1
|
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.
Collapse
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, ,
| |
Collapse
|
2
|
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.
Collapse
Affiliation(s)
- Wei Wei
- Correspondence: ; Tel.: +1-301-504-0786
| | | |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
- Assunta Bertaccini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, 40127 Bologna, Italy
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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'.
Collapse
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
| |
Collapse
|
6
|
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, Civera AV, Yuen J, Zappalà L, Bosco D, Chiumenti M, Di Serio F, Galetto L, Marzachì C, Pautasso M, Jacques MA. Pest categorisation of the 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:e05929. [PMID: 32626484 PMCID: PMC7008834 DOI: 10.2903/j.efsa.2020.5929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Plant Health performed a pest categorisation of nine phytoplasmas of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. (hereafter “host plants”) known to occur only outside the EU or having a limited presence in the EU. This opinion covers the (i) reference strains of ‘Candidatus Phytoplasma australiense’, ‘Ca. P. fraxini’, ‘Ca. P. hispanicum’, ‘Ca. P. trifolii’, ‘Ca. P. ziziphi’, (ii) related strains infecting the host plants of ‘Ca. P. aurantifolia’, ‘Ca. P. pruni’, and ‘Ca. P. pyri’, and (iii) an unclassified phytoplasma causing Buckland valley grapevine yellows. Phytoplasmas can be detected by available methods and are efficiently transmitted by vegetative propagation, with plants for planting acting as a major entry pathway and a long‐distance spread mechanism. Phytoplasmas are also transmitted in a persistent and propagative manner by some insect families of the Fulgoromorpha, Cicadomorpha and Sternorrhyncha (order Hemiptera). No transovarial, pollen or seed transmission has been reported. The natural host range of the categorised phytoplasmas varies from one to more than 90 plant species, thus increasing the possible entry pathways. The host plants are widely cultivated in the EU. All the categorised phytoplasmas can enter and spread through the trade of host plants for planting, and by vectors. Establishment of these phytoplasmas is not expected to be limited by EU environmental conditions. The introduction of these phytoplasmas in the EU would have an economic impact. There are measures to reduce the risk of entry, establishment, spread and impact. Uncertainties result from limited information on distribution, biology and epidemiology. All the phytoplasmas categorised here meet the criteria evaluated by EFSA to qualify as potential Union quarantine pests, and they do not qualify as potential regulated non‐quarantine pests, because they are non‐EU phytoplasmas.
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Wulff NA, Fassini CG, Marques VV, Martins EC, Coletti DAB, Teixeira DDC, Sanches MM, Bové JM. Molecular Characterization and Detection of 16SrIII Group Phytoplasma Associated with Huanglongbing Symptoms. PHYTOPATHOLOGY 2019; 109:366-374. [PMID: 30226423 DOI: 10.1094/phyto-03-18-0081-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
When huanglongbing (HLB) was found in Brazil in 2004, 'Candidatus Liberibacter americanus' was infecting most of the trees while 'Ca. L. asiaticus' was present in a minor proportion. Currently, 'Ca. L. asiaticus' is the predominant bacterium associated with HLB in citrus trees in São Paulo (SP) and Minas Gerais (MG) States, the major citrus-growing regions in Brazil. A phytoplasma from the 16SrIX group was associated with HLB symptoms in Brazil in 2007, in plants free of Liberibacter spp. In this report, HLB samples testing negative for 'Ca. L. asiaticus', 'Ca. L. americanus', and 16SrIX phytoplasma were infected with 16SrIII phytoplasmas. Coinfection with 'Ca. L. asiaticus' and 16SrIII was also found. The 16S ribosomal RNA (rRNA) gene sequences from 22 samples were obtained and sequenced, confirming that the 16SrIII group phytoplasma is associated with HLB symptoms in SP and MG States. Ten single-nucleotide polymorphisms (SNPs) were found in the 1,427-bp 16S rRNA gene sequences from 16SrIII phytoplasmas from citrus, whereas none was detected in 16S rRNA gene sequences among 16SrIX phytoplasma from citrus. Ribosomal protein (rp) rpsSrplVrpsC gene sequences were amplified with 16SrIII group-specific primers, sequenced from a subset of nine samples, and assembled into three groups based on eight SNPs. SNPs in 16S rRNA gene and rp gene sequences are common in 16SrIII phytoplasmas from other hosts and this phytoplasma group is widespread in South America. 16SrIII phytoplasmas highly related are commonly found in Melia azedarach, a widespread tree in Brazil and Argentina. The finding of a new phytoplasma associated with HLB symptoms belonging to the 16SrIII group reinforces the need to develop diagnostic tools to assess HLB-associated microbiomes.
Collapse
Affiliation(s)
- Nelson Arno Wulff
- 1 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040 and PPG Biotecnologia, IQ/UNESP Araraquara, SP, 14800-060. Brazil
| | - Camila Giacomo Fassini
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Viviani Vieira Marques
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Elaine Cristina Martins
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | | | - Diva do Carmo Teixeira
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | | | - Joseph Marie Bové
- 2 Departamento de Pesquisa & Desenvolvimento, Fundecitrus, Araraquara, SP, 14807-040, Brazil
- 4 UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux, INRA, 71 avenue Edouard Bourlaux, CS20032, F-33882 Villenave d'Ornon Cedex, France
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Oren A. A plea for linguistic accuracy - also for Candidatus taxa. Int J Syst Evol Microbiol 2017; 67:1085-1094. [PMID: 27926819 DOI: 10.1099/ijsem.0.001715] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
While all names of new taxa submitted to the International Journal of Systematic and Evolutionary Microbiology, either in direct submissions or in validation requests for names effectively published elsewhere, are subject to nomenclatural review to ensure that they are acceptable based on the rules of the International Code of Nomenclature of Prokaryotes, the names of Candidatus taxa have not been subjected to such a review. Formally, this was not necessary because the rank of Candidatus is not covered by the Code, and the names lack the priority afforded validly published names. However, many Candidatus taxa of different ranks are widely discussed in the scientific literature, and a proposal to incorporate the nomenclature of uncultured prokaryotes under the provisions of the Code is currently pending. Therefore, an evaluation of the names of Candidatus taxa published thus far is very timely. Out of the ~400 Candidatus names found in the literature, 120 contradict the current rules of the Code or are otherwise problematic. A list of those names of Candidatus taxa that need correction is presented here and alternative names that agree with the provisions of the Code are proposed.
Collapse
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Fernández FD, Galdeano E, Kornowski MV, Arneodo JD, Conci LR. Description of ‘Candidatus Phytoplasma meliae’, a phytoplasma associated with Chinaberry (Melia azedarach L.) yellowing in South America. Int J Syst Evol Microbiol 2016; 66:5244-5251. [DOI: 10.1099/ijsem.0.001503] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Franco Daniel Fernández
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino 60 cuadras km 5 ½ (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
| | - Marcela Victoria Kornowski
- Estación Experimental Agropecuaria Montecarlo-INTA, Av. El Libertador 2472 (3384), Montecarlo, Argentina
| | - Joel Demián Arneodo
- Instituto de Microbiología y Zoología Agrícola (IMyZA), INTA, Nicolas Repetto y de los Reseros s/n (1686), Hurlingham, Argentina
| | - Luis Rogelio Conci
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino 60 cuadras km 5 ½ (X5020ICA), Córdoba, Argentina
| |
Collapse
|
13
|
Zhao Y, Davis RE. Criteria for phytoplasma 16Sr group/subgroup delineation and the need of a platform for proper registration of new groups and subgroups. Int J Syst Evol Microbiol 2016; 66:2121-2123. [DOI: 10.1099/ijsem.0.000999] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yan Zhao
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center,ARS-USDA, Beltsville, MD 20705,USA
| | - Robert E. Davis
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center,ARS-USDA, Beltsville, MD 20705,USA
| |
Collapse
|
14
|
Šafárˇová D, Zemánek T, Válová P, Navrátil M. 'Candidatus Phytoplasma cirsii', a novel taxon from creeping thistle [Cirsium arvense (L.) Scop]. Int J Syst Evol Microbiol 2016; 66:1745-1753. [PMID: 26849880 DOI: 10.1099/ijsem.0.000937] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Creeping thistle [Cirsium arvense (L.) Scop.] and dahlia (Dahlia sp.) plants showing typical symptoms of phytoplasma infection including yellowing, stunting, inflorescence and proliferation, were sampled; the presence of phytoplasma was confirmed by standard PCR using universal primers. RFLP analysis allowed classification of the detected phytoplasma strains CirYS, CirYS1 and DahlP within the 16SrXI group, the unique restriction profile F2nR2 fragment obtained in silico by iPhyClassifier indicated that they belong to the new 16SrXI-E subgroup. Genetic analysis of the 16S rRNA gene revealed that the studied strains shared less than 97.5% similarity with all of the previously described 'Candidatus Phytoplasma' species. The closest relatives are 'Candidatus Phytoplasma cynodontis' and 'Candidatus Phytoplasma oryzae' with 96.8% and 96.6% similarity. All strains studied bear three specific regions in the 16S rRNA gene, discriminating them from the other phytoplasma species. Phylogenetic analysis of the 16S rRNA and secA genes confirmed this specificity, as the creeping thistle and dahlia phytoplasma strains clustered in a distinguishable lineage group. The uniqueness of the genetic analysis agrees with the biological characterization of the studied phytoplasma strains, their host range, and geographical distribution. The strains only infect dicotyledonous plants in Europe, contrary to their closest relatives. Based on their unique properties, it could be concluded that the studied phytoplasma strains represent a discrete group that is proposed as a novel taxon 'Candidatus Phytoplasma cirsii', with strain CirYS as a reference strain.
Collapse
Affiliation(s)
- Dana Šafárˇová
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelu˚ 27, 783 71, Olomouc, Czech Republic
| | - Tomáš Zemánek
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelu˚ 27, 783 71, Olomouc, Czech Republic
| | - Pavla Válová
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelu˚ 27, 783 71, Olomouc, Czech Republic
| | - Milan Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University, Šlechtitelu˚ 27, 783 71, Olomouc, Czech Republic
| |
Collapse
|
15
|
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
| |
Collapse
|
16
|
Fernández FD, Meneguzzi NG, Guzmán FA, Kirschbaum DS, Conci VC, Nome CF, Conci LR. Detection and identification of a novel 16SrXIII subgroup phytoplasma associated with strawberry red leaf disease in Argentina. Int J Syst Evol Microbiol 2015; 65:2741-2747. [DOI: 10.1099/ijs.0.000276] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strawberry red leaf phytoplasma was found in strawberry plants from production fields in Lules (Tucumán province) and Bella Vista (Corrientes province), Argentina. Characteristic strawberry red leaf symptoms were stunting, young leaves with yellowing at the edges, mature leaves which curled and were reddish at the abaxial face, flower and fruit deformation and death. The pathogen was detected with phytoplasma-universal primer pairs P1/P7 followed by R16F2n/R16R2 as nested primers in 13 diseased plants. Based on RFLP and sequence analysis of the amplified 16S rRNA gene, the phytoplasma was related to the 16SrXIII group (Mexican periwinkle virescence). In silico the RFLP profile of all the samples analysed revealed the presence of a unique pattern, showing that the novel phytoplasma is different from all the phytoplasmas currently composing the 16SrXIII group. The phylogenetic analysis was consistent with RFLP analysis as the strawberry red leaf phytoplasma was grouped within the 16SrXIII group, but formed a particular cluster. On this basis, the Strawberry red leaf phytoplasma associated with strawberry red leaf disease was assigned to a new subgroup, 16SrXIII-F.
Collapse
Affiliation(s)
- Franco D. Fernández
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino a 60 cuadras km 5 ½. (X5020ICA), Córdoba, Argentina
| | - Natalia G. Meneguzzi
- Estación Experimental Agropecuaria Famaillá-INTA, Ruta Prov. 301 km 32 (4132), Famaillá, Tucumán, Argentina
| | - Fabiana A. Guzmán
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino a 60 cuadras km 5 ½. (X5020ICA), Córdoba, Argentina
| | - Daniel S. Kirschbaum
- Estación Experimental Agropecuaria Famaillá-INTA, Ruta Prov. 301 km 32 (4132), Famaillá, Tucumán, Argentina
| | - Vilma C. Conci
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino a 60 cuadras km 5 ½. (X5020ICA), Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Claudia F. Nome
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino a 60 cuadras km 5 ½. (X5020ICA), Córdoba, Argentina
| | - Luis R. Conci
- Universidad Católica de Córdoba; UCC, Córdoba, Argentina
- Instituto de Patología Vegetal (IPAVE), CIAP-INTA, Camino a 60 cuadras km 5 ½. (X5020ICA), Córdoba, Argentina
| |
Collapse
|
17
|
Specific PCR and real-time PCR assays for detection and quantitation of 'Candidatus Phytoplasma phoenicium'. Mol Cell Probes 2014; 29:63-70. [PMID: 25543009 DOI: 10.1016/j.mcp.2014.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/24/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022]
Abstract
Almond witches' broom (AlmWB) is a fast-spreading lethal disease of almond, peach and nectarine associated with 'Candidatus Phytoplasma phoenicium'. The development of PCR and quantitative real-time PCR (qPCR) assays for the sensitive and specific detection of the phytoplasma is of prime importance for early detection of 'Ca. P. phoenicium' and for epidemiological studies. The developed qPCR assay herein uses a TaqMan(®) probe labeled with Black Hole Quencher Plus. The specificity of the PCR and that of the qPCR detection protocols were tested on 17 phytoplasma isolates belonging to 11 phytoplasma 16S rRNA groups, on samples of almond, peach, nectarine, native plants and insects infected or uninfected with the phytoplasma. The developed assays showed high specificity against 'Ca. P. phoenicium' and no cross-reactivity against any other phytoplasma, plant or insect tested. The sensitivity of the developed PCR and qPCR assays was similar to the conventional nested PCR protocol using universal primers. The qPCR assay was further validated by quantitating AlmWB phytoplasma in different hosts, plant parts and potential insect vectors. The highest titers of 'Ca. P. phoenicium' were detected in the phloem tissues of stems and roots of almond and nectarine trees, where they averaged from 10(5) to 10(6) genomic units per nanogram of host DNA (GU/ng of DNA). The newly developed PCR and qPCR protocols are reliable, specific and sensitive methods that are easily applicable to high-throughput diagnosis of AlmWB in plants and insects and can be used for surveys of potential vectors and alternative hosts.
Collapse
|
18
|
Harrison NA, Davis RE, Oropeza C, Helmick EE, Narváez M, Eden-Green S, Dollet M, Dickinson M. ‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique. Int J Syst Evol Microbiol 2014; 64:1890-1899. [DOI: 10.1099/ijs.0.060053-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus
Phytoplasma
’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus
Phytoplasma
’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.
Collapse
Affiliation(s)
- Nigel A. Harrison
- University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Davie, FL 33314, USA
| | - Robert E. Davis
- Molecular Plant Pathology Laboratory, USDA–Agricultural Research Service, Beltsville, MD 20705, USA
| | - Carlos Oropeza
- Centro de Investigación Científica de Yucatán (CICY), CP 97200 Mérida, Yucatan, Mexico
| | - Ericka E. Helmick
- University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Davie, FL 33314, USA
| | - María Narváez
- Centro de Investigación Científica de Yucatán (CICY), CP 97200 Mérida, Yucatan, Mexico
| | | | - Michel Dollet
- CIRAD, Etiologie – dépérissement, UPR 29, Campus international de Baillarguet, 34398 Montpellier cedex 5, France
| | - Matthew Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| |
Collapse
|
19
|
Bertaccini A, Duduk B, Paltrinieri S, Contaldo N. Phytoplasmas and Phytoplasma Diseases: A Severe Threat to Agriculture. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.512191] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
20
|
Bagadia P, Polashock J, Bottner-Parker K, Zhao Y, Davis R, Lee IM. Characterization and molecular differentiation of 16SrI-E and 16SrIX-E phytoplasmas associated with blueberry stunt disease in New Jersey. Mol Cell Probes 2013. [DOI: 10.1016/j.mcp.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
21
|
‘Candidatus Phytoplasma malaysianum’, a novel taxon associated with virescence and phyllody of Madagascar periwinkle (Catharanthus roseus). Int J Syst Evol Microbiol 2013; 63:540-548. [DOI: 10.1099/ijs.0.041467-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study addressed the taxonomic position and group classification of a phytoplasma responsible for virescence and phyllody symptoms in naturally diseased Madagascar periwinkle plants in western Malaysia. Unique regions in the 16S rRNA gene from the Malaysian periwinkle virescence (MaPV) phytoplasma distinguished the phytoplasma from all previously described ‘
Candidatus
Phytoplasma
’ species. Pairwise sequence similarity scores, calculated through alignment of full-length 16S rRNA gene sequences, revealed that the MaPV phytoplasma 16S rRNA gene shared 96.5 % or less sequence similarity with that of previously described ‘
Ca.
Phytoplasma
’ species, justifying the recognition of the MaPV phytoplasma as a reference strain of a novel taxon, ‘Candidatus Phytoplasma malaysianum’. The 16S rRNA gene F2nR2 fragment from the MaPV phytoplasma exhibited a distinct restriction fragment length polymorphism (RFLP) profile and the pattern similarity coefficient values were lower than 0.85 with representative phytoplasmas classified in any of the 31 previously delineated 16Sr groups; therefore, the MaPV phytoplasma was designated a member of a new 16Sr group, 16SrXXXII. Phytoplasmas affiliated with this novel taxon and the new group included diverse strains infecting periwinkle, coconut palm and oil palm in Malaysia. Three phytoplasmas were characterized as representatives of three distinct subgroups, 16SrXXXII-A, 16SrXXXII-B and 16SrXXXII-C, respectively.
Collapse
|
22
|
Davis RE, Zhao Y, Dally EL, Lee IM, Jomantiene R, Douglas SM. ‘Candidatus Phytoplasma pruni’, a novel taxon associated with X-disease of stone fruits, Prunus spp.: multilocus characterization based on 16S rRNA, secY, and ribosomal protein genes. Int J Syst Evol Microbiol 2013; 63:766-776. [DOI: 10.1099/ijs.0.041202-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-disease is one of the most serious diseases known in peach (Prunus persica). Based on RFLP analysis of 16S rRNA gene sequences, peach X-disease phytoplasma strains from eastern and western United States and eastern Canada were classified in 16S rRNA gene RFLP group 16SrIII, subgroup A. Phylogenetic analyses of 16S rRNA gene sequences revealed that the X-disease phytoplasma strains formed a distinct subclade within the phytoplasma clade, supporting the hypothesis that they represented a lineage distinct from those of previously described ‘Candidatus
Phytoplasma
’ species. Nucleotide sequence alignments revealed that all studied X-disease phytoplasma strains shared less than 97.5 % 16S rRNA gene sequence similarity with previously described ‘Candidatus
Phytoplasma
’ species. Based on unique properties of the DNA, we propose recognition of X-disease phytoplasma strain PX11CT1R as representative of a novel taxon, ‘Candidatus
Phytoplasma pruni’. Results from nucleotide and phylogenetic analyses of secY and ribosomal protein (rp) gene sequences provided additional molecular markers of the ‘Ca. Phytoplasma pruni’ lineage. We propose that the term ‘Ca.
Phytoplasma pruni’ be applied to phytoplasma strains whose 16S rRNA gene sequences contain the oligonucleotide sequences of unique regions that are designated in the formally published description of the taxon. Such strains include X-disease phytoplasma and - within the tolerance of a single base difference in one unique sequence - peach rosette, peach red suture, and little peach phytoplasmas. Although not employed for taxon delineation in this work, we further propose that secY, rp, and other genetic loci from the reference strain of a taxon, and where possible oligonucleotide sequences of unique regions of those genes that distinguish taxa within a given 16Sr group, be incorporated in emended descriptions and as part of future descriptions of ‘Candidatus
Phytoplasma
’ taxa.
Collapse
Affiliation(s)
- Robert E. Davis
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Yan Zhao
- Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ellen L. Dally
- 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
| | - Rasa Jomantiene
- Phytovirus Laboratory, Nature Research Centre, Vilnius, LT–08412, Lithuania
| | - Sharon M. Douglas
- The Connecticut Agricultural Experiment Station, New Haven, CT 06511, USA
| |
Collapse
|
23
|
Win NKK, Lee SY, Bertaccini A, Namba S, Jung HY. ‘Candidatus Phytoplasma balanitae’ associated with witches’ broom disease of Balanites triflora. Int J Syst Evol Microbiol 2013; 63:636-640. [DOI: 10.1099/ijs.0.041566-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phytoplasma was identified in naturally infected wild Balanites triflora plants exhibiting typical witches’ broom symptoms (Balanites witches’ broom: BltWB) in Myanmar. The 16S rRNA gene sequence revealed that BltWB phytoplasma had the highest similarity to that of ‘Candidatus Phytoplasma ziziphi’ and it was also closely related to that of ‘Candidatus
Phytoplasma ulmi
’. Phylogenetic analysis of the 16S rRNA gene sequences indicated that the BltWB phytoplasma clustered as a discrete subclade with Elm yellows phytoplasmas. RFLP analysis of the 16S rRNA gene including the 16S–23S spacer region differentiated the BltWB phytoplasma from ‘Ca.
P. ziziphi
’, ‘Ca.
P. ulmi
’ and ‘Candidatus
Phytoplasma trifolii
’. Analysis of additional ribosomal protein (rp) and translocase protein (secY) gene sequences and phylogenetic analysis of BltWB showed that this phytoplasma was clearly distinguished from those of other ‘Candidatus
Phytoplasma
’ taxa. Taking into consideration the unique plant host and the restricted geographical occurrence in addition to the 16S rRNA gene sequence similarity, the BltWB phytoplasma is proposed to represent a novel taxon, ‘Candidatus Phytoplasma balanitae’.
Collapse
Affiliation(s)
- Nang Kyu Kyu Win
- Department of Agricultural Biology, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Seung-Yeol Lee
- Department of Agricultural Biology, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Assunta Bertaccini
- DiSTA, Patologia vegetale, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Shigetou Namba
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Hee-Young Jung
- Department of Agricultural Biology, School of Applied Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| |
Collapse
|
24
|
Martini M, Marcone C, Mitrović J, Maixner M, Delić D, Myrta A, Ermacora P, Bertaccini A, Duduk B. 'Candidatus Phytoplasma convolvuli', a new phytoplasma taxon associated with bindweed yellows in four European countries. Int J Syst Evol Microbiol 2012; 62:2910-2915. [PMID: 22247217 DOI: 10.1099/ijs.0.038612-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants of Convolvulus arvensis exhibiting symptoms of undersized leaves, shoot proliferation and yellowing, collectively defined as bindweed yellows, were sampled in different regions of Europe and assessed for phytoplasma infection by PCR amplification using phytoplasma universal rRNA operon primer pairs. Positive results were obtained for all diseased plants. RFLP analysis of amplicons comprising the16S rRNA gene alone or the16S rRNA gene and 16-23S intergenic spacer region indicated that the detected phytoplasmas were distinguishable from all other previously described rRNA gene sequences. Analysis of 16S rRNA gene sequences derived from seven selected phytoplasma strains (BY-S57/11, BY-S62/11, BY-I1015, BY-I1016, BY-BH1, BY-BH2 and BY-G) showed that they were nearly identical (99.9-100% gene sequence similarity) but shared less than 97.5% similarity with comparable sequences of other phytoplasmas. Thus, BY phytoplasmas represent a new taxon whose closest relatives are stolbur phytoplasma strains and 'Candidatus Phytoplasma fragariae' with which they share 97.2% and 97.1% 16S rRNA gene sequence similarity, respectively. Phylogenetic analysis of 16S rRNA gene sequences confirmed that bindweed yellows phytoplasma strains collectively represent a distinct lineage within the phytoplasma clade and share a common ancestor with previously published or proposed 'Candidatus Phytoplasma' taxa within a major branch including aster yellows and stolbur phytoplasmas. On the basis of unique 16S rRNA gene sequences and biological properties that include a single host plant species and a geographical distribution limited to parts of Europe, the bindweed yellows (BY) phytoplasmas represent a coherent but discrete taxon, 'Candidatus Phytoplasma convolvuli', with strain BY-S57/11 (GenBank accession no. JN833705) as the reference strain.
Collapse
Affiliation(s)
- Marta Martini
- Department of Agriculture and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Carmine Marcone
- Department of Pharmaceutical and Biomedical Sciences, University of Salerno, 84084 Fisciano (SA), Italy
| | - Jelena Mitrović
- Institute of Pesticides and Environmental Protection, 11080 Belgrade, Serbia
| | - Michael Maixner
- Julius Kühn-Institute, Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, 54470 Bernkastel-Kues, Germany
| | - Duška Delić
- University of Banjaluka, Faculty of Agriculture, 7800 Banjaluka, Bosnia and Herzegovina
| | - Arben Myrta
- Certis Europe B.V., 21047 Saronno (VA), Italy
| | - Paolo Ermacora
- Department of Agriculture and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Assunta Bertaccini
- Department of Agricultural Sciences (DipSA), Plant Pathology, Alma Mater Studiorum University of Bologna, Bologna, 40127, Italy
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, 11080 Belgrade, Serbia
| |
Collapse
|
25
|
Kube M, Mitrovic J, Duduk B, Rabus R, Seemüller E. Current view on phytoplasma genomes and encoded metabolism. ScientificWorldJournal 2011; 2012:185942. [PMID: 22550465 PMCID: PMC3322544 DOI: 10.1100/2012/185942] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/20/2011] [Indexed: 11/21/2022] Open
Abstract
Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma' genomes that include those of ‘Ca. P. asteris' strains OY-M and AY-WB, ‘Ca. P. australiense,' and ‘Ca. P. mali'. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali' is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.
Collapse
Affiliation(s)
- Michael Kube
- Department of Crop and Animal Sciences, Humboldt-University of Berlin, Lentzeallee 55/57, 14195 Berlin, Germany.
| | | | | | | | | |
Collapse
|