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

Abstract 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 colle...

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Autores principales:	Joe Parker, Andrew J. Helmstetter, Dion Devey, Tim Wilkinson, Alexander S. T. Papadopulos
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/43c00ac457a74a439e92f27d3667693a
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spelling	oai:doaj.org-article:43c00ac457a74a439e92f27d3667693a2021-12-02T15:06:22ZField-based species identification of closely-related plants using real-time nanopore sequencing10.1038/s41598-017-08461-52045-2322https://doaj.org/article/43c00ac457a74a439e92f27d3667693a2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08461-5https://doaj.org/toc/2045-2322Abstract 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.Joe ParkerAndrew J. HelmstetterDion DeveyTim WilkinsonAlexander S. T. PapadopulosNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-8 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Joe Parker Andrew J. Helmstetter Dion Devey Tim Wilkinson Alexander S. T. Papadopulos Field-based species identification of closely-related plants using real-time nanopore sequencing
description	Abstract 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.
format	article
author	Joe Parker Andrew J. Helmstetter Dion Devey Tim Wilkinson Alexander S. T. Papadopulos
author_facet	Joe Parker Andrew J. Helmstetter Dion Devey Tim Wilkinson Alexander S. T. Papadopulos
author_sort	Joe Parker
title	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_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_sort	field-based species identification of closely-related plants using real-time nanopore sequencing
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/43c00ac457a74a439e92f27d3667693a
work_keys_str_mv	AT joeparker fieldbasedspeciesidentificationofcloselyrelatedplantsusingrealtimenanoporesequencing AT andrewjhelmstetter fieldbasedspeciesidentificationofcloselyrelatedplantsusingrealtimenanoporesequencing AT diondevey fieldbasedspeciesidentificationofcloselyrelatedplantsusingrealtimenanoporesequencing AT timwilkinson fieldbasedspeciesidentificationofcloselyrelatedplantsusingrealtimenanoporesequencing AT alexanderstpapadopulos fieldbasedspeciesidentificationofcloselyrelatedplantsusingrealtimenanoporesequencing
_version_	1718388444431908864

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

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