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Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII)
Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Society for General Microbiology
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884932/ https://www.ncbi.nlm.nih.gov/pubmed/19622670 http://dx.doi.org/10.1099/ijs.0.010249-0 |
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author | Zhao, Yan Wei, Wei Lee, Ing-Ming Shao, Jonathan Suo, Xiaobing Davis, Robert E. |
author_facet | Zhao, Yan Wei, Wei Lee, Ing-Ming Shao, Jonathan Suo, Xiaobing Davis, Robert E. |
author_sort | Zhao, Yan |
collection | PubMed |
description | Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html. |
format | Text |
id | pubmed-2884932 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Society for General Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-28849322010-07-06 Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) Zhao, Yan Wei, Wei Lee, Ing-Ming Shao, Jonathan Suo, Xiaobing Davis, Robert E. Int J Syst Evol Microbiol Evolution, Phylogeny and Biodiversity Phytoplasmas, the causal agents of numerous plant diseases, are insect-vector-transmitted, cell-wall-less bacteria descended from ancestral low-G+C-content Gram-positive bacteria in the Bacillus–Clostridium group. Despite their monophyletic origin, widely divergent phytoplasma lineages have evolved in adaptation to specific ecological niches. Classification and taxonomic assignment of phytoplasmas have been based primarily on molecular analysis of 16S rRNA gene sequences because of the inaccessibility of measurable phenotypic characters suitable for conventional microbial characterization. In the present study, an interactive online tool, iPhyClassifier, was developed to expand the efficacy and capacity of the current 16S rRNA gene sequence-based phytoplasma classification system. iPhyClassifier performs sequence similarity analysis, simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) profiles. Based on calculated RFLP pattern similarity coefficients and overall sequence similarity scores, iPhyClassifier makes instant suggestions on tentative phytoplasma 16Sr group/subgroup classification status and ‘Candidatus Phytoplasma’ species assignment. Using iPhyClassifier, we revised and updated the classification of strains affiliated with the peach X-disease phytoplasma group. The online tool can be accessed at http://www.ba.ars.usda.gov/data/mppl/iPhyClassifier.html. Society for General Microbiology 2009-10 /pmc/articles/PMC2884932/ /pubmed/19622670 http://dx.doi.org/10.1099/ijs.0.010249-0 Text en Copyright © 2009, IUMS http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Evolution, Phylogeny and Biodiversity Zhao, Yan Wei, Wei Lee, Ing-Ming Shao, Jonathan Suo, Xiaobing Davis, Robert E. Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title | Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title_full | Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title_fullStr | Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title_full_unstemmed | Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title_short | Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) |
title_sort | construction of an interactive online phytoplasma classification tool, iphyclassifier, and its application in analysis of the peach x-disease phytoplasma group (16sriii) |
topic | Evolution, Phylogeny and Biodiversity |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884932/ https://www.ncbi.nlm.nih.gov/pubmed/19622670 http://dx.doi.org/10.1099/ijs.0.010249-0 |
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