Are we ready to detect nematode diversity by next generation sequencing?

In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful impl...

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Autores principales: Peham, Thomas, Steiner, Florian M., Schlick‐Steiner, Birgit C., Arthofer, Wolfgang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2017
Materias:
Hypotheses
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478071/
https://www.ncbi.nlm.nih.gov/pubmed/28649327
http://dx.doi.org/10.1002/ece3.2998
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author Peham, Thomas
Steiner, Florian M.
Schlick‐Steiner, Birgit C.
Arthofer, Wolfgang
author_facet Peham, Thomas
Steiner, Florian M.
Schlick‐Steiner, Birgit C.
Arthofer, Wolfgang
author_sort Peham, Thomas
collection PubMed
description In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.
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spelling pubmed-54780712017-06-23 Are we ready to detect nematode diversity by next generation sequencing? Peham, Thomas Steiner, Florian M. Schlick‐Steiner, Birgit C. Arthofer, Wolfgang Ecol Evol Hypotheses In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers. John Wiley and Sons Inc. 2017-04-27 /pmc/articles/PMC5478071/ /pubmed/28649327 http://dx.doi.org/10.1002/ece3.2998 Text en © 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Hypotheses
Peham, Thomas
Steiner, Florian M.
Schlick‐Steiner, Birgit C.
Arthofer, Wolfgang
Are we ready to detect nematode diversity by next generation sequencing?
title Are we ready to detect nematode diversity by next generation sequencing?
title_full Are we ready to detect nematode diversity by next generation sequencing?
title_fullStr Are we ready to detect nematode diversity by next generation sequencing?
title_full_unstemmed Are we ready to detect nematode diversity by next generation sequencing?
title_short Are we ready to detect nematode diversity by next generation sequencing?
title_sort are we ready to detect nematode diversity by next generation sequencing?
topic Hypotheses
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478071/
https://www.ncbi.nlm.nih.gov/pubmed/28649327
http://dx.doi.org/10.1002/ece3.2998
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