Article: 6-10× pyrosequencing is a practical approach for whole prokaryote genome studies

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Title6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
AuthorsLi, J1
Jiang, J1
Leung, FC1
KeywordsLow depth
Pyrosequencing
Simulation study
Whole genome sequencing
Issue Date2012
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene
CitationGene, 2012, v. 494 n. 1, p. 57-64 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.gene.2011.11.051
AbstractNext generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20 × in depth proposed by official protocols but usually done with over 20 × in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10 × sequencing in qualified runs with 400. bp reads could produce high quality draft assembly (> 98% genome coverage, < 100 contigs with N50 size > 100 kb, single base accuracy > 99.99, indel error rate < 0.01%, false gene loss/duplication rate < 0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics. © 2011 Elsevier B.V.
ISSN0378-1119
2011 Impact Factor: 2.341
2011 SCImago Journal Rankings: 0.238
DOIhttp://dx.doi.org/10.1016/j.gene.2011.11.051
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorLi, J
dc.contributor.authorJiang, J
dc.contributor.authorLeung, FC
dc.date.accessioned2012-03-27T09:07:33Z
dc.date.available2012-03-27T09:07:33Z
dc.date.issued2012
dc.description.abstractNext generation 454 pyrosequencing technology for whole bacterial genome sequencing involves a deep sequencing strategy with at least 15-20 × in depth proposed by official protocols but usually done with over 20 × in practices. In this study, we carried out a comprehensive evaluation of quality of the de novo assemblies based on realistic pyrosequencing simulated data from 1480 prokaryote genomes and 7 runs of machine-generated data. Our results demonstrated that for most of the prokaryote genomes, 6-10 × sequencing in qualified runs with 400. bp reads could produce high quality draft assembly (> 98% genome coverage, < 100 contigs with N50 size > 100 kb, single base accuracy > 99.99, indel error rate < 0.01%, false gene loss/duplication rate < 0.5%). Our study proves the power of low depth pyrosequencing strategy, which provides a cost-effective way for sequencing whole prokaryote genomes in a short time and enables further studies in microbial population diversity and comparative genomics. © 2011 Elsevier B.V.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationGene, 2012, v. 494 n. 1, p. 57-64 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.gene.2011.11.051
dc.identifier.citeulike10137301
dc.identifier.doihttp://dx.doi.org/10.1016/j.gene.2011.11.051
dc.identifier.epage64
dc.identifier.hkuros199087
dc.identifier.isiWOS:000300542800008
Funding AgencyGrant Number
Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, University of Hong Kong
Funding Information:

This project was partially supported by the Strategic Research Themes of Infection and Immunology and Initiatives of Clean Energy, The University of Hong Kong. We are grateful to Dr. Andreas Tauch, Miao He and Brendan Wren for kindly providing the raw reads data from their projects.

dc.identifier.issn0378-1119
2011 Impact Factor: 2.341
2011 SCImago Journal Rankings: 0.238
dc.identifier.issue1
dc.identifier.pmid22192914
dc.identifier.scopuseid_2-s2.0-84856101175
dc.identifier.spage57
dc.identifier.urihttp://hdl.handle.net/10722/146038
dc.identifier.volume494
dc.languageeng
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/gene
dc.publisher.placeNetherlands
dc.relation.ispartofGene
dc.relation.referencesReferences in Scopus
dc.subject.meshGenome
dc.subject.meshProkaryotic Cells
dc.subject.meshSequence Analysis, DNA - methods
dc.subjectLow depth
dc.subjectPyrosequencing
dc.subjectSimulation study
dc.subjectWhole genome sequencing
dc.title6-10× pyrosequencing is a practical approach for whole prokaryote genome studies
dc.typeArticle
Author Affiliations
  1. The University of Hong Kong