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Field-based species identification of closely-related plants using real-time nanopore sequencing

Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and an...

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Autores principales: Parker, Joe, Helmstetter, Andrew J., Devey, Dion, Wilkinson, Tim, Papadopulos, Alexander S. T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566789/
https://www.ncbi.nlm.nih.gov/pubmed/28827531
http://dx.doi.org/10.1038/s41598-017-08461-5
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author Parker, Joe
Helmstetter, Andrew J.
Devey, Dion
Wilkinson, Tim
Papadopulos, Alexander S. T.
author_facet Parker, Joe
Helmstetter, Andrew J.
Devey, Dion
Wilkinson, Tim
Papadopulos, Alexander S. T.
author_sort Parker, Joe
collection PubMed
description Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible.
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spelling pubmed-55667892017-09-01 Field-based species identification of closely-related plants using real-time nanopore sequencing Parker, Joe Helmstetter, Andrew J. Devey, Dion Wilkinson, Tim Papadopulos, Alexander S. T. Sci Rep Article Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based RTnS analysis of closely-related plant species (Arabidopsis spp.) has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification and phylogenomics. Samples were collected and sequenced in a single day by RTnS using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification. Individually annotated RTnS reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with RTnS and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based RTnS makes real-time, rapid specimen identification and genome wide analyses possible. Nature Publishing Group UK 2017-08-21 /pmc/articles/PMC5566789/ /pubmed/28827531 http://dx.doi.org/10.1038/s41598-017-08461-5 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Parker, Joe
Helmstetter, Andrew J.
Devey, Dion
Wilkinson, Tim
Papadopulos, Alexander S. T.
Field-based species identification of closely-related plants using real-time nanopore sequencing
title Field-based species identification of closely-related plants using real-time nanopore sequencing
title_full Field-based species identification of closely-related plants using real-time nanopore sequencing
title_fullStr Field-based species identification of closely-related plants using real-time nanopore sequencing
title_full_unstemmed Field-based species identification of closely-related plants using real-time nanopore sequencing
title_short Field-based species identification of closely-related plants using real-time nanopore sequencing
title_sort field-based species identification of closely-related plants using real-time nanopore sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566789/
https://www.ncbi.nlm.nih.gov/pubmed/28827531
http://dx.doi.org/10.1038/s41598-017-08461-5
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