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Che H, Yu S, Chen W, Zheng W, Cao X, Luo D. Molecular Identification and Characterization of Novel Taxonomic Subgroups and New Host Plants in 16SrI and 16SrII Group Phytoplasmas and Their Evolutionary Diversity on Hainan Island, China. PLANT DISEASE 2024:PDIS12232682RE. [PMID: 38175658 DOI: 10.1094/pdis-12-23-2682-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Phytoplasmas are a group of plant prokaryotic pathogens distributed worldwide. To comprehensively reveal the diversity of the pathogens and the diseases they cause on Hainan, a tropical island with abundant biodiversity in China, a survey of phytoplasmal diseases was performed from 2009 to 2022. Herein, molecular identification and genetic analysis were conducted based on the conserved genes of phytoplasmas. The results indicated that phytoplasmas could be detected in 138 samples from 18 host plants among 215 samples suspected to be infected by the pathogens. The phytoplasma strains from 27 diseased samples of 4 host plants belonged to the 16SrI group and the strains from 111 samples of 14 hosts belonged to the 16SrII group. Among them, 12 plants, including important tropical cash crops such as Phoenix dactylifera, cassava, sugarcane, and Piper nigrum, were first identified as hosts of phytoplasmas on Hainan Island. Based on BLAST and iPhyClassifier analyses, seven novel 16Sr subgroups were proposed to describe the relevant phytoplasma strains, comprising the 16SrI-AP, 16SrI-AQ, and 16SrI-AR subgroups within the 16SrI group and the 16SrII-Y, 16SrII-Z, 16SrII-AB, and 16SrII-AC subgroups within the 16SrII group. Genetic variation and phylogenetic analysis indicated that the phytoplasma strains identified in this study and those reported previously on Hainan Island mainly belong to four 16Sr groups (including I, II, V, and XXXII) and could infect 44 host plants, among which the 16SrI and 16SrII groups were the prevalent 16Sr groups associated with 43 host plant species. The diversity of host plants infected by the phytoplasmas made it difficult to monitor and control their related diseases. Therefore, strengthening inspection and quarantine during the introduction and transit of the related phytoplasmal host crops would effectively curb the spread and prevalence of the phytoplasmas and their related lethal diseases.
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Affiliation(s)
- Haiyan Che
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan Province, China
| | - Shaoshuai Yu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, Hainan Province, China
| | - Wang Chen
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, College of Agriculture, Yangtze University, Jingzhou 434000, Hubei Province, China
| | - Wenhu Zheng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan Province, China
| | - Xueren Cao
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan Province, China
| | - Daquan Luo
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan Province, China
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2
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Toth R, Ilic AM, Huettel B, Duduk B, Kube M. Divergence within the Taxon ' Candidatus Phytoplasma asteris' Confirmed by Comparative Genome Analysis of Carrot Strains. Microorganisms 2024; 12:1016. [PMID: 38792845 PMCID: PMC11123874 DOI: 10.3390/microorganisms12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Phytoplasmas are linked to diseases in hundreds of economically important crops, including carrots. In carrots, phytoplasmosis is associated with leaf chlorosis and necrosis, coupled with inhibited root system development, ultimately leading to significant economic losses. During a field study conducted in Baden-Württemberg (Germany), two strains of the provisional taxon 'Candidatus Phytoplasma asteris' were identified within a carrot plot. For further analysis, strains M8 and M33 underwent shotgun sequencing, utilising single-molecule-real-time (SMRT) long-read sequencing and sequencing-by-synthesis (SBS) paired-end short-read sequencing techniques. Hybrid assemblies resulted in complete de novo assemblies of two genomes harboring circular chromosomes and two plasmids. Analyses, including average nucleotide identity and sequence comparisons of established marker genes, confirmed the phylogenetic divergence of 'Ca. P. asteris' and a different assignment of strains to the 16S rRNA subgroup I-A for M33 and I-B for M8. These groups exhibited unique features, encompassing virulence factors and genes, associated with the mobilome. In contrast, pan-genome analysis revealed a highly conserved gene set related to metabolism across these strains. This analysis of the Aster Yellows (AY) group reaffirms the perception of phytoplasmas as bacteria that have undergone extensive genome reduction during their co-evolution with the host and an increase of genome size by mobilome.
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Affiliation(s)
- Rafael Toth
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | - Anna-Marie Ilic
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
| | | | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, 11080 Belgrade, Serbia;
| | - Michael Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, 70599 Stuttgart, Germany; (R.T.); (A.-M.I.)
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Romero B, Mithöfer A, Olivier C, Wist T, Prager SM. The Role of Plant Defense Signaling Pathways in Phytoplasma-Infected and Uninfected Aster Leafhoppers' Oviposition, Development, and Settling Behavior. J Chem Ecol 2024:10.1007/s10886-024-01488-9. [PMID: 38532167 DOI: 10.1007/s10886-024-01488-9] [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: 08/29/2023] [Revised: 03/08/2024] [Accepted: 03/17/2024] [Indexed: 03/28/2024]
Abstract
In plant-microbe-insect systems, plant-mediated responses involve the regulation and interactions of plant defense signaling pathways of phytohormones jasmonic acid (JA), ethylene (ET), and salicylic acid (SA). Phytoplasma subgroup 16SrI is the causal agent of Aster Yellows (AY) disease and is primarily transmitted by populations of aster leafhoppers (Macrosteles quadrilineatus Forbes). Aster Yellows infection in plants is associated with the downregulation of the JA pathway and increased leafhopper oviposition. The extent to which the presence of intact phytohormone-mediated defensive pathways regulates aster leafhopper behavioral responses, such as oviposition or settling preferences, remains unknown. We conducted no-choice and two-choice bioassays using a selection of Arabidopsis thaliana lines that vary in their defense pathways and repeated the experiments using AY-infected aster leafhoppers to evaluate possible differences associated with phytoplasma infection. While nymphal development was similar among the different lines and groups of AY-uninfected and AY-infected insects, the number of offspring and individual female egg load of AY-uninfected and AY-infected insects differed in lines with mutated components of the JA and SA signaling pathways. In most cases, AY-uninfected insects preferred to settle on wild-type (WT) plants over mutant lines; no clear pattern was observed in the settling preference of AY-infected insects. These findings support previous observations in other plant pathosystems and suggest that plant signaling pathways and infection with a plant pathogen can affect insect behavioral responses in more than one manner. Potential differences with previous work on AY could be related to the specific subgroup of phytoplasma involved in each case.
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Affiliation(s)
- Berenice Romero
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Chrystel Olivier
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Tyler Wist
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Sean M Prager
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
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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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Pardo JM, Chittarath K, Vongphachanh P, Hang LT, Oeurn S, Arinaitwe W, Rodriguez R, Sophearith S, Malik AI, Cuellar WJ. Cassava Witches' Broom Disease in Southeast Asia: A Review of Its Distribution and Associated Symptoms. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112217. [PMID: 37299196 DOI: 10.3390/plants12112217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
Cassava witches' broom disease (CWBD) is one of the main diseases of cassava in Southeast Asia (SEA). Affected cassava plants show reduced internodal length and proliferation of leaves (phyllody) in the middle and top part of the plant, which results in reduced root yields of 50% or more. It is thought to be caused by phytoplasma; however, despite its widespread distribution in SEA still little is known about CWBD pathology. The overarching goal of this study was to review and corroborate published information on CWBD biology and epidemiology considering recent field observations. We report the following: (1) CWBD symptoms are conserved and persistent in SEA and are distinct from what has been reported as witches' broom in Argentina and Brazil. (2) In comparison with cassava mosaic disease, another major disease of cassava in SEA, symptoms of CWBD develop later. (3) Phytoplasma detected in CWBD-affected plants belong to different ribosomal groups and there is no association study available indicating phytoplasma as the causing agent of CWBD. These findings are essential clues for designing surveillance and management strategies and for future studies to better understand the biology, tissue localization and spatial spread of CWBD in SEA and other potential risk areas.
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Affiliation(s)
- Juan M Pardo
- Cassava Program, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Khonesavanh Chittarath
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Pinkham Vongphachanh
- Plant Protection Center (PPC), Department of Agriculture, Ministry of Agriculture and Forestry, Vientiane P.O. Box 811, Laos
| | - Le Thi Hang
- Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Ha Noi 100000, Vietnam
| | - Samoul Oeurn
- Plant Protection Sanitary and Phytosanitary Department, General Directorate of Agriculture (GDA), Phnom Penh 120406, Cambodia
| | - Warren Arinaitwe
- Cassava Program Asia Office, International Center for Tropical Agriculture (CIAT), Vientiane P.O. Box 783, Laos
| | - Rafael Rodriguez
- Cassava Program, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
| | - Sok Sophearith
- Cassava Program Cambodia Office, International Center for Tropical Agriculture (CIAT), Phnom Penh 120904, Cambodia
| | - Al Imran Malik
- Cassava Program Asia Office, International Center for Tropical Agriculture (CIAT), Vientiane P.O. Box 783, Laos
| | - Wilmer J Cuellar
- Cassava Program, International Center for Tropical Agriculture (CIAT), The Americas Hub, Km 17 Recta Cali-Palmira, Cali 763537, Colombia
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Janik K, Panassiti B, Kerschbamer C, Burmeister J, Trivellone V. Phylogenetic Triage and Risk Assessment: How to Predict Emerging Phytoplasma Diseases. BIOLOGY 2023; 12:biology12050732. [PMID: 37237544 DOI: 10.3390/biology12050732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
Phytoplasma diseases pose a substantial threat to diverse crops of agricultural importance. Management measures are usually implemented only after the disease has already occurred. Early detection of such phytopathogens, prior to disease outbreak, has rarely been attempted, but would be highly beneficial for phytosanitary risk assessment, disease prevention and mitigation. In this study, we present the implementation of a recently proposed proactive disease management protocol (DAMA: Document, Assess, Monitor, Act) for a group of vector-borne phytopathogens. We used insect samples collected during a recent biomonitoring program in southern Germany to screen for the presence of phytoplasmas. Insects were collected with malaise traps in different agricultural settings. DNA was extracted from these mass trap samples and subjected to PCR-based phytoplasma detection and mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding. Phytoplasma DNA was detected in two out of the 152 insect samples analyzed. Phytoplasma identification was performed using iPhyClassifier based on 16S rRNA gene sequence and the detected phytoplasmas were assigned to 'Candidatus Phytoplasma asteris'-related strains. Insect species in the sample were identified by DNA metabarcoding. By using established databases, checklists, and archives, we documented historical associations and records of phytoplasmas and its hosts in the study region. For the assessment in the DAMA protocol, phylogenetic triage was performed in order to determine the risk for tri-trophic interactions (plant-insect-phytoplasma) and associated disease outbreaks in the study region. A phylogenetic heat map constitutes the basis for risk assessment and was used here to identify a minimum number of seven leafhopper species suggested to be monitored by stakeholders in this region. A proactive stance in monitoring changing patterns of association between hosts and pathogens can be a cornerstone in capabilities to prevent future phytoplasma disease outbreaks. To the best of our knowledge, this is the first time that the DAMA protocol has been applied in the field of phytopathology and vector-borne plant diseases.
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Affiliation(s)
- Katrin Janik
- Laimburg Research Centre, Functional Genomics, Laimburg 6-Pfatten (Vadena), 39040 Auer, South Tyrol, Italy
| | | | - Christine Kerschbamer
- Laimburg Research Centre, Functional Genomics, Laimburg 6-Pfatten (Vadena), 39040 Auer, South Tyrol, Italy
| | - Johannes Burmeister
- Institute for Organic Farming, Soil and Resource Management, Bavarian State Research Center for Agriculture, 85354 Freising, Germany
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
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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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Inaba J, Shao J, Trivellone V, Zhao Y, Dietrich CH, Bottner-Parker KD, Ivanauskas A, Wei W. Guilt by Association: DNA Barcoding-Based Identification of Potential Plant Hosts of Phytoplasmas from Their Insect Carriers. PHYTOPATHOLOGY 2023; 113:413-422. [PMID: 36287619 DOI: 10.1094/phyto-09-22-0323-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytoplasmas are small phloem-restricted and insect-transmissible bacteria that infect many plant species, including important crops and ornamental plants, causing severe economic losses. Our previous studies screened phytoplasmas in hundreds of leafhoppers collected from natural habitats worldwide and identified multiple genetically different phytoplasmas in seven leafhopper species (potential insect vectors). As an initial step toward determining the impact of these phytoplasmas on the ecosystem, ribulose 1,5-biphosphate carboxylase large subunit (rbcL), a commonly used plant DNA barcoding marker, was employed to identify the plant species that the phytoplasma-harboring leafhoppers feed on. The DNA of 17 individual leafhoppers was PCR amplified using universal rbcL primers. PCR products were cloned, and five clones per amplicon were randomly chosen for Sanger sequencing. Moreover, Illumina high-throughput sequencing on selected PCR products was conducted and confirmed no missing targets in Sanger sequencing. The nucleotide BLAST results revealed 14 plant species, including six well-known plant hosts of phytoplasmas such as tomato, alfalfa, and maize. The remaining species have not been documented as phytoplasma hosts, expanding our knowledge of potential plant hosts. Notably, the DNA of tomato and maize (apparently cultivated in well-managed croplands) was detected in some phytoplasma-harboring leafhopper species sampled in non-crop lands, suggesting the spillover/spillback risk of phytoplasma strains between crop and non-crop areas. Furthermore, our results indicate that barcoding (or metabarcoding) is a valuable tool to study the three-way interactions among phytoplasmas, plant hosts, and vectors. The findings contribute to a better understanding of phytoplasma host range, host shift, and disease epidemiology.
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Affiliation(s)
- Junichi Inaba
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Jonathan Shao
- Statistics Group, NEA Bioinformatics, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820
| | - Yan Zhao
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820
| | - Kristi D Bottner-Parker
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Algirdas Ivanauskas
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
| | - Wei Wei
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705
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Wang G, Wu W, Tan S, Liang Y, He C, Chen H, Huang X, Yi K. Development of a Specific Nested PCR Assay for the Detection of 16SrI Group Phytoplasmas Associated with Sisal Purple Leafroll Disease in Sisal Plants and Mealybugs. PLANTS (BASEL, SWITZERLAND) 2022; 11:2817. [PMID: 36365270 PMCID: PMC9658197 DOI: 10.3390/plants11212817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Sisal purple leafroll disease (SPLD) is currently the most destructive disease affecting sisal in China, yet its aetiology remains unclear. In our previous research, it was verified to be associated with phytoplasmas, and nested PCR based on the 16S rRNA gene using universal primers R16mF2/R16mR1 followed by R16F2n/R16R2 was confirmed as the most effective molecular method for the detection of phytoplasmas associated with SPLD (SPLDaP). However, the method has a shortcoming of inaccuracy, for it could produce false positive results. To further manage the disease, accurate detection is needed. In this study, we developed a specific nested PCR assay using universal primers R16F2n/R16R2, followed by a set of primers designed on 16Sr gene sequences amplified from SPLDaP, nontarget bacteria from sisal plants, and other phytoplasma subgroups or groups. This established method is accurate, specific, and effective for detection of 16SrI group phytoplasma in sisal, and its sensitivity is up to 10 fg/μL of total DNA. It also minimized the false positive problem of nested PCR using universal primers R16mF2/R16mR1 followed by R16F2n/R16R2. This method was further used to verify the presence of phytoplasma in Dysmicoccusneobrevipes, and the results showed that D. neobrevipes could be infected by SPLDaP and thus could be a candidate for vector transmission assays.
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Affiliation(s)
- Guihua Wang
- College of Ecology and Environment, Hainan University, Haikou 570228, China
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- College of Forestry, Hainan University, Haikou 570228, China
| | - Weihuai Wu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yanqiong Liang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Chunping He
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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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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11
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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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12
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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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13
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Tseng YW, Chang HH, Chang CJ, Jan FJ. First Report of ' Candidatus Phytoplasma asteris' (16SrI group) Associated with Murraya exotica Witches'-Broom Disease in Taiwan. PLANT DISEASE 2022; 106:3199. [PMID: 35549325 DOI: 10.1094/pdis-02-22-0312-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Murraya exotica L., commonly known as orange jasmine, is an evergreen shrub belonging to the Rutaceae family. It has long been used as traditional Chinese medicine for treating abdominal pain, toothache, scabies, and other disorders (Liu et al. 2018). M. exotica is widely grown as a garden bush in Taiwan. A prokaryotic pathogen, 'Candidatus Liberibacter asiaticus' (Damsteegt et al. 2010), reportedly could infect M. exotica, but there is no reported phytoplasma disease in M. exotica. In June 2020, M. exotica plants exhibiting witches'-broom (WB), leaf yellowing, and small leaves (Fig. s1) were observed in a horticultural landscaping field in Taichung City, Taiwan. It was estimated that more than 70% of M. exotica plants within a single area were affected. DNA was extracted separately from petioles of five symptomatic and one asymptomatic plants using a modified CTAB method (Echevarría-Machado et al. 2005) and used for nested PCR with two universal primers, P1 (Deng and Hiruki 1991)/P7 (Schneider et al. 1995) followed by R16F2n/R16R2 (Gundersen and Lee 1996) to amplify a 1.2-kb 16S rRNA fragment. PCR was also conducted by primers, rp(I)F1A/rp(I)R1A to amplify a partial ribosomal protein S3 and L22 (rplV-rpsC) fragment (Lee et al. 2004). Expected 1.2-kb bands were amplified from DNA extracted from all symptomatic plants, whereas no bands were amplified from that of the asymptomatic plant. The amplicons were cloned, sequenced with an ABI 3730 automatic sequencer (Applied Biosystems, Hammonton, NJ, USA) in Biotechnology Centre DNA-sequencing facility at National Chung Hsing University (NCHU) and deposited in GenBank. BLAST analysis revealed that 16S rDNA sequences (MZ373297 and MZ373298) shared 100% identity to each other and both shared 99.4% identity with those of several phytoplasma strains, e.g., rapeseed phyllody phytoplasma (CP055264), Brassica sp. phyllody phytoplasma (MN877914), Plumbago auriculata leaf yellowing phytoplasma (MN239504), and aster yellows phytoplasma (MK992774), which all belonging to the 16SrI group, by using the CLUSTAL W Methods of MegAlign program (DNASTAR, Inc., Madison, WI, USA). Further analysis using iPhyClassifier tool (https://plantpathology.ba.ars.usda.gov) indicated that the virtual restriction fragment length polymorphism (RFLP) patterns derived from the 16S rDNA F2nR2 fragment of the M. exotica WB phytoplasma was most similar to the reference pattern of the 16SrI-B subgroup, with a pattern similarity coefficient of 0.97 and shared 99.3% sequence identity to 'Candidatus Phytoplasma asteris' (M30790). The partial rplV-rpsC gene sequence (OM275408) showed 99.7% of sequence identities to those of rapeseed phyllody phytoplasma (CP055264), plum witches'-broom phytoplasma (MH061366) and oilseed rape phytoplasma (KX551965), by using the CLUSTAL W Methods of MegAlign program. Taken together, we concluded that the phytoplasma strain associated with M. exotica WB disease was a strain belonging to a 16SrI. To the best of our knowledge, this is the first report of M. exotica being infected by a phytoplasma in the aster yellows group, and M. exotica may also serve as an intermediate reservoir host to other plants, e.g., wax apple, periwinkle and roselle, of 16SrI phytoplasma.
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Affiliation(s)
- Yi-Wen Tseng
- National Chung Hsing University, 34916, Department of Plant Pathology, Taichung, Taiwan;
| | - Ho-Hsiung Chang
- National Chung Hsing University, 34916, Department of Plant Pathology, Taichung, Taiwan;
| | - Chung Jan Chang
- University of Georgia College of Agricultural and Environmental Sciences - Griffin Campus, 92569, Department of Plant Pathology, Griffin, Georgia, United States;
| | - Fuh-Jyh Jan
- National Chung Hsing University, 34916, Department of Plant Pathology, Taichung, Taiwan;
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14
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Wang XJ, Luo Q, Li T, Meng PH, Pu YT, Liu JX, Zhang J, Liu H, Tan GF, Xiong AS. Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants. HORTICULTURE RESEARCH 2022; 9:uhac076. [PMID: 38239769 PMCID: PMC10795576 DOI: 10.1093/hr/uhac076] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/17/2022] [Indexed: 01/22/2024]
Abstract
Many of the world's most important vegetables and medicinal crops, including carrot, celery, coriander, fennel, and cumin, belong to the Apiaceae family. In this review, we summarize the complex origins of Apiaceae and the current state of research on the family, including traditional and molecular breeding practices, bioactive compounds, medicinal applications, nanotechnology, and omics research. Numerous molecular markers, regulatory factors, and functional genes have been discovered, studied, and applied to improve vegetable and medicinal crops in Apiaceae. In addition, current trends in Apiaceae application and research are also briefly described, including mining new functional genes and metabolites using omics research, identifying new genetic variants associated with important agronomic traits by population genetics analysis and GWAS, applying genetic transformation, the CRISPR-Cas9 gene editing system, and nanotechnology. This review provides a reference for basic and applied research on Apiaceae vegetable and medicinal plants.
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Affiliation(s)
- Xiao-Jing Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guizhou 550025, China
| | - Qing Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping-Hong Meng
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Yu-Ting Pu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guizhou 550025, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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15
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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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16
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Phytoplasma diseases of plants: molecular diagnostics and way forward. World J Microbiol Biotechnol 2021; 37:102. [PMID: 34009500 DOI: 10.1007/s11274-021-03061-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Phytoplasmas are obligate phytopathogenic bacteria associated with devastating diseases in hundreds of crops across the world. They have been responsible for huge economic losses in many crop plants for decades now. Isolation and establishment of axenic culture of phytoplasma in complex media is a recent progress in phytoplasma research. Earlier methods for phytoplasma disease detection included symptom profiling, microscopy, serology and dodder transmission studies. With advancement in the field of molecular biology, phytoplasma diagnostics and characterisation witnessed radical improvement. Starting from PCR amplification which often necessities a nested PCR on account of low titre of phytoplasmas, to the closed tube quantitative PCR assays and then the ddPCR, an array of diagnostics have been developed for phytoplasma. The isothermal diagnostic platforms are the latest addition to this and the Loop Mediated Isothermal Amplification (LAMP) assay has been applied for the detection of phytoplasma from several hosts. The futuristic approach in phytoplasma detection will be very likely provided by an integration of nanotechnology and molecular diagnostics. Phytoplasma disease management majorly relies on early detection, vector control, use of disease free planting materials and cultivation of resistant varieties. Hence understanding the molecular mechanism of phytoplasma-host interaction is as important as timely and accurate detection, in the management of phytoplasma diseases. Further, the changing climatic scenario and global warming may lead to an upsurge in the phytoplasma diseases spread and severity across the world, making disease management even more challenging.
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17
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Wei W, Trivellone V, Dietrich CH, Zhao Y, Bottner-Parker KD, Ivanauskas A. Identification of Phytoplasmas Representing Multiple New Genetic Lineages from Phloem-Feeding Leafhoppers Highlights the Diversity of Phytoplasmas and Their Potential Vectors. Pathogens 2021; 10:352. [PMID: 33809759 PMCID: PMC8002289 DOI: 10.3390/pathogens10030352] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 01/18/2023] Open
Abstract
Phytoplasmas are obligate transkingdom bacterial parasites that infect a variety of plant species and replicate in phloem-feeding insects in the order Hemiptera, mainly leafhoppers (Cicadellidae). The insect capacity in acquisition, transmission, survival, and host range directly determines the epidemiology of phytoplasmas. However, due to the difficulty of insect sampling and the lack of follow-up transmission trials, the confirmed phytoplasma insect hosts are still limited compared with the identified plant hosts. Recently, quantitative polymerase chain reaction (qPCR)-based quick screening of 227 leafhoppers collected in natural habitats unveiled the presence of previously unknown phytoplasmas in six samples. In the present study, 76 leafhoppers, including the six prescreened positive samples, were further examined to identify and characterize the phytoplasma strains by semi-nested PCR. A total of ten phytoplasma strains were identified in leafhoppers from four countries including South Africa, Kyrgyzstan, Australia, and China. Based on virtual restriction fragment length polymorphism (RFLP) analysis, these ten phytoplasma strains were classified into four distinct ribosomal (16Sr) groups (16SrI, 16SrIII, 16SrXIV, and 16SrXV), representing five new subgroups (16SrI-AO, 16SrXIV-D, 16SrXIV-E, 16SrXIV-F, and 16SrXV-C). The results strongly suggest that the newly identified phytoplasma strains not only represent new genetic subgroup lineages, but also extend previously undiscovered geographical distributions. In addition, ten phytoplasma-harboring leafhoppers belonged to seven known leafhopper species, none of which were previously reported insect vectors of phytoplasmas. The findings from this study provide fresh insight into genetic diversity, geographical distribution, and insect host range of phytoplasmas. Further transmission trials and screening of new potential host plants and weed reservoirs in areas adjacent to collection sites of phytoplasma harboring leafhoppers will contribute to a better understanding of phytoplasma transmission and epidemiology.
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Affiliation(s)
- Wei Wei
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Valeria Trivellone
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA; (V.T.); (C.H.D.)
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL 61820, USA; (V.T.); (C.H.D.)
| | - Yan Zhao
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Kristi D. Bottner-Parker
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
| | - Algirdas Ivanauskas
- Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA; (Y.Z.); (K.D.B.-P.); (A.I.)
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18
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Panda P, Nigam A, Rao GP. Multilocus gene analysis reveals the presence of two phytoplasma groups in Impatiens balsamina showing flat stem and phyllody. 3 Biotech 2021; 11:122. [PMID: 33633922 PMCID: PMC7878611 DOI: 10.1007/s13205-021-02666-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/23/2021] [Indexed: 11/29/2022] Open
Abstract
Rose balsam (Impatiens balsamina) is an important ornamental species grown worldwide for its attractive flowers and also having medicinal properties. Flat stem, little leaf, and phyllody symptoms were observed in I. balsamina nurseries in Uttar Pradesh and Tripura states of India during surveys from 2018 to 2020, with an incidence from 6 to 27%. Amplicons of ~ 1.2 kb were amplified in all the tested symptomatic samples of I. balsamina using universal phytoplasma primer pairs from different surveyed locations, but not from the asymptomatic plants. Pairwise sequence comparison, phylogeny, and virtual RFLP analysis of 16S rRNA gene sequences identified the phytoplasmas as 16SrI-B subgroup strain from Tripura (Lembucherra) and 16SrII-D subgroup strain from Uttar Pradesh (Gorakhpur and Faizabad). Phytoplasma presence and identity was further confirmed by amplifying secA, rp, secY, and tuf genes. This is the first report of 16SrI-B and 16SrII-D phytoplasmas detection in I. balsamina in the world.
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Affiliation(s)
- Priyam Panda
- Discipline of Life Sciences, Indira Gandhi National Open University, New Delhi, 110068 India
| | - Amrita Nigam
- Discipline of Life Sciences, Indira Gandhi National Open University, New Delhi, 110068 India
| | - G. P. Rao
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Santos Junior MN, de Macêdo Neres NS, Campos GB, Bastos BL, Timenetsky J, Marques LM. A Review of Ureaplasma diversum: A Representative of the Mollicute Class Associated With Reproductive and Respiratory Disorders in Cattle. Front Vet Sci 2021; 8:572171. [PMID: 33681318 PMCID: PMC7930009 DOI: 10.3389/fvets.2021.572171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/13/2021] [Indexed: 12/22/2022] Open
Abstract
The Mollicutes class encompasses wall-less microbes with a reduced genome. They may infect plants, insects, humans, and animals including those on farms and in livestock. Ureaplasma diversum is a mollicute associated with decreased reproduction mainly in the conception rate in cattle, as well as weight loss and decreased quality in milk production. Therefore, U. diversum infection contributes to important economic losses, mainly in large cattle-producing countries such as the United States, China, Brazil, and India. The characteristics of Mollicutes, virulence, and pathogenic variations make it difficult to control their infections. Genomic analysis, prevalence studies, and immunomodulation assays help better understand the pathogenesis of bovine ureaplasma. Here we present the main features of transmission, virulence, immune response, and pathogenesis of U. diversum in bovines.
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Affiliation(s)
- Manoel Neres Santos Junior
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
- Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
| | - Nayara Silva de Macêdo Neres
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Guilherme Barreto Campos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Bruno Lopes Bastos
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Lucas Miranda Marques
- Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil
- Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
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20
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Clements J, Bradford BZ, Garcia M, Piper S, Huang W, Zwolinska A, Lamour K, Hogenhout S, Groves RL. 'Candidatus Phytoplasma asteris' subgroups display distinct disease progression dynamics during the carrot growing season. PLoS One 2021; 16:e0239956. [PMID: 33539350 PMCID: PMC7861454 DOI: 10.1371/journal.pone.0239956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/20/2021] [Indexed: 11/19/2022] Open
Abstract
Aster Yellows phytoplasma (AYp; ‘Candidatus Phytoplasma asteris’) is an obligate bacterial pathogen that is the causative agent of multiple diseases in herbaceous plants. While this phytoplasma has been examined in depth for its disease characteristics, knowledge about the spatial and temporal dynamics of pathogen spread is lacking. The phytoplasma is found in plant’s phloem and is vectored by leafhoppers (Cicadellidae: Hemiptera), including the aster leafhopper, Macrosteles quadrilineatus Forbes. The aster leafhopper is a migratory insect pest that overwinters in the southern United States, and historical data suggest these insects migrate from southern overwintering locations to northern latitudes annually, transmitting and driving phytoplasma infection rates as they migrate. A more in-depth understanding of the spatial, temporal and genetic determinants of Aster Yellows disease progress will lead to better integrated pest management strategies for Aster Yellows disease control. Carrot, Daucus carota L., plots were established at two planting densities in central Wisconsin and monitored during the 2018 growing season for Aster Yellows disease progression. Symptomatic carrots were sampled and assayed for the presence of the Aster Yellows phytoplasma. Aster Yellows disease progression was determined to be significantly associated with calendar date, crop density, location within the field, and phytoplasma subgroup.
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Affiliation(s)
- Justin Clements
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, ID, United States of America
| | - Benjamin Z. Bradford
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Marjorie Garcia
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Shannon Piper
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Agnieszka Zwolinska
- Department of Virology and Bacteriology, National Research Institute, Poznan, Poland
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States of America
| | - Saskia Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Russell L. Groves
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States of America
- * E-mail:
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21
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Jović J, Marinković S, Jakovljević M, Krstić O, Cvrković T, Mitrović M, Toševski I. Symptomatology, (Co)occurrence and Differential Diagnostic PCR Identification of ' Ca. Phytoplasma solani' and ' Ca. Phytoplasma convolvuli' in Field Bindweed. Pathogens 2021; 10:pathogens10020160. [PMID: 33546447 PMCID: PMC7913610 DOI: 10.3390/pathogens10020160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 11/16/2022] Open
Abstract
Field bindweed (Convolvulus arvensis) is one of the major natural plant hosts and reservoirs of ‘Candidatus Phytoplasma solani’ (‘Ca. P. solani’), the causal agent of plant diseases in diverse agricultural crops, including Bois noir (BN) disease of grapevine. Phylogenetically, the most closely related phytoplasma to ‘Ca. P. solani’, the ‘Ca. P. convolvuli’, induces disease in field bindweed that is known by its symptoms as bindweed yellows (BY). The occurrence, coinfection and symptoms association of the two phytoplasmas in shared host plants were the subject of this study. Specific primers for the amplification of the elongation factor Tu gene (tuf) were developed for the identification of ‘Ca. P. convolvuli’ (by conventional nested PCR), as well as primers for simultaneous detection of ‘Ca. P. solani’ and ‘Ca. P. convolvuli’ by duplex SYBR Green real-time PCR. Among symptomatic bindweed plants, 25 and 41% were infected with a single phytoplasma species, ‘Ca. P. solani’ and ‘Ca. P. convolvuli’, respectively, while 34% were infected with both phytoplasmas. None of the non-symptomatic control plants carried phytoplasma, while non-symptomatic plants from our previous epidemiological studies in BN-affected vineyards were confirmed to be infected solely with ‘Ca. P. solani’. Stamp gene typing revealed Rqg50 and Rqg31 ‘Ca. P. solani’ genotypes in plants coinfected with ‘Ca. P. convolvuli’, while three diverse genotypes (Rqg50, GGY and Rpm35) were identified in a single locality with symptomatic bindweeds infected solely with ‘Ca. P. solani’. Variations in symptoms and their association with each of the phytoplasmas are described and documented. The symptom of bushy appearance could be single out as specific for ‘Ca. P. convolvuli’ infection, while occurrence of ‘Ca. P. solani’ could not be unequivocally associated with specific alterations in infected bindweeds. The results are discussed in the context of the epidemiological and ecological complexity of ‘Ca. P. solani’-induced diseases and the relationship between the two phytoplasma relatives in shared host plant.
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Affiliation(s)
- Jelena Jović
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
- Correspondence: or
| | - Slavica Marinković
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
| | - Miljana Jakovljević
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
| | - Oliver Krstić
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
| | - Tatjana Cvrković
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
| | - Milana Mitrović
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
| | - Ivo Toševski
- Department of Plant Pests, Institute for Plant Protection and Environment, 11080 Zemun, Serbia; (S.M.); (M.J.); (O.K.); (T.C.); (M.M.); (I.T.)
- CABI, 2800 Delémont, Switzerland
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22
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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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23
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Franco-Lara L, García JA, Bernal YE, Rodríguez RA. Diversity of the 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma fraxini' isolates that infect urban trees in Bogotá, Colombia. Int J Syst Evol Microbiol 2021; 70:6508-6517. [PMID: 33174835 DOI: 10.1099/ijsem.0.004553] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas have been associated with a disease that affects trees of at least 11 species from different botanic families in Bogotá, Colombia. 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma fraxini' are the major groups of phytoplasma in the area of Bogotá. In this study, the genetic diversity within 'Ca. P. asteris' and 'Ca. P. fraxini' was studied in five urban tree species: Croton species (Euphorbiaceae), Fraxinus uhdei (Oleaceae), Magnolia grandiflora (Magnoliaceae), Populus nigra (Salicaceae) and Quercus humboldtii (Fagaceae). Analyses of the 16S rRNA gene using nested PCR, RFLP and sequencing showed that phytoplasmas of 'Ca. P. asteris' could be assigned to: subgroup 16SrI-B; a new subgroup named 16SrI-AF, with a restriction pattern similar to that of 16SrI-B; and a new subgroup named 16SrI-AG, with a restriction pattern similar to that of 16SrI-K and 16SrI-AH with a restriction pattern similar to that of 16SrI-AC. 'Ca. P. fraxini' isolates belonged to a new subgroup named 16SrVII-G, with a restriction pattern similar to that of 16SrVII-A. To complement the identification of the phytoplasma strains, we amplified nonribosomal genes such as leuS and secA. Unexpectedly, it was observed that in 16 trees in which 16S rRNA gene analysis showed the presence of 'Ca. P. fraxini' only, the leuS or secA primers amplified sequences exclusively affiliated to 'Ca. P. asteris. In those plants, sequences belonging to 'Ca. P. fraxini' leuS or secA genes were not amplified. The present work contributes to the identification of novel strains of both species in Colombia, and supports previous suggestions that phytoplasmas in South America are highly variable.
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Affiliation(s)
- Liliana Franco-Lara
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Jennifer Andrea García
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Yuly Eilen Bernal
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km2 vía Cajicá-Zipaquirá, Colombia.,Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
| | - Rubén Adolfo Rodríguez
- Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, Km 2 vía Cajicá-Zipaquirá, Cundinamarca, Colombia
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24
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Galetto L, Abbà S, Rossi M, Ripamonti M, Palmano S, Bosco D, Marzachì C. Silencing of ATP synthase β reduces phytoplasma multiplication in a leafhopper vector. JOURNAL OF INSECT PHYSIOLOGY 2021; 128:104176. [PMID: 33253714 DOI: 10.1016/j.jinsphys.2020.104176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
The leafhopper Euscelidius variegatus is a natural vector of the chrysanthemum yellows phytoplasma (CYp) and a laboratory vector of the Flavescence dorée phytoplasma (FDp). Previous studies indicated a crucial role for insect ATP synthase α and β subunits during phytoplasma infection of the vector species. Gene silencing of ATP synthase β was obtained by injection of specific dsRNAs in E. variegatus. Here we present the long-lasting nature of such silencing, its effects on the small RNA profile, the significant reduction of the corresponding protein expression, and the impact on phytoplasma acquisition capability. The specific transcript expression was silenced at least up to 37 days post injection with an average reduction of 100 times in insects injected with dsRNAs targeting ATP synthase β (dsATP) compared with those injected with dsRNAs targeting green fluorescent protein (dsGFP), used as negative controls. Specific silencing of this gene was also confirmed at protein level at 15 days after the injection. Total sRNA reads mapping to dsATP and dsGFP sequences in analysed libraries showed in both cases a peak of 21 nt, a length consistent with the generation of dsRNA-derived siRNAs by RNAi pathway. Reads mapped exclusively to the fragment corresponding to the injected dsATPs, probably indicating the absence of a secondary machinery for siRNA synthesis. Insects injected either with dsATP or dsGFP successfully acquired CYp and FDp during feeding on infected plants. However, the average phytoplasma amount in dsATP insects was significantly lower than that measured in dsGFP specimens, indicating a probable reduction of the pathogen multiplication when ATP synthase β was silenced. The role of the insect ATP synthase β during phytoplasma infection process is discussed.
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Affiliation(s)
- Luciana Galetto
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy.
| | - Simona Abbà
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy.
| | - Marika Rossi
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy.
| | - Matteo Ripamonti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy; Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Sabrina Palmano
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy.
| | - Domenico Bosco
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy; Dipartimento di Scienze Agrarie, Forestali ed Alimentari DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy.
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, IPSP-CNR, Strada delle Cacce 73 10135 Torino, Italy.
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25
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Bragard C, Dehnen‐Schmutz K, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Reignault PL, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Bosco D, Chiumenti M, Di Serio F, Galetto L, Marzachì C, Pautasso M, Jacques M. List of non-EU phytoplasmas of tuber-forming Solanum spp. EFSA J 2020; 18:e06355. [PMID: 33376552 PMCID: PMC7757786 DOI: 10.2903/j.efsa.2020.6355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Plant Health prepared a list of non-EU phytoplasmas of tuber-forming Solanum spp. A systematic literature review and search of databases identified 12 phytoplasmas infecting S. tuberosum. These phytoplasmas were assigned to three categories. The first group (a) consists of seven non-EU phytoplasmas, known to occur only outside the EU ('Candidatus Phytoplasma americanum', 'Ca. P. australiense', 'Ca. P. fragariae'-related strain (YN-169, YN-10G) and 'Ca. P. hispanicum') or having only limited presence in the EU ('Ca. P. aurantifolia'-related strains, 'Ca. P. pruni'-related strains and 'Ca. P. trifolii'). The second group (b) consists of three phytoplasmas originally described or reported from the EU. The third group (c) consists of two phytoplasmas with substantial presence in the EU, whose presence in S. tuberosum is not fully supported by the available literature. Phytoplasmas of categories (b) and (c) were excluded at this stage from further categorisation efforts. Three phytoplasmas from category (a) ('Ca. P. australiense', 'Ca. P. hispanicum' and 'Ca. P. trifolii') were excluded from further categorisation, as a pest categorisation has already been performed by EFSA. Comments provided by the EU Member States were integrated in the opinion. The main uncertainties of this listing concern: the taxonomy, the geographic distribution and prevalence and host range. The following phytoplasmas considered as non-EU and whose presence in S. tuberosum is fully supported by literature (category (a)) are categorised by the Panel in a separate opinion: 'Ca. P. americanum', 'Ca. P. fragariae'-related strain (YN-169, YN-10G), 'Ca. P. aurantifolia'-related strains and 'Ca. P. pruni'-related strains.
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26
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Kogej Z, Dermastia M, Mehle N. Development and Validation of a New TaqMan Real-Time PCR for Detection of ' Candidatus Phytoplasma pruni'. Pathogens 2020; 9:E642. [PMID: 32784551 PMCID: PMC7459698 DOI: 10.3390/pathogens9080642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/22/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Abstract
Phytoplasmas of the 16SrIII group are wide spread, and have a broad plant host range. Among these, 'Candidatus phytoplasma pruni' ('Ca. P. pruni'; phytoplasmas of 16SrIII subgroup A) can cause serious diseases in Prunus species and 'Ca. P. pruni'-related strains can infect other plant species, including grapevines. In this study, a new real-time PCR detection system was developed for 'Ca. P. pruni' using TaqMan chemistry. This test was designed to detect 'Ca. P. pruni', by amplifying the species-specific secY gene. In addition, a test to amplify the group-specific 16S rRNA gene region was also developed. The performances of both tests were evaluated. The test that amplifies the secY gene provided reliable and quick detection of 'Ca. P. pruni'. Using the newly developed and validated test, 'Ca. P. pruni' was not found in any of the 434 field samples collected from different plants species grown in different regions of Slovenia.
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Affiliation(s)
- Zala Kogej
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia;
| | | | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia;
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27
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Cho ST, Kung HJ, Huang W, Hogenhout SA, Kuo CH. Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis. Front Microbiol 2020; 11:1531. [PMID: 32754131 PMCID: PMC7366425 DOI: 10.3389/fmicb.2020.01531] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/12/2020] [Indexed: 11/29/2022] Open
Abstract
Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘Candidatus Phytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share < 94% ANI and < 75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Jui Kung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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28
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Bosco D, Chiumenti M, Di Serio F, Galetto L, Marzachì C, Pautasso M, Jacques MA. List of non-EU phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. EFSA J 2020; 18:e05930. [PMID: 32626485 PMCID: PMC7008801 DOI: 10.2903/j.efsa.2020.5930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Plant Health prepared a list of non‐EU phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review and search of databases identified 27 phytoplasmas infecting one or more of the host genera under consideration. These phytoplasmas were assigned to three categories. The first group (a) consists of 10 non‐EU phytoplasmas, known to occur only outside the EU (‘Candidatus Phytoplasma australiense’, ‘Ca. P. hispanicum’, ‘Ca. P. pruni’‐related strain (NAGYIII), ‘Ca. P. pyri’‐related strain (PYLR) and Buckland valley grapevine yellows phytoplasma) or having only limited presence in the EU (‘Ca. P. aurantifolia’‐related strains, ‘Ca. P. fraxini’, ‘Ca. P. phoenicium’, ‘Ca. P. trifolii’ and ‘Ca. P. ziziphi’). The second group (b) consists of three non‐EU phytoplasmas, whose presence in the target plant species is not fully supported by the available literature. The third group (c) consists of 14 phytoplasmas with substantial presence in the EU (i.e. they are originally described or reported from the EU or known to occur or be widespread in some EU Member States or frequently reported in the EU). Phytoplasmas of categories (b) and (c) were excluded at this stage from further categorisation efforts. One phytoplasma from category (a) (‘Ca. P. phoenicium’) was excluded from further categorisation, as a pest risk assessment has been performed by EPPO. Comments provided by the EU Member States were integrated in the opinion. The main uncertainties of this listing concern: the geographic distribution and prevalence, the taxonomy, biology and host range. The phytoplasmas considered as non‐EU and whose presence in target plant species is fully supported by literature (category (a)) are categorised by the Panel in a separate opinion.
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29
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Stillson PT, Szendrei Z. Identifying Leafhopper Targets for Controlling Aster Yellows in Carrots and Celery. INSECTS 2020; 11:E411. [PMID: 32630777 PMCID: PMC7412092 DOI: 10.3390/insects11070411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022]
Abstract
Aster yellows phytoplasma (Candidatus Phytoplasma asteris) is a multi-host plant pathogen and is transmitted by at least 24 leafhopper species. Pathogen management is complex and requires a thorough understanding of vector dynamics. In the American Midwest, aster yellows is of great concern for vegetable farmers who focus on controlling one vector, Macrosteles quadrilineatus-the aster leafhopper. However, vegetable-associated leafhopper communities can be diverse. To investigate whether additional species are important aster yellows vectors, we surveyed leafhopper communities at commercial celery and carrot farms in Michigan from 2018 to 2019 and conducted real-time PCR to determine infection status. Leafhoppers were collected within crop fields and field edges and identified with DNA barcoding. Overall, we collected 5049 leafhoppers, with the most abundant species being M. quadrilineatus (57%) and Empoasca fabae-the potato leafhopper (23%). Our results revealed the most abundant aster yellows vector in Michigan in both crops is M. quadrilineatus, but we also found that E. fabae may be a potential vector for this pathogen. While several taxa reside in and near these crops, we did not find strong evidence that they contribute to phytoplasma infection. These findings indicate that M. quadrilineatus should be the primary target for controlling this pathogen.
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Affiliation(s)
| | - Zsofia Szendrei
- Department of Entomology, Michigan State University, East Lansing, MI 48823, USA;
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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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Clements J, Garcia M, Bradford B, Crubaugh L, Piper S, Duerr E, Zwolinska A, Hogenhout S, Groves RL. Genetic Variation Among Geographically Disparate Isolates of Aster Yellows Phytoplasma in the Contiguous United States. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:604-611. [PMID: 31900490 PMCID: PMC7136194 DOI: 10.1093/jee/toz356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Aster Yellows phytoplasma (AYp; Candidatus Phytoplasma asteris) is associated with diseases of herbaceous plants, including ornamentals and important commercial vegetable and grain crops. The aster leafhopper (ALH; Macrosteles quadrilineatus Forbes) is the predominant vector of these bacteria, though other leafhopper species can acquire and transmit AYp. Potentially inoculative leafhoppers are reported to overwinter in the southern United States and migrate to northern latitudes in the spring. Examining the genetic similarities and differences in AYp associated with southern and northern populations of ALH may provide insight into the role that migrating ALH play in AYp disease development. To investigate similarities among geographically distinct populations of ALH and characterize the variation in AYp associated within these populations, we identified genetic variations in subgroup designation and the relative proportions of secreted AY-WB proteins from field-collected populations of AYp isolated from ALH from select locations in the southern (Arkansas, Kansas, Oklahoma, and Texas) and the northern United States (Wisconsin) in 2016, 2017, and 2018. Isolated phytoplasma were tested for variation of AYp genotypes, numbers of potentially inoculative (AYp-positive) ALH, and presence of specific AYp virulence (effector) genes. Geographically distinct populations of ALH collected in northern and southern regions were similar in CO1 genotype but carried different proportions of AYp genotypes. While similar AYp strains were detected in geographically distinct locations, the proportion of each genotype varied over time.
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Affiliation(s)
- Justin Clements
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | - Marjorie Garcia
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | - Benjamin Bradford
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | - Linda Crubaugh
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | - Shannon Piper
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | - Emily Duerr
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
| | | | | | - Russell L Groves
- Department of Entomology, University of Wisconsin-Madison, Madison, WI
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Singh A, Lakhanpaul S. Detection, characterization and evolutionary aspects of S54LP of SP (SAP54 Like Protein of Sesame Phyllody): a phytoplasma effector molecule associated with phyllody development in sesame ( Sesamum indicum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:445-458. [PMID: 32205922 PMCID: PMC7078397 DOI: 10.1007/s12298-020-00764-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 05/05/2023]
Abstract
SAP54, an effector protein secreted by phytoplasmas has been reported to induce phyllody. S54LP of SP (SAP54 Like Protein of Sesame Phyllody), a SAP54 ortholog from phyllody and witches' broom affected sesame (Sesamum indicum L.) was amplified, cloned and sequenced. Comparative sequence and phylogenetic analysis of diverse phytoplasma strains was carried out to delineate the evolution of S54LP of SP. The degree of polymorphism across SAP54 orthologs and the evolutionary forces acting on this effector protein were ascertained. Site-specific selection across SAP54 orthologs was estimated using Fixed Effects Likelihood (FEL) approach. Nonsynonymous substitutions were detected in the SAP54 orthologs' sequences from phytoplasmas belonging to same (sub) group. Phylogenetic analysis based on S54LP of SP grouped phytoplasmas belonging to same 16SrDNA (sub) groups into different clusters. Analysis of selection forces acting on SAP54 orthologs from nine different phytoplasma (sub)groups, affecting plant species belonging to twelve different families across ten countries showed the orthologs to be under purifying (negative) selection. One amino acid residue was found to be under pervasive diversifying (positive) selection and a total of three amino acid sites were found to be under pervasive purifying (negative) selection. The location of these amino acids in the signal peptide and mature protein was studied with an aim to understand their role in protein-protein interaction. Asparagine residues (at positions 68 and 84) were found to be under pervasive purifying selection suggesting their functional importance in the effector protein. Our study suggests lack of coevolution between SAP54 and 16SrDNA. Signal peptide appears to evolve at a rate slightly higher than the mature protein. Overall, SAP54 and its orthologs are evolving under purifying selection confirming their functional importance in phytoplasma virulence.
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Affiliation(s)
- Amrita Singh
- Department of Botany, University of Delhi, Delhi, 110007 India
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Pecher P, Moro G, Canale MC, Capdevielle S, Singh A, MacLean A, Sugio A, Kuo CH, Lopes JRS, Hogenhout SA. Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog 2019; 15:e1008035. [PMID: 31557268 PMCID: PMC6802841 DOI: 10.1371/journal.ppat.1008035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 10/21/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022] Open
Abstract
Phytoplasmas are insect-transmitted bacterial pathogens that colonize a wide range of plant species, including vegetable and cereal crops, and herbaceous and woody ornamentals. Phytoplasma-infected plants often show dramatic symptoms, including proliferation of shoots (witch's brooms), changes in leaf shapes and production of green sterile flowers (phyllody). Aster Yellows phytoplasma Witches' Broom (AY-WB) infects dicots and its effector, secreted AYWB protein 11 (SAP11), was shown to be responsible for the induction of shoot proliferation and leaf shape changes of plants. SAP11 acts by destabilizing TEOSINTE BRANCHED 1-CYCLOIDEA-PROLIFERATING CELL FACTOR (TCP) transcription factors, particularly the class II TCPs of the CYCLOIDEA/TEOSINTE BRANCHED 1 (CYC/TB1) and CINCINNATA (CIN)-TCP clades. SAP11 homologs are also present in phytoplasmas that cause economic yield losses in monocot crops, such as maize, wheat and coconut. Here we show that a SAP11 homolog of Maize Bushy Stunt Phytoplasma (MBSP), which has a range primarily restricted to maize, destabilizes specifically TB1/CYC TCPs. SAP11MBSP and SAP11AYWB both induce axillary branching and SAP11AYWB also alters leaf development of Arabidopsis thaliana and maize. However, only in maize, SAP11MBSP prevents female inflorescence development, phenocopying maize tb1 lines, whereas SAP11AYWB prevents male inflorescence development and induces feminization of tassels. SAP11AYWB promotes fecundity of the AY-WB leafhopper vector on A. thaliana and modulates the expression of A. thaliana leaf defence response genes that are induced by this leafhopper, in contrast to SAP11MBSP. Neither of the SAP11 effectors promote fecundity of AY-WB and MBSP leafhopper vectors on maize. These data provide evidence that class II TCPs have overlapping but also distinct roles in regulating development and defence in a dicot and a monocot plant species that is likely to shape SAP11 effector evolution depending on the phytoplasma host range.
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Affiliation(s)
- Pascal Pecher
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Gabriele Moro
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Maria Cristina Canale
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, University of São Paulo, Piracicaba, Brazil
| | - Sylvain Capdevielle
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Archana Singh
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Allyson MacLean
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Akiko Sugio
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Joao R. S. Lopes
- Luiz de Queiroz College of Agriculture, Department of Entomology and Acarology, University of São Paulo, Piracicaba, Brazil
| | - Saskia A. Hogenhout
- John Innes Centre, Department of Crop Genetics, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Cho ST, Lin CP, Kuo CH. Genomic Characterization of the Periwinkle Leaf Yellowing (PLY) Phytoplasmas in Taiwan. Front Microbiol 2019; 10:2194. [PMID: 31608032 PMCID: PMC6761752 DOI: 10.3389/fmicb.2019.02194] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/06/2019] [Indexed: 12/17/2022] Open
Abstract
The periwinkle leaf yellowing (PLY) disease was first reported in Taiwan in 2005. This disease was caused by an uncultivated bacterium in the genus “Candidatus phytoplasma.” In subsequent years, this bacterium was linked to other plant diseases and caused losses in agriculture. For genomic investigation of this bacterium and its relatives, we conducted whole genome sequencing of a PLY phytoplasma from an infected periwinkle collected in Taoyuan. The de novo genome assembly produced eight contigs with a total length of 824,596 bp. The annotation contains 775 protein-coding genes, 63 pseudogenes, 32 tRNA genes, and two sets of rRNA operons. To characterize the genomic diversity across populations, a second strain that infects green onions in Yilan was collected for re-sequencing analysis. Comparison between these two strains identified 337 sequence polymorphisms and 10 structural variations. The metabolic pathway analysis indicated that the PLY phytoplasma genome contains two regions with highly conserved gene composition for carbohydrate metabolism. Intriguingly, each region contains several pseudogenes and the remaining functional genes in these two regions complement each other, suggesting a case of duplication followed by differential gene losses. Comparative analysis with other available phytoplasma genomes indicated that this PLY phytoplasma belongs to the 16SrI-B subgroup in the genus, with “Candidatus Phytoplasma asteris” that causes the onion yellowing (OY) disease in Japan as the closest known relative. For characterized effectors that these bacteria use to manipulate their plant hosts, the PLY phytoplasma has homologs for SAP11, SAP54/PHYL1, and TENGU. For genome structure comparison, we found that potential mobile unit (PMU) insertions may be the main factor that drives genome rearrangements in these bacteria. A total of 10 PMU-like regions were found in the PLY phytoplasma genome. Two of these PMUs were found to harbor one SAP11 homolog each, with one more similar to the 16SrI-B type and the other more similar to the 16SrI-A type, suggesting possible horizontal transfer. Taken together, this work provided a first look into population genomics of the PLY phytoplasmas in Taiwan, as well as identified several evolutionary processes that contributed to the genetic diversification of these plant-pathogenic bacteria.
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Affiliation(s)
- Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chan-Pin Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Pierro R, Semeraro T, Luvisi A, Garg H, Vergine M, De Bellis L, Gill HK. The Distribution of Phytoplasmas in South and East Asia: An Emerging Threat to Grapevine Cultivation. FRONTIERS IN PLANT SCIENCE 2019; 10:1108. [PMID: 31572418 PMCID: PMC6749065 DOI: 10.3389/fpls.2019.01108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/13/2019] [Indexed: 05/31/2023]
Abstract
Grapevine is largely cultivated in several parts of the world, and a spurt in its cultivation has occurred in the last two decades in grapevine cultivated areas of South and East Asia, mainly in China, India, Japan, Korea, Thailand, and Indonesia. Grapevine yellows (GY) represent one of the most important diseases in viticultural areas of the world, and they have been assigned to five different groups: aster yellows [AY (16SrI)], peanut witches' broom [PnWB (16SrII)], X-disease (16SrIII), elm yellows [EY (16SrV)], and Stolbur (16SrXII). This study provides a comprehensive overview of the presence of phytoplasma strains and their vectors associated with GY complex, and their potential impact on viticulture of the South and East Asia. In general, both AY and EY were reported on several herbaceous plants and/or cultivated plants in South and East Asia, along with its vectors that were largely reported in China and sporadically in Japan. Interestingly, AY and EY are yet not found in South and East Asia grapevine regions; however, their presence on different plant species suggests the potential spread of the pathogens that may occur in grapevine regions in the near future. Additionally, a few reports also suggest the presence of Stolbur group in Asian countries, along with one study that found a Stolbur-related strain in China on Vitis vinifera. Similarly, PnWB was also frequently reported in India and China on several plant species, but not in grapes. Conversely, sporadic detections of phytoplasma strains related to X-disease in Thailand, South Korea, and China indicate that their potential influence in viticulture is rather negligible. Our review suggests that monitoring and control strategies against GY are essential in order to prevent epidemic phytoplasma spread, especially in vine-allocated areas in Asia.
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Affiliation(s)
- Roberto Pierro
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Teodoro Semeraro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Harsh Garg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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36
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Pradit N, Rodriguez-Saona C, Kawash J, Polashock J. Phytoplasma Infection Influences Gene Expression in American Cranberry. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Phytoplasma detection and identification is primarily based on PCR followed by restriction fragment length polymorphism analysis. This method detects and differentiates phytoplasmas including those not yet identified. The protocol describes the application of this method for identification of phytoplasmas at 16S rRNA (16Sr) group and 16Sr subgroup levels on amplicons and also in silico on the same sequences.
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Abstract
Phytoplasmas are among the most recently discovered plant pathogens. They are wall-less prokaryotes restricted to phloem tissue, associated with diseases affecting several hundred plant species. The impact of phytoplasma diseases on agriculture is impressive and, at the present day, no effective curative strategy has been developed. The availability of rapid and sensitive techniques for phytoplasma detection as well as the possibility to study their relationship with the host plants is a prerequisite for the management of phytoplasma-associated diseases.
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Affiliation(s)
- L Pagliari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - R Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy.
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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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Fránová J, Koloniuk I, Lenz O, Sakalieva D. Molecular diversity of "Candidatus Phytoplasma mali" strains associated with apple proliferation disease in Bulgarian germplasm collection. Folia Microbiol (Praha) 2018; 64:373-382. [PMID: 30377990 DOI: 10.1007/s12223-018-0660-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
A quarantine organism, "Candidatus Phytoplasma mali," is the causal agent of apple proliferation, one of the most important apple diseases in Europe. The genetic diversity of this pathogen in Central and Southern Europe has already been reported; however, almost no data exists from Eastern Europe. In this study, "Ca. P. mali" strains, which were identified in 14 apple trees from the Bulgarian germplasm collection, were characterized by restriction fragment length polymorphism (RFLP) and sequence analysis of four genomic loci. In total, nine distinct genetic lineages were recognized based on the combination of the following detected RFLP profiles: two profiles for the 16S-23S rDNA region (16SrX-A2, -A3), four profiles for the secY gene (one previously known: secY(X)-A, and three new: secY-C, secY-D, secY-E), three profiles for the rpl22-rps3 genes (rpX-A, rpX-B, rpX-F), and one profile for the nitroreductase- and rhodanese-like gene (AT-1). Phylogenetic analysis of the Bulgarian and other European "Ca. P. mali" strains based on 16S-23S rRNA gene sequences confirmed RFLP grouping, regardless of the phytoplasma origin. In a phylogenetic tree based on the secY data, only German strains formed separate clade from the other strains. The tree based on rp genes did not correspond to RFLP profiles. Unexpectedly, when using nitroreductase and rhodanese-like gene sequences, the Bulgarian strains clustered separately from the other European strains. Apart from the identification of different "Ca. P. mali" strains, the paper also recommends the unification of the rpX-subgroup nomenclature to avoid future confusions. Both aims of this paper provide valuable tools to understand the epidemiology of this quarantine pathogen.
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Affiliation(s)
- Jana Fránová
- Department of Plant Virology, Institute of Plant Molecular Biology, The Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic.
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, The Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - Ondřej Lenz
- Department of Plant Virology, Institute of Plant Molecular Biology, The Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
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A Multiplex-PCR Method for Diagnosis of AY-Group Phytoplasmas. Methods Mol Biol 2018. [PMID: 30362001 DOI: 10.1007/978-1-4939-8837-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Polymerase chain reaction (PCR) methods using phytoplasma-specific primers are widely used to detect phytoplasmas from infected plants and insects. Here, I describe a method of multiplex-PCR to amplify nine gene fragments in PCR reactions from AY-group phytoplasmas. Strain-identification was possible after electrophoresis and direct sequencing was also possible after PCR. The combinations of primers can be easily modified, so this method could be applied to other phytoplasma strains.
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PCR-Based Sequence Analysis on Multiple Genes Other than 16S rRNA Gene for Differentiation of Phytoplasmas. Methods Mol Biol 2018. [PMID: 30361998 DOI: 10.1007/978-1-4939-8837-2_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]
Abstract
Differentiation and classification of phytoplasmas have been primarily based on the highly conserved 16S rRNA gene, for which "universal" primers are available. To date, 36 ribosomal (16Sr) groups and more than 150 subgroups have been delineated by RFLP analysis of 16S rRNA gene sequences. However, in recent years, the use of moderately conserved genes as additional genetic markers has enhanced the resolving power in delineating distinct phytoplasma strains among members of some 16Sr subgroups.This chapter describes the methodology of amplification, differentiation, and classification of phytoplasma based on less-conserved non-ribosomal genes, named rp and secY. Actual and virtual RFLP analyses of amplicons obtained by semi-universal or group-specific rp and secY gene-based primers are used for finer differentiation of phytoplasma strains within a given group. The rp and secY gene-based classification not only readily resolves 16Sr subgroups within a given 16Sr group, but also provides finer differentiation of closely related phytoplasma strains within a given 16Sr subgroup.
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Genome Sequence of a Plant-Pathogenic Bacterium, "Candidatus Phytoplasma asteris" Strain TW1. Microbiol Resour Announc 2018; 7:MRA01109-18. [PMID: 30533656 PMCID: PMC6256679 DOI: 10.1128/mra.01109-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022] Open
Abstract
A draft genome sequence is presented for a strain of "Candidatus Phytoplasma asteris" affecting canola plants in Saskatoon, Canada. This phytopathogenic bacterium was determined to be a 16SrI strain and features 16S rRNA-encoding gene sequence heterogeneity.
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Davis RE, Dally EL, Zhao Y, Wolf TK. Genotyping Points to Divergent Evolution of 'Candidatus Phytoplasma asteris' Strains Causing North American Grapevine Yellows and Strains Causing Aster Yellows. PLANT DISEASE 2018; 102:1696-1702. [PMID: 30125195 DOI: 10.1094/pdis-10-17-1690-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Grapevine yellows diseases occur in cultivated grapevine (Vitis vinifera L.) on several continents, where the diseases are known by different names depending upon the identities of the causal phytoplasmas. In this study, phytoplasma strains associated with grapevine yellows disease (North American grapevine yellows [NAGY]) in vineyards of Pennsylvania were characterized as belonging to 16S ribosomal RNA (rRNA) gene restriction fragment length polymorphism group 16SrI (aster yellows phytoplasma group), subgroup 16SrI-B (I-B), and variant subgroup I-B*. The strains (NAGYI strains) were subjected to genotyping based on analyses of 16S rRNA and secY genes, and to in silico three-dimensional modeling of the SecY protein. Although the NAGYI strains are closely related to aster yellows (AY) phytoplasma strains and are classified like AY strains in subgroup I-B or in variant subgroup I-B*, the results from genotyping and protein modeling may signal ongoing evolutionary divergence of NAGYI strains from related strains in subgroup 16SrI-B.
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Affiliation(s)
- Robert E Davis
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Ellen L Dally
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Yan Zhao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Tony K Wolf
- Alson H. Smith, Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA 22602
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Xu XJ, Chang WC, Gao R, Wei DF, Chen XZ, Li XD. First Report of 'Candidatus Phytoplasma asteris' Subgroup 16SrI-AE Associated with Winter Jasmine Witches' Broom in Shandong, China. PLANT DISEASE 2018; 102:PDIS12172026PDN. [PMID: 30067164 DOI: 10.1094/pdis-12-17-2026-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- X-J Xu
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - W-C Chang
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - R Gao
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China, and Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China
| | - D-F Wei
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - X-Z Chen
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
| | - X-D Li
- Shandong Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, China
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Pagliari L, Buoso S, Santi S, Van Bel AJE, Musetti R. What Slows Down Phytoplasma Proliferation? Speculations on the Involvement of AtSEOR2 Protein in Plant Defence Signalling. PLANT SIGNALING & BEHAVIOR 2018; 13:e1473666. [PMID: 29969363 PMCID: PMC6103281 DOI: 10.1080/15592324.2018.1473666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 03/22/2018] [Indexed: 05/13/2023]
Abstract
Considering the crude methods used to control phytoplasma diseases, a deeper knowledge on the defence mechanisms recruited by the plant to face phytoplasma invasion is required. Recently, we demonstrated that Arabidopsis mutants lacking AtSEOR1 gene showed a low phytoplasma titre. In wild type plants AtSEOR1 and AtSEOR2 are tied in filamentous proteins. Knockout of the AtSEOR1 gene may pave the way for an involvement of free AtSEOR2 proteins in defence mechanisms. Among the proteins conferring resistance against pathogenic bacteria, AtRPM1-interacting protein has been found to interact with AtSEOR2 in a high-quality, matrix-based yeast-two hybrid assay. For this reason, we investigated the expression levels of Arabidopsis AtRIN4, and the associated AtRPM1 and AtRPS2 genes in healthy and Chrysanthemum yellows-infected wild-type and Atseor1ko lines.
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Affiliation(s)
- L. Pagliari
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - S. Buoso
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - S. Santi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - A. J. E. Van Bel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
| | - R. Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Sparks ME, Bottner-Parker KD, Gundersen-Rindal DE, Lee IM. Draft genome sequence of the New Jersey aster yellows strain of 'Candidatus Phytoplasma asteris'. PLoS One 2018; 13:e0192379. [PMID: 29408883 PMCID: PMC5800598 DOI: 10.1371/journal.pone.0192379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/20/2018] [Indexed: 01/21/2023] Open
Abstract
The NJAY (New Jersey aster yellows) strain of ‘Candidatus Phytoplasma asteris’ is a significant plant pathogen responsible for causing severe lettuce yellows in the U.S. state of New Jersey. A draft genome sequence was prepared for this organism. A total of 177,847 reads were assembled into 75 contigs > 518 bp with a total base value of 652,092 and an overall [G+C] content of 27.1%. A total of 733 protein coding genes were identified. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MAPF00000000. This draft genome was used for genome- and gene-based comparative phylogenetic analyses with other phytoplasmas, including the closely related ‘Ca. Phytoplasma asteris’ strain, aster yellows witches’- broom (AY-WB). NJAY and AY-WB exhibit approximately 0.5% dissimilarity at the nucleotide level among their shared genomic segments. Evidence indicated that NJAY harbors four plasmids homologous to those known to encode pathogenicity determinants in AY-WB, as well as a chromosome-encoded mobile unit. Apparent NJAY orthologs to the important AY-WB virulence factors, SAP11 and SAP54, were identified. A number of secreted proteins, both membrane-bound and soluble, were encoded, with many bearing similarity to known AY-WB effector molecules and others representing possible secreted proteins that may be novel to the NJAY lineage.
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Affiliation(s)
- Michael E. Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | | | - Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Ing-Ming Lee
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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48
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Gopala, Rao GP. Molecular characterization of phytoplasma associated with four important ornamental plant species in India and identification of natural potential spread sources. 3 Biotech 2018; 8:116. [PMID: 29430377 PMCID: PMC5801105 DOI: 10.1007/s13205-018-1126-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/17/2018] [Indexed: 10/18/2022] Open
Abstract
Phytoplasma suspected symptoms of phyllody, witches' broom, leaf yellowing, stunting and little leaf were observed in Chrysanthemum morifolium, Bougainvillea glabra, Jasminum sambac and Callistephus chinensis during survey of flower nurseries and experimental ornamental fields at Delhi, Maharashtra, Tamil Nadu and Karnataka from 2014 to 2016. Pleomorphic bodies typical to phytoplasma structures were observed in the phloem sieve elements of ultrathin sections of all the four symptomatic ornamental plants (stem tissue) in transmission electron microscope. Amplification of 1.8 and 1.2 kb phytoplasma DNA products was observed in all the four test plants in PCR assays using universal primer pairs P1/P7 followed by nested primer pair R16F2n/R16R2, respectively. Pairwise sequence comparison, phylogeny and virtual RFLP analysis of 16S rDNA sequences confirmed the association of two phytoplasma subgroups (16SrI-B and 16SrII-D) in four ornamental plant species. 'Ca. P. aurantifolia' subgroup D (16SrII-D) was found associated with chrysanthemum phyllody and leaf yellowing at Delhi and Tamil Nadu, bougainvillea little leaf and yellowing at Delhi and Chinese aster phyllody at Bengaluru, Karnataka. However, jasmine little leaf and yellowing at Bengaluru, Karnataka and chrysanthemum stunting at Pune were found to be associated with 'Ca. P. asteris' subgroup B-related strains (16SrI-B). The identification of 16SrII-D subgroup phytoplasma infecting bougainvillea and 16SrI-B subgroup infecting jasmine are the new reports to the world. Besides weed species, Cannabis sativa showing witches' broom in jasmine fields at Bengaluru and Parthenium hysterophorus showing witches' broom symptoms in chrysanthemum fields at Delhi were identified to be caused by phytoplasma strains classified under subgroups 16SrI-B and 16SrII-D, respectively, by PCR assays and 16Sr DNA sequence comparison analysis. Among the three major leafhopper species identified, only Hishimonas phycitis was identified positive for 16SrI-B and 16SrII-D subgroups of phytoplasmas from chrysanthemum fields at Delhi and jasmine fields at Bengaluru, respectively. The identity of similar phytoplasma strains infecting ornamental species in leafhopper and the weed species in the present study suggested that H. phycitis and weeds may act as potential natural sources for secondary spread of the identified phytoplasma strains.
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Affiliation(s)
- Gopala
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012 India
| | - G. P. Rao
- Division of Plant Pathology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012 India
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49
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Trolinger JC, McGovern RJ, Elmer WH, Rechcigl NA, Shoemaker CM. Diseases of Chrysanthemum. HANDBOOK OF PLANT DISEASE MANAGEMENT 2018. [DOI: 10.1007/978-3-319-39670-5_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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50
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Naderali N, Nejat N, Vadamalai G, Davis RE, Wei W, Harrison NA, Kong L, Kadir J, Tan YH, Zhao Y. 'Candidatus Phytoplasma wodyetiae', a new taxon associated with yellow decline disease of foxtail palm (Wodyetia bifurcata) in Malaysia. Int J Syst Evol Microbiol 2017; 67:3765-3772. [PMID: 28905707 DOI: 10.1099/ijsem.0.002187] [Citation(s) in RCA: 35] [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
Landscape-grown foxtail palm (Wodyetia bifurcata A. K. Irvine) trees displaying symptoms of severe foliar chlorosis, stunting, general decline and mortality reminiscent of coconut yellow decline disease were observed in Bangi, Malaysia, during 2012. DNA samples from foliage tissues of 15 symptomatic palms were analysed by employing a nested PCR assay primed by phytoplasma universal ribosomal RNA operon primer pairs, P1/P7 followed by R16F2n/R2. The assay yielded amplicons of a single band of 1.25 kb from DNA samples of 11 symptomatic palms. Results from cloning and sequence analysis of the PCR-amplified 16S rRNA gene segments revealed that, in three palms, three mutually distinct phytoplasmas comprising strains related to 'Candidatus Phytoplasma asteris' and 'Candidatus Phytoplasma cynodontis', as well as a novel phytoplasma, were present as triple infections. The 16S rRNA gene sequence derived from the novel phytoplasma shared less than 96 % nucleotide sequence identity with that of each previously describedspecies of the provisional genus 'Ca. Phytoplasma', justifying its recognition as the reference strain of a new taxon, 'Candidatus Phytoplasma wodyetiae'. Virtual RFLP profiles of the R16F2n/R2 portion of the 16S rRNA gene and the pattern similarity coefficient value (0.74) supported the delineation of 'Ca. Phytoplasma wodyetiae' as the sole representative subgroup A member of a new phytoplasma ribosomal group, 16SrXXXVI.
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Affiliation(s)
- Neda Naderali
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia
| | - Naghmeh Nejat
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia.,School of Science, Health Innovations Research Institute, RMIT University, Melbourne, Victoria, Australia
| | - Ganesan Vadamalai
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia.,Plant Protection Department, Universiti Putra Malaysia, 43400, Malaysia
| | - Robert E Davis
- 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
| | - Nigel A Harrison
- Department of Plant Pathology, Fort Lauderdale Research and Education Center, University of Florida, Fort Lauderdale, FL 33314, USA
| | - LihLing Kong
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia
| | - Jugah Kadir
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia
| | - Yee-How Tan
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Malaysia
| | - Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
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