and allows the simultaneous determination of sequences corresponding to seven different markers. In this proof-of-concept study, hybridization-based MLST was demonstrated to be an efficient way to generate data regarding ‘Ca. Phytoplasma’ species/strain differentiation.
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Affiliation(s)
- Karolina Pusz-Bochenska
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edel Perez-Lopez
- Centre de Recherche et D'innovation sur les Végétaux (CRIV), Faculté des Sciences de L'agriculture et de L'alimentation, Département de Phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Tyler J. Wist
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Harvinder Bennypaul
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Daniel Sanderson
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Margaret Green
- Canadian Food Inspection Agency (CFIA), Sidney Laboratory, Centre for Plant Health, North Saanich, BC, Canada
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Tim J. Dumonceaux,
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