De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where...

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Autores principales:	Harish Nagarajan, Jessica E Butler, Anna Klimes, Yu Qiu, Karsten Zengler, Joy Ward, Nelson D Young, Barbara A Methé, Bernhard Ø Palsson, Derek R Lovley, Christian L Barrett
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a37fbc30ee124fdc8fe736ec459fb4f8
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spelling	oai:doaj.org-article:a37fbc30ee124fdc8fe736ec459fb4f82021-12-02T20:21:07ZDe Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.1932-620310.1371/journal.pone.0010922https://doaj.org/article/a37fbc30ee124fdc8fe736ec459fb4f82010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20544019/?tool=EBIhttps://doaj.org/toc/1932-6203State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400) that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.Harish NagarajanJessica E ButlerAnna KlimesYu QiuKarsten ZenglerJoy WardNelson D YoungBarbara A MethéBernhard Ø PalssonDerek R LovleyChristian L BarrettPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 6, p e10922 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Harish Nagarajan Jessica E Butler Anna Klimes Yu Qiu Karsten Zengler Joy Ward Nelson D Young Barbara A Methé Bernhard Ø Palsson Derek R Lovley Christian L Barrett De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
description	State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400) that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.
format	article
author	Harish Nagarajan Jessica E Butler Anna Klimes Yu Qiu Karsten Zengler Joy Ward Nelson D Young Barbara A Methé Bernhard Ø Palsson Derek R Lovley Christian L Barrett
author_facet	Harish Nagarajan Jessica E Butler Anna Klimes Yu Qiu Karsten Zengler Joy Ward Nelson D Young Barbara A Methé Bernhard Ø Palsson Derek R Lovley Christian L Barrett
author_sort	Harish Nagarajan
title	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
title_short	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
title_full	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
title_fullStr	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
title_full_unstemmed	De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
title_sort	de novo assembly of the complete genome of an enhanced electricity-producing variant of geobacter sulfurreducens using only short reads.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/a37fbc30ee124fdc8fe736ec459fb4f8
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De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

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