Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria

Actinomycetota (Actinobacteria) is an ecologically and industrially important phylum which is challenging to extract pure high-molecular-weight (HMW) DNA from. This protocol provides a parallelized, cost-effective, and straightforward approach for consistently extracting pure HMW DNA using modified...

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Autores principales: Alvarez-Arevalo, Maria, Sterndorff, Eva Baggesgaard, Faurdal, David, Jørgensen, Tue Sparholt, Mourched, Anna-Sophie, Vuksanovic, Oliwia, Saha, Subhasish, Weber, Tilmann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9792953/
https://www.ncbi.nlm.nih.gov/pubmed/36527715
http://dx.doi.org/10.1016/j.xpro.2022.101955
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author Alvarez-Arevalo, Maria
Sterndorff, Eva Baggesgaard
Faurdal, David
Jørgensen, Tue Sparholt
Mourched, Anna-Sophie
Vuksanovic, Oliwia
Saha, Subhasish
Weber, Tilmann
author_facet Alvarez-Arevalo, Maria
Sterndorff, Eva Baggesgaard
Faurdal, David
Jørgensen, Tue Sparholt
Mourched, Anna-Sophie
Vuksanovic, Oliwia
Saha, Subhasish
Weber, Tilmann
author_sort Alvarez-Arevalo, Maria
collection PubMed
description Actinomycetota (Actinobacteria) is an ecologically and industrially important phylum which is challenging to extract pure high-molecular-weight (HMW) DNA from. This protocol provides a parallelized, cost-effective, and straightforward approach for consistently extracting pure HMW DNA using modified non-toxic commercial kits suitable for higher throughput applications. We further provide a workflow for sequencing and assembly of complete genomes using an optimized Oxford Nanopore rapid barcoding protocol and Illumina data error correction.
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spelling pubmed-97929532022-12-28 Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria Alvarez-Arevalo, Maria Sterndorff, Eva Baggesgaard Faurdal, David Jørgensen, Tue Sparholt Mourched, Anna-Sophie Vuksanovic, Oliwia Saha, Subhasish Weber, Tilmann STAR Protoc Protocol Actinomycetota (Actinobacteria) is an ecologically and industrially important phylum which is challenging to extract pure high-molecular-weight (HMW) DNA from. This protocol provides a parallelized, cost-effective, and straightforward approach for consistently extracting pure HMW DNA using modified non-toxic commercial kits suitable for higher throughput applications. We further provide a workflow for sequencing and assembly of complete genomes using an optimized Oxford Nanopore rapid barcoding protocol and Illumina data error correction. Elsevier 2022-12-16 /pmc/articles/PMC9792953/ /pubmed/36527715 http://dx.doi.org/10.1016/j.xpro.2022.101955 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocol
Alvarez-Arevalo, Maria
Sterndorff, Eva Baggesgaard
Faurdal, David
Jørgensen, Tue Sparholt
Mourched, Anna-Sophie
Vuksanovic, Oliwia
Saha, Subhasish
Weber, Tilmann
Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title_full Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title_fullStr Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title_full_unstemmed Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title_short Extraction and Oxford Nanopore sequencing of genomic DNA from filamentous Actinobacteria
title_sort extraction and oxford nanopore sequencing of genomic dna from filamentous actinobacteria
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9792953/
https://www.ncbi.nlm.nih.gov/pubmed/36527715
http://dx.doi.org/10.1016/j.xpro.2022.101955
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