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Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences

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 (RF...

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Autores principales: Pérez-López, Edel, Olivier, Chrystel Y., Luna-Rodríguez, Mauricio, Dumonceaux, Tim J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244502/
https://www.ncbi.nlm.nih.gov/pubmed/27667728
http://dx.doi.org/10.1099/ijsem.0.001501
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author Pérez-López, Edel
Olivier, Chrystel Y.
Luna-Rodríguez, Mauricio
Dumonceaux, Tim J.
author_facet Pérez-López, Edel
Olivier, Chrystel Y.
Luna-Rodríguez, Mauricio
Dumonceaux, Tim J.
author_sort Pérez-López, Edel
collection PubMed
description 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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spelling pubmed-52445022017-03-27 Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences Pérez-López, Edel Olivier, Chrystel Y. Luna-Rodríguez, Mauricio Dumonceaux, Tim J. Int J Syst Evol Microbiol Note 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. Microbiology Society 2016-12 2016-12 /pmc/articles/PMC5244502/ /pubmed/27667728 http://dx.doi.org/10.1099/ijsem.0.001501 Text en © 2016 Her Majesty The Queen in Right of Canada as represented by the Minister of Agriculture http://creativecommons.org/licenses/by/4.0/ This is an open access article under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.
spellingShingle Note
Pérez-López, Edel
Olivier, Chrystel Y.
Luna-Rodríguez, Mauricio
Dumonceaux, Tim J.
Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title_full Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title_fullStr Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title_full_unstemmed Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title_short Phytoplasma classification and phylogeny based on in silico and in vitro RFLP analysis of cpn60 universal target sequences
title_sort phytoplasma classification and phylogeny based on in silico and in vitro rflp analysis of cpn60 universal target sequences
topic Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244502/
https://www.ncbi.nlm.nih.gov/pubmed/27667728
http://dx.doi.org/10.1099/ijsem.0.001501
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