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riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those codin...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009695/ https://www.ncbi.nlm.nih.gov/pubmed/29608703 http://dx.doi.org/10.1093/nar/gky212 |
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author | Waters, Nicholas R Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton |
author_facet | Waters, Nicholas R Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton |
author_sort | Waters, Nicholas R |
collection | PubMed |
description | The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome. |
format | Online Article Text |
id | pubmed-6009695 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60096952018-06-25 riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions Waters, Nicholas R Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton Nucleic Acids Res Methods Online The vast majority of bacterial genome sequencing has been performed using Illumina short reads. Because of the inherent difficulty of resolving repeated regions with short reads alone, only ∼10% of sequencing projects have resulted in a closed genome. The most common repeated regions are those coding for ribosomal operons (rDNAs), which occur in a bacterial genome between 1 and 15 times, and are typically used as sequence markers to classify and identify bacteria. Here, we exploit the genomic context in which rDNAs occur across taxa to improve assembly of these regions relative to de novo sequencing by using the conserved nature of rDNAs across taxa and the uniqueness of their flanking regions within a genome. We describe a method to construct targeted pseudocontigs generated by iteratively assembling reads that map to a reference genome’s rDNAs. These pseudocontigs are then used to more accurately assemble the newly sequenced chromosome. We show that this method, implemented as riboSeed, correctly bridges across adjacent contigs in bacterial genome assembly and, when used in conjunction with other genome polishing tools, can assist in closure of a genome. Oxford University Press 2018-06-20 2018-03-28 /pmc/articles/PMC6009695/ /pubmed/29608703 http://dx.doi.org/10.1093/nar/gky212 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Online Waters, Nicholas R Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title | riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title_full | riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title_fullStr | riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title_full_unstemmed | riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title_short | riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
title_sort | riboseed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009695/ https://www.ncbi.nlm.nih.gov/pubmed/29608703 http://dx.doi.org/10.1093/nar/gky212 |
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