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High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and a...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803254/ https://www.ncbi.nlm.nih.gov/pubmed/29416032 http://dx.doi.org/10.1038/s41467-018-03016-2 |
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author | Michael, Todd P. Jupe, Florian Bemm, Felix Motley, S. Timothy Sandoval, Justin P. Lanz, Christa Loudet, Olivier Weigel, Detlef Ecker, Joseph R. |
author_facet | Michael, Todd P. Jupe, Florian Bemm, Felix Motley, S. Timothy Sandoval, Justin P. Lanz, Christa Loudet, Olivier Weigel, Detlef Ecker, Joseph R. |
author_sort | Michael, Todd P. |
collection | PubMed |
description | The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal. |
format | Online Article Text |
id | pubmed-5803254 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-58032542018-02-09 High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell Michael, Todd P. Jupe, Florian Bemm, Felix Motley, S. Timothy Sandoval, Justin P. Lanz, Christa Loudet, Olivier Weigel, Detlef Ecker, Joseph R. Nat Commun Article The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal. Nature Publishing Group UK 2018-02-07 /pmc/articles/PMC5803254/ /pubmed/29416032 http://dx.doi.org/10.1038/s41467-018-03016-2 Text en © The Author(s) 2018 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 Michael, Todd P. Jupe, Florian Bemm, Felix Motley, S. Timothy Sandoval, Justin P. Lanz, Christa Loudet, Olivier Weigel, Detlef Ecker, Joseph R. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title | High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title_full | High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title_fullStr | High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title_full_unstemmed | High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title_short | High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell |
title_sort | high contiguity arabidopsis thaliana genome assembly with a single nanopore flow cell |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5803254/ https://www.ncbi.nlm.nih.gov/pubmed/29416032 http://dx.doi.org/10.1038/s41467-018-03016-2 |
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