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Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Al-Sadi AM, Al-Subhi AM, Foissac X, Salar P, Cai H, Yang JY, Davis R, Jones L, Rodoni B, Constable FE. The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486824 DOI: 10.1099/ijsem.0.005977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely 'Candidatus Phytoplasma aurantifolia' and 'Ca. Phytoplasma australasia'. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | | | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | - Abdullah M Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ali M Al-Subhi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Xavier Foissac
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Pascal Salar
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Hong Cai
- The Key Laboratory for Plant Pathology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
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2
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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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3
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Wei W, Shao J, Bottner-Parker KD, Zhao Y. Draft Genome Sequence Resource of CBPPT1, a ' Candidatus Phytoplasma trifolii'-Related Strain Associated with Potato Purple Top Disease in the Columbia Basin, U.S.A. PLANT DISEASE 2023; 107:922-925. [PMID: 36587246 DOI: 10.1094/pdis-08-22-1788-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Affiliation(s)
- Wei Wei
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD 20705
| | - Jonathan Shao
- Statistics Group, Northeast Area Bioinformatics, USDA-ARS, Beltsville, MD 20705
| | | | - Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD 20705
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4
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Gao P, Song B, Xu R, Sun X, Lin H, Xu F, Li B, Sun W. Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58523-58535. [PMID: 34115291 DOI: 10.1007/s11356-021-14595-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.
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Affiliation(s)
- Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
- School of Environment, Henan Normal University, Xinxiang, Henan, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang, Henan, China.
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5
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Trivellone V, Wei W, Filippin L, Dietrich CH. Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas. Ecol Evol 2021; 11:6493-6503. [PMID: 34141234 PMCID: PMC8207438 DOI: 10.1002/ece3.7502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/03/2022] Open
Abstract
Phytoplasmas (Mollicutes, Acholeplasmataceae), vector-borne obligate bacterial plant parasites, infect nearly 1,000 plant species and unknown numbers of insects, mainly leafhoppers (Hemiptera, Deltocephalinae), which play a key role in transmission and epidemiology. Although the plant-phytoplasma-insect association has been evolving for >300 million years, nearly all known phytoplasmas have been discovered as a result of the damage inflicted by phytoplasma diseases on crops. Few efforts have been made to study phytoplasmas occurring in noneconomically important plants in natural habitats. In this study, a subsample of leafhopper specimens preserved in a large museum biorepository was analyzed to unveil potential new associations. PCR screening for phytoplasmas performed on 227 phloem-feeding leafhoppers collected worldwide from natural habitats revealed the presence of 6 different previously unknown phytoplasma strains. This indicates that museum collections of herbivorous insects represent a rich and largely untapped resource for discovery of new plant pathogens, that natural areas worldwide harbor a diverse but largely undiscovered diversity of phytoplasmas and potential insect vectors, and that independent epidemiological cycles occur in such habitats, posing a potential threat of disease spillover into agricultural systems. Larger-scale future investigations will contribute to a better understanding of phytoplasma genetic diversity, insect host range, and insect-borne phytoplasma transmission and provide an early warning for the emergence of new phytoplasma diseases across global agroecosystems.
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Affiliation(s)
- Valeria Trivellone
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
| | - Wei Wei
- Molecular Plant Pathology LaboratoryBeltsville Agricultural Research CenterAgricultural Research ServiceUnited States Department of AgricultureBeltsvilleMDUSA
| | - Luisa Filippin
- CREA–VECouncil for Agricultural Research and EconomicsResearch Centre for Viticulture and EnologyConegliano, TrevisoItaly
| | - Christopher H. Dietrich
- Illinois Natural History SurveyPrairie Research InstituteUniversity of IllinoisChampaignILUSA
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6
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Chen Q, He Z, Zhuo Y, Li S, Yang W, Hu L, Zhong H. Rubidium chloride modulated the fecal microbiota community in mice. BMC Microbiol 2021; 21:46. [PMID: 33588762 PMCID: PMC7885239 DOI: 10.1186/s12866-021-02095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes. Results The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level. Conclusions Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02095-4.
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Affiliation(s)
- Qian Chen
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuting Zhuo
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Wenjing Yang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Liang Hu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Hui Zhong
- School of Life Sciences, Central South University, Changsha, 410013, China.
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7
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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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8
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Draft Genome Sequence of " Candidatus Phytoplasma pruni" (X-Disease Group, Subgroup 16SrIII-B) Strain ChTDIII from Argentina. Microbiol Resour Announc 2020; 9:9/38/e00792-20. [PMID: 32943565 PMCID: PMC7498431 DOI: 10.1128/mra.00792-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herein, we report the draft genome sequence of "Candidatus Phytoplasma pruni" strain ChTDIII (subgroup 16SrIII-B). The final assembly consists of 790,517 nucleotides organized in 67 contigs (minimal size, 1 kb), with a G+C content of 29.4% and encoding 672 proteins.
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9
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Fernández FD, Galdeano E, Conci LR. Phytoplasmas diversity and identification of new aster yellows subgroup (16SrI) associated with weed species in Argentina. Int J Syst Evol Microbiol 2020; 70:35-43. [PMID: 31922469 DOI: 10.1099/ijsem.0.003704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Symptoms of phytoplasma infection were observed in different weed species, Bidens subalternans, Conyza bonariensis, Heterosperma ovatifolium and Conium maculatum, collected from diverse geographical regions in Argentina. To confirm the association of phytoplasma infection with symptomatic plants, PCR, RFLP and phylogenetic analyses based on 16S rRNA-encoding sequences were performed. In this work, we report the presence of phytoplasmas from group 16SrVII (subgroup 16VII-B) infecting C. bonariensis and B. subalternans and from group 16SrIII (subgroup 16SrIII-X) B. subalternans, H. ovatifolium, and C. maculatum. Phytoplasmas from the aster yellows group were detected infecting C. bonariensis and B. subalternans. Analysis of 16S rRNA-encoding genes revealed the presence of two distinct operons, rrnB (16SrI-B) and newly described rrnA, which is different from the reference RFLP patterns of all previously established 16SrI-subgroups. A single rp operon sequence analysis reveals the presence of simple infection and confirms a description of a novel subgroup. On the basis of these results we propose a designation of new subgroup 16SrI-(B/AJ) AJ (rp-AJ). To our knowledge, this is the first report of phytoplasmas infecting Bidens subalternans¸ Heterosperma ovatifolium and Conium maculatum.
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Affiliation(s)
- Franco D Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Unidad de Fitopatología y Modelización Agrícola (UFYMA), Córdoba.,Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino 60 cuadras Kmt 5.5. X5020ICA, Córdoba, Argentina
| | - Ernestina Galdeano
- Instituto de Botánica del Nordeste, (CONICET-UNNE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131 (3400). Corrientes, Argentina
| | - Luis R Conci
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino 60 cuadras Kmt 5.5. X5020ICA, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Unidad de Fitopatología y Modelización Agrícola (UFYMA), Córdoba
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10
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Banerjee A, Pérez-López E, Mossman K. Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies. Front Microbiol 2018; 9:2863. [PMID: 30524418 PMCID: PMC6262150 DOI: 10.3389/fmicb.2018.02863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Arinjay Banerjee
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, Michael DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, ON, Canada
| | - Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karen Mossman
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, Michael DeGroote Centre for Learning and Discovery, McMaster University, Hamilton, ON, Canada
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11
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Music MS, Samarzija I, Hogenhout SA, Haryono M, Cho ST, Kuo CH. The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences. Syst Appl Microbiol 2018; 42:117-127. [PMID: 30455068 DOI: 10.1016/j.syapm.2018.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 11/15/2022]
Abstract
Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach. The de novo assembly generated a draft genome with 19 contigs totalling 821,322bp, which corresponded to more than 80% of the estimated genome size. Further completion of the genome was challenging due to the high occurrence of repetitive sequences. The majority of repeats consisted of gene arrangements characteristic of phytoplasma potential mobile units (PMUs). These regions showed variation in gene orders intermixed with genes of unknown functions and lack of similarity to other phytoplasma genes, suggesting that they were prone to rearrangements and acquisition of new sequences via recombination. The availability of this high-quality draft genome also provided a foundation for genome-scale genotypic analysis (e.g., average nucleotide identity and average amino acid identity) and molecular phylogenetic analysis. Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones. The 'Ca. P. solani' SA-1 genome also contained putative secreted protein/effector genes, including a homologue of SAP11, found in many other phytoplasma species.
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Affiliation(s)
- Martina Seruga Music
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Ivana Samarzija
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK.
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
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12
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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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Detection and Typing of "Candidatus Phytoplasma " spp. in Host DNA Extracts Using Oligonucleotide-Coupled Fluorescent Microspheres. Methods Mol Biol 2018. [PMID: 28600765 DOI: 10.1007/978-1-4939-7037-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The use of oligonucleotide-coupled fluorescent microspheres is a rapid, sequencing-independent, and reliable way to diagnose bacterial diseases. Previously described applications of oligonucleotide-coupled fluorescent microspheres for the detection and identification of bacteria in human clinical samples have been successfully adapted to detect and differentiate "Ca. Phytoplasma" species using as a target the chaperonin 60-encoding gene. In this chapter, we describe in detail the design and validation of oligonucleotide capture probes, and their application in the assay aiming to differentiate phytoplasma strains infecting Brassica napus and Camelina sativa plants grown in the same geographic location at the same time.
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14
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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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15
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Molecular characterization of a phytoplasma affiliated with the 16SrVII group representative of the novel 16SrVII-F subgroup. Int J Syst Evol Microbiol 2017; 67:3122-3126. [DOI: 10.1099/ijsem.0.001823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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May M, Brown DR. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Mollicutes. Minutes of the closed meeting, 3rd July 2016, Brisbane, Australia. Int J Syst Evol Microbiol 2017; 67:2482-2484. [PMID: 28693682 DOI: 10.1099/ijsem.0.001818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford, Maine, USA
| | - Daniel R Brown
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA
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Blain NP, Helgason BL, Germida JJ. Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site. Can J Microbiol 2017; 63:502-515. [DOI: 10.1139/cjm-2017-0039] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Bitumount Provincial Historic site is the location of 2 of the world’s first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil)−1, plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarbon-contaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.
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Affiliation(s)
- Natalie P. Blain
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada
| | - Bobbi L. Helgason
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - James J. Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N5A8, Canada
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Anabestani A, Izadpanah K, Abbà S, Galetto L, Ghorbani A, Palmano S, Siampour M, Veratti F, Marzachì C. Identification of putative effector genes and their transcripts in three strains related to 'Candidatus Phytoplasma aurantifolia'. Microbiol Res 2017; 199:57-66. [PMID: 28454710 DOI: 10.1016/j.micres.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/22/2017] [Accepted: 03/04/2017] [Indexed: 11/25/2022]
Abstract
Molecular mechanisms underlying phytoplasma interactions with host plants are largely unknown. In this study attempts were made to identify effectors of three phytoplasma strains related to 'Ca. P. aurantifolia', crotalaria phyllody (CrP), faba bean phyllody (FBP), and witches' broom disease of lime (WBDL), using information from draft genome of peanut witches' broom phytoplasma. Seven putative effectors were identified in WBDL genome (SAP11, SAP21, Eff64, Eff115, Eff197, Eff211 and EffSAP67), five (SAP11, SAP21, Eff64, Eff99 and Eff197) in CrP and two (SAP11, Eff64) in FBP. No homologs to Eff64, Eff197 and Eff211 in phytoplasmas of other phylogenetic groups were found. SAP11 and Eff64 homologs of 'Ca. P. aurantifolia' strains shared at least 95.9% identity and were detected in the three phytoplasmas, supporting their role within the group. Five of the putative effectors (SAP11, SAP21, Eff64, Eff115, and Eff99) were transcribed from total RNA extracts of periwinkle plants infected with these phytoplasmas. Transcription profiles of selected putative effectors of CrP, FBP and WBDL indicated that SAP11 transcripts were the most abundant in the three phytoplasmas. SAP21 transcript levels were comparable to those of SAP11 for CrP and not measurable for the other phytoplasmas. Eff64 had the lowest transcription level irrespective of sampling date and phytoplasma isolate. Eff115 transcript levels were the highest in WBDL infected plants. This work reports the first sequence information for 14 putative effectors in three strains related to 'Ca. P. aurantifolia', and offers novel insight into the transcription profile of five of them during infection of periwinkle.
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Affiliation(s)
- Ameneh Anabestani
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy; Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Keramat Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Simona Abbà
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Luciana Galetto
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Sabrina Palmano
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Majid Siampour
- Department of Plant Protection, Shahrekord University, Shahrekord, Iran
| | - Flavio Veratti
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy
| | - Cristina Marzachì
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, I-10135, Torino, Italy.
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Fernández FD, Meneguzzi NG, Conci LR. Identification of three novel subgroups within the X-disease group phytoplasma associated with strawberry redness disease. Int J Syst Evol Microbiol 2017; 67:753-758. [DOI: 10.1099/ijsem.0.001636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Franco D Fernández
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA. Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina
| | - Natalia G Meneguzzi
- Estación Experimental Agropecuaria Famaillá-INTA, Ruta Prov. 301 km 32 (4132), Famaillá, Tucumán, Argentina
| | - Luis R Conci
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA. Av. 11 de septiembre 4755, X5014MGO, Córdoba, Argentina
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20
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Pérez-López E, Olivier CY, Luna-Rodríguez M, Dumonceaux TJ. Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences. Int J Syst Evol Microbiol 2016; 66:5600-5613. [PMID: 27667728 PMCID: PMC5244502 DOI: 10.1099/ijsem.0.001501] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplasmas are unculturable, phytopathogenic bacteria that cause economic losses worldwide. As unculturable micro-organisms, phytoplasma taxonomy has been based on the use of the 16S rRNA-encoding gene to establish 16Sr groups and subgroups based on the restriction fragment length polymorphism (RFLP) pattern resulting from the digestion of amplicon (in vitro) or sequence (in silico) with seventeen restriction enzymes. Problems such as heterogeneity of the ribosomal operon and the inability to differentiate closely related phytoplasma strains has motivated the search for additional markers capable of providing finer differentiation of phytoplasma strains. In this study we developed and validated a scheme to classify phytoplasmas based on the use of cpn60 universal target (cpn60 UT) sequences. Ninety-six cpn60 UT sequences from strains belonging to 19 16Sr subgroups were subjected to in silico RFLP using pDRAW32 software, resulting in 25 distinctive RFLP profiles. Based on these results we delineated cpn60 UT groups and subgroups, and established a threshold similarity coefficient for groups and subgroups classifying all the strains analysed in this study. The nucleotide identity among the reference strains, the correspondence between in vitro and in silico RFLP, and the phylogenetic relationships of phytoplasma strains based on cpn60 UT sequences are also discussed.
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Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas Xalapa, Veracruz, México
| | - Chrystel Y. Olivier
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada
| | - Mauricio Luna-Rodríguez
- Laboratorio de Alta Tecnología de Xalapa - DGI, Universidad Veracruzana, Médicos 5, Unidad del Bosque Xalapa, Veracruz, México
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Correspondence Tim J. Dumonceaux
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Prezelj N, Covington E, Roitsch T, Gruden K, Fragner L, Weckwerth W, Chersicola M, Vodopivec M, Dermastia M. Metabolic Consequences of Infection of Grapevine (Vitis vinifera L.) cv. "Modra frankinja" with Flavescence Dorée Phytoplasma. FRONTIERS IN PLANT SCIENCE 2016; 7:711. [PMID: 27242887 PMCID: PMC4876132 DOI: 10.3389/fpls.2016.00711] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/09/2016] [Indexed: 05/18/2023]
Abstract
Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp-grapevine interaction in infected grapevines of cv. "Modra frankinja" under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defense response status.
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Affiliation(s)
- Nina Prezelj
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
| | - Elizabeth Covington
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of CopenhagenTaastrup, Denmark
- Global Change Research Centre, Czech Globe AS CR, v.v.i.Drásov, Czech Republic
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of ViennaVienna, Austria
- Vienna Metabolomics Center (VIME), University of ViennaVienna, Austria
| | - Marko Chersicola
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
- Jožef Stefan International Postgraduate SchoolLjubljana, Slovenia
| | - Maja Vodopivec
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
| | - Marina Dermastia
- Department of Biotechnology and Systems Biology, National Institute of BiologyLjubljana, Slovenia
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Pérez-López E, Luna-Rodríguez M, Olivier CY, Dumonceaux TJ. The underestimated diversity of phytoplasmas in Latin America. Int J Syst Evol Microbiol 2016; 66:492-513. [DOI: 10.1099/ijsem.0.000726] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Edel Pérez-López
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Avenida de Las Culturas Veracruzanas, Xalapa, Veracruz, Mexico
| | - Mauricio Luna-Rodríguez
- DGI-LATEX, Universidad Veracruzana, Avenida de Las Culturas Veracruzanas, Xalapa, Veracruz, Mexico
| | - Chrystel Y. Olivier
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
| | - Tim J. Dumonceaux
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Role of the major antigenic membrane protein in phytoplasma transmission by two insect vector species. BMC Microbiol 2015; 15:193. [PMID: 26424332 PMCID: PMC4589916 DOI: 10.1186/s12866-015-0522-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/18/2015] [Indexed: 11/17/2022] Open
Abstract
Background Phytoplasmas are bacterial plant pathogens (class Mollicutes), transmitted by phloem feeding leafhoppers, planthoppers and psyllids in a persistent/propagative manner. Transmission of phytoplasmas is under the control of behavioral, environmental and geographical factors, but molecular interactions between membrane proteins of phytoplasma and vectors may also be involved. The aim of the work was to provide experimental evidence that in vivo interaction between phytoplasma antigenic membrane protein (Amp) and vector proteins has a role in the transmission process. In doing so, we also investigated the topology of the interaction at the gut epithelium and at the salivary glands, the two barriers encountered by the phytoplasma during vector colonization. Methods Experiments were performed on the ‘Candidatus Phytoplasma asteris’ chrysanthemum yellows strain (CYP), and the two leafhopper vectors Macrosteles quadripunctulatus Kirschbaum and Euscelidius variegatus Kirschbaum. To specifically address the interaction of CYP Amp at the gut epithelium barrier, insects were artificially fed with media containing either the recombinant phytoplasma protein Amp, or the antibody (A416) or both, and transmission, acquisition and inoculation efficiencies were measured. An abdominal microinjection protocol was employed to specifically address the interaction of CYP Amp at the salivary gland barrier. Phytoplasma suspension was added with Amp or A416 or both, injected into healthy E. variegatus adults and then infection and inoculation efficiencies were measured. An internalization assay was developed, consisting of dissected salivary glands from healthy E. variegatus exposed to phytoplasma suspension alone or together with A416 antibody. The organs were then either observed in confocal microscopy or subjected to DNA extraction and phytoplasma quantification by qPCR, to visualize and quantify possible differences among treatments in localization/presence/number of CYP cells. Results Artificial feeding and abdominal microinjection protocols were developed to address the two barriers separately. The in vivo interactions between Amp of ‘Candidatus Phytoplasma asteris’ Chrysanthemum yellows strain (CYP) and vector proteins were studied by evaluating their effects on phytoplasma transmission by Euscelidius variegatus and Macrosteles quadripunctulatus leafhoppers. An internalization assay was developed, consisting of dissected salivary glands from healthy E. variegatus exposed to phytoplasma suspension alone or together with anti-Amp antibody. To visualize possible differences among treatments in localization/presence of CYP cells, the organs were observed in confocal microscopy. Pre-feeding of E. variegatus and M. quadripunctulatus on anti-Amp antibody resulted in a significant decrease of acquisition efficiencies in both species. Inoculation efficiency of microinjected E. variegatus with CYP suspension and anti-Amp antibody was significantly reduced compared to that of the control with phytoplasma suspension only. The possibility that this was due to reduced infection efficiency or antibody-mediated inhibition of phytoplasma multiplication was ruled out. These results provided the first indirect proof of the role of Amp in the transmission process. Conclusion Protocols were developed to assess the in vivo role of the phytoplasma native major antigenic membrane protein in two phases of the vector transmission process: movement through the midgut epithelium and colonization of the salivary glands. These methods will be useful also to characterize other phytoplasma-vector combinations. Results indicated for the first time that native CYP Amp is involved in vivo in specific crossing of the gut epithelium and salivary gland colonization during early phases of vector infection. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0522-5) contains supplementary material, which is available to authorized users.
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24
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Nejat N, Cahill DM, Vadamalai G, Ziemann M, Rookes J, Naderali N. Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection. Mol Genet Genomics 2015; 290:1899-910. [PMID: 25893418 DOI: 10.1007/s00438-015-1046-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/06/2015] [Indexed: 12/25/2022]
Abstract
Invasive phytoplasmas wreak havoc on coconut palms worldwide, leading to high loss of income, food insecurity and extreme poverty of farmers in producing countries. Phytoplasmas as strictly biotrophic insect-transmitted bacterial pathogens instigate distinct changes in developmental processes and defence responses of the infected plants and manipulate plants to their own advantage; however, little is known about the cellular and molecular mechanisms underlying host-phytoplasma interactions. Further, phytoplasma-mediated transcriptional alterations in coconut palm genes have not yet been identified. This study evaluated the whole transcriptome profiles of naturally infected leaves of Cocos nucifera ecotype Malayan Red Dwarf in response to yellow decline phytoplasma from group 16SrXIV, using RNA-Seq technique. Transcriptomics-based analysis reported here identified genes involved in coconut innate immunity. The number of down-regulated genes in response to phytoplasma infection exceeded the number of genes up-regulated. Of the 39,873 differentially expressed unigenes, 21,860 unigenes were suppressed and 18,013 were induced following infection. Comparative analysis revealed that genes associated with defence signalling against biotic stimuli were significantly overexpressed in phytoplasma-infected leaves versus healthy coconut leaves. Genes involving cell rescue and defence, cellular transport, oxidative stress, hormone stimulus and metabolism, photosynthesis reduction, transcription and biosynthesis of secondary metabolites were differentially represented. Our transcriptome analysis unveiled a core set of genes associated with defence of coconut in response to phytoplasma attack, although several novel defence response candidate genes with unknown function have also been identified. This study constitutes valuable sequence resource for uncovering the resistance genes and/or susceptibility genes which can be used as genetic tools in disease resistance breeding.
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Affiliation(s)
- Naghmeh Nejat
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia.
| | - David M Cahill
- School of Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Ganesan Vadamalai
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia
| | - Mark Ziemann
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - James Rookes
- School of Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Neda Naderali
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia
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