Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.

Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an i...

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Autores principales:	Shuiquan Tang, Yunchen Gong, Elizabeth A Edwards
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/aebf233e92b9400992ff53597db26e27
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spelling	oai:doaj.org-article:aebf233e92b9400992ff53597db26e272021-11-18T08:03:58ZSemi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.1932-620310.1371/journal.pone.0052038https://doaj.org/article/aebf233e92b9400992ff53597db26e272012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284863/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an in silico gap-resolution strategy that can substantially improve assembly. This strategy resolves assembly gaps in scaffolds using pre-assembled contigs, followed by verification with read mapping. It is capable of resolving assembly gaps caused by repetitive elements and subspecies polymorphisms. Using this strategy, we realized the de novo assembly of the first two Dehalobacter genomes from the metagenomes of two anaerobic mixed microbial cultures capable of reductive dechlorination of chlorinated ethanes and chloroform. Only four additional PCR reactions were required even though the initial assembly with Newbler v. 2.5 produced 101 contigs within 9 scaffolds belonging to two Dehalobacter strains. By applying this strategy to the re-assembly of a recently published genome of Bacteroides, we demonstrate its potential utility for other sequencing projects, both metagenomic and genomic.Shuiquan TangYunchen GongElizabeth A EdwardsPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e52038 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shuiquan Tang Yunchen Gong Elizabeth A Edwards Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
description	Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an in silico gap-resolution strategy that can substantially improve assembly. This strategy resolves assembly gaps in scaffolds using pre-assembled contigs, followed by verification with read mapping. It is capable of resolving assembly gaps caused by repetitive elements and subspecies polymorphisms. Using this strategy, we realized the de novo assembly of the first two Dehalobacter genomes from the metagenomes of two anaerobic mixed microbial cultures capable of reductive dechlorination of chlorinated ethanes and chloroform. Only four additional PCR reactions were required even though the initial assembly with Newbler v. 2.5 produced 101 contigs within 9 scaffolds belonging to two Dehalobacter strains. By applying this strategy to the re-assembly of a recently published genome of Bacteroides, we demonstrate its potential utility for other sequencing projects, both metagenomic and genomic.
format	article
author	Shuiquan Tang Yunchen Gong Elizabeth A Edwards
author_facet	Shuiquan Tang Yunchen Gong Elizabeth A Edwards
author_sort	Shuiquan Tang
title	Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
title_short	Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
title_full	Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
title_fullStr	Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
title_full_unstemmed	Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.
title_sort	semi-automatic in silico gap closure enabled de novo assembly of two dehalobacter genomes from metagenomic data.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/aebf233e92b9400992ff53597db26e27
work_keys_str_mv	AT shuiquantang semiautomaticinsilicogapclosureenableddenovoassemblyoftwodehalobactergenomesfrommetagenomicdata AT yunchengong semiautomaticinsilicogapclosureenableddenovoassemblyoftwodehalobactergenomesfrommetagenomicdata AT elizabethaedwards semiautomaticinsilicogapclosureenableddenovoassemblyoftwodehalobactergenomesfrommetagenomicdata
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Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data.

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