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Rapid Sequencing of Multiple RNA Viruses in Their Native Form
Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subge...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398364/ https://www.ncbi.nlm.nih.gov/pubmed/30858830 http://dx.doi.org/10.3389/fmicb.2019.00260 |
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author | Wongsurawat, Thidathip Jenjaroenpun, Piroon Taylor, Mariah K. Lee, Jasper Tolardo, Aline Lavado Parvathareddy, Jyothi Kandel, Sangam Wadley, Taylor D. Kaewnapan, Bualan Athipanyasilp, Niracha Skidmore, Andrew Chung, Donghoon Chaimayo, Chutikarn Whitt, Michael Kantakamalakul, Wannee Sutthent, Ruengpung Horthongkham, Navin Ussery, David W. Jonsson, Colleen B. Nookaew, Intawat |
author_facet | Wongsurawat, Thidathip Jenjaroenpun, Piroon Taylor, Mariah K. Lee, Jasper Tolardo, Aline Lavado Parvathareddy, Jyothi Kandel, Sangam Wadley, Taylor D. Kaewnapan, Bualan Athipanyasilp, Niracha Skidmore, Andrew Chung, Donghoon Chaimayo, Chutikarn Whitt, Michael Kantakamalakul, Wannee Sutthent, Ruengpung Horthongkham, Navin Ussery, David W. Jonsson, Colleen B. Nookaew, Intawat |
author_sort | Wongsurawat, Thidathip |
collection | PubMed |
description | Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subgenomic mRNA/mRNA simultaneously, (iii) detect a complex transcriptomic architecture without the need for assembly, (iv) enable real-time detection. Using this protocol, positive-ssRNA, negative-ssRNA, with/without a poly(A)-tail, segmented/non-segmented genomes were mixed and sequenced in parallel. Mapping of the generated sequences on the reference genomes showed 100% length recovery with up to 97% identity. This work provides a proof of principle and the validity of this strategy, opening up a wide range of applications to study RNA viruses. |
format | Online Article Text |
id | pubmed-6398364 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-63983642019-03-11 Rapid Sequencing of Multiple RNA Viruses in Their Native Form Wongsurawat, Thidathip Jenjaroenpun, Piroon Taylor, Mariah K. Lee, Jasper Tolardo, Aline Lavado Parvathareddy, Jyothi Kandel, Sangam Wadley, Taylor D. Kaewnapan, Bualan Athipanyasilp, Niracha Skidmore, Andrew Chung, Donghoon Chaimayo, Chutikarn Whitt, Michael Kantakamalakul, Wannee Sutthent, Ruengpung Horthongkham, Navin Ussery, David W. Jonsson, Colleen B. Nookaew, Intawat Front Microbiol Microbiology Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subgenomic mRNA/mRNA simultaneously, (iii) detect a complex transcriptomic architecture without the need for assembly, (iv) enable real-time detection. Using this protocol, positive-ssRNA, negative-ssRNA, with/without a poly(A)-tail, segmented/non-segmented genomes were mixed and sequenced in parallel. Mapping of the generated sequences on the reference genomes showed 100% length recovery with up to 97% identity. This work provides a proof of principle and the validity of this strategy, opening up a wide range of applications to study RNA viruses. Frontiers Media S.A. 2019-02-25 /pmc/articles/PMC6398364/ /pubmed/30858830 http://dx.doi.org/10.3389/fmicb.2019.00260 Text en Copyright © 2019 Wongsurawat, Jenjaroenpun, Taylor, Lee, Tolardo, Parvathareddy, Kandel, Wadley, Kaewnapan, Athipanyasilp, Skidmore, Chung, Chaimayo, Whitt, Kantakamalakul, Sutthent, Horthongkham, Ussery, Jonsson and Nookaew. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Wongsurawat, Thidathip Jenjaroenpun, Piroon Taylor, Mariah K. Lee, Jasper Tolardo, Aline Lavado Parvathareddy, Jyothi Kandel, Sangam Wadley, Taylor D. Kaewnapan, Bualan Athipanyasilp, Niracha Skidmore, Andrew Chung, Donghoon Chaimayo, Chutikarn Whitt, Michael Kantakamalakul, Wannee Sutthent, Ruengpung Horthongkham, Navin Ussery, David W. Jonsson, Colleen B. Nookaew, Intawat Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title | Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title_full | Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title_fullStr | Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title_full_unstemmed | Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title_short | Rapid Sequencing of Multiple RNA Viruses in Their Native Form |
title_sort | rapid sequencing of multiple rna viruses in their native form |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398364/ https://www.ncbi.nlm.nih.gov/pubmed/30858830 http://dx.doi.org/10.3389/fmicb.2019.00260 |
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