Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities

A PCR-DGGE primer pair, Tyl2F-Tyl4R, specific to plant parasitic and fungivorous nematodes was designed based on the 18S rRNA gene. The results of community analysis using the primers showed that they are specific to the order Tylenchida. This primer pair detected species belonging to Tylenchida wit...

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Autor principal: Kushida, Atsuhiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology 2013
Materias:
Short Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070663/
https://www.ncbi.nlm.nih.gov/pubmed/23595022
http://dx.doi.org/10.1264/jsme2.ME12158
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author Kushida, Atsuhiko
author_facet Kushida, Atsuhiko
author_sort Kushida, Atsuhiko
collection PubMed
description A PCR-DGGE primer pair, Tyl2F-Tyl4R, specific to plant parasitic and fungivorous nematodes was designed based on the 18S rRNA gene. The results of community analysis using the primers showed that they are specific to the order Tylenchida. This primer pair detected species belonging to Tylenchida with high sensitivity and high resolution. The number of detected species of plant parasitic and fungivorous nematodes and their band intensity were much improved compared with PCR-DGGE analysis using the SSU18A-SSU9R primer, which is commonly used for nematode community analysis. It was confirmed that using a group-specific primer was effective for nematode community analysis with PCR-DGGE.
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spelling pubmed-40706632014-07-24 Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities Kushida, Atsuhiko Microbes Environ Short Communication A PCR-DGGE primer pair, Tyl2F-Tyl4R, specific to plant parasitic and fungivorous nematodes was designed based on the 18S rRNA gene. The results of community analysis using the primers showed that they are specific to the order Tylenchida. This primer pair detected species belonging to Tylenchida with high sensitivity and high resolution. The number of detected species of plant parasitic and fungivorous nematodes and their band intensity were much improved compared with PCR-DGGE analysis using the SSU18A-SSU9R primer, which is commonly used for nematode community analysis. It was confirmed that using a group-specific primer was effective for nematode community analysis with PCR-DGGE. Japanese Society of Microbial Ecology/The Japanese Society of Soil Microbiology 2013-06 2013-04-17 /pmc/articles/PMC4070663/ /pubmed/23595022 http://dx.doi.org/10.1264/jsme2.ME12158 Text en Copyright © 2013 by the Japanese Society of Microbial Ecology / the Japanese Society of Soil Microbiology http://creativecommons.org/licenses/by/3.0 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 Short Communication
Kushida, Atsuhiko
Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title_full Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title_fullStr Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title_full_unstemmed Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title_short Design and Evaluation of PCR Primers for Denaturing Gradient Gel Electrophoresis Analysis of Plant Parasitic and Fungivorous Nematode Communities
title_sort design and evaluation of pcr primers for denaturing gradient gel electrophoresis analysis of plant parasitic and fungivorous nematode communities
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070663/
https://www.ncbi.nlm.nih.gov/pubmed/23595022
http://dx.doi.org/10.1264/jsme2.ME12158
work_keys_str_mv AT kushidaatsuhiko designandevaluationofpcrprimersfordenaturinggradientgelelectrophoresisanalysisofplantparasiticandfungivorousnematodecommunities

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