Article: A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

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TitleA cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
AuthorsJiang, J1
Li, J1
Kwan, H3
Au, C3
Wan Law, P3
Li, L3
Kam, K2
Lun Ling, J3
Leung, FC1
KeywordsProkaryota
Issue Date2012
PublisherBioMed Central Ltd.. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/
CitationBmc Research Notes, 2012, v. 5 [How to Cite?]
DOI: http://dx.doi.org/10.1186/1756-0500-5-80
AbstractBackground: Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. Findings. Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ∼90% of 100 assemblies with < 10 scaffolds and ∼95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. Conclusions: A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks. © 2012 Jiang et al; BioMed Central Ltd.
ISSN1756-0500
2011 SCImago Journal Rankings: 0.159
DOIhttp://dx.doi.org/10.1186/1756-0500-5-80
PubMed Central IDPMC3296665
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorJiang, J
dc.contributor.authorLi, J
dc.contributor.authorKwan, H
dc.contributor.authorAu, C
dc.contributor.authorWan Law, P
dc.contributor.authorLi, L
dc.contributor.authorKam, K
dc.contributor.authorLun Ling, J
dc.contributor.authorLeung, FC
dc.date.accessioned2012-03-27T09:07:34Z
dc.date.available2012-03-27T09:07:34Z
dc.date.issued2012
dc.description.abstractBackground: Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. Findings. Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ∼90% of 100 assemblies with < 10 scaffolds and ∼95% of 100 assemblies with < 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is > 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. Conclusions: A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks. © 2012 Jiang et al; BioMed Central Ltd.
dc.description.naturepublished_or_final_version
dc.identifier.citationBmc Research Notes, 2012, v. 5 [How to Cite?]
DOI: http://dx.doi.org/10.1186/1756-0500-5-80
dc.identifier.citeulike10294559
dc.identifier.doihttp://dx.doi.org/10.1186/1756-0500-5-80
dc.identifier.hkuros199089
dc.identifier.issn1756-0500
2011 SCImago Journal Rankings: 0.159
dc.identifier.pmcidPMC3296665
dc.identifier.pmid22289569
dc.identifier.scopuseid_2-s2.0-84862812240
dc.identifier.urihttp://hdl.handle.net/10722/146040
dc.identifier.volume5
dc.languageeng
dc.publisherBioMed Central Ltd.. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/
dc.publisher.placeUnited Kingdom
dc.relation.ispartofBMC Research Notes
dc.relation.referencesReferences in Scopus
dc.rightsBMC Research Notes. Copyright © BioMed Central Ltd..
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License
dc.subjectProkaryota
dc.titleA cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
dc.typeArticle
Author Affiliations
  1. The University of Hong Kong
  2. Centre for Health Protection
  3. Chinese University of Hong Kong