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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, H4
Au, C4
Wan Law, P4
Li, L4
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
2012 SCImago Journal Rankings: 0.518
 
DOIhttp://dx.doi.org/10.1186/1756-0500-5-80
 
PubMed Central IDPMC3296665
 
ReferencesReferences in Scopus
 
DC FieldValue
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
2012 SCImago Journal Rankings: 0.518
 
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
 
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<contributor.author>Kwan, H</contributor.author>
<contributor.author>Au, C</contributor.author>
<contributor.author>Wan Law, P</contributor.author>
<contributor.author>Li, L</contributor.author>
<contributor.author>Kam, K</contributor.author>
<contributor.author>Lun Ling, J</contributor.author>
<contributor.author>Leung, FC</contributor.author>
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<description.abstract>Background: 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) &#8764;90% of 100 assemblies with &lt; 10 scaffolds and &#8764;95% of 100 assemblies with &lt; 150 contigs; 2) average contig N50 size is over 331 kb; 3) average single base accuracy is &gt; 99.99%; 4) average false gene duplication rate is &lt; 0.7%; 5) average false gene loss rate is &lt; 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. &#169; 2012 Jiang et al; BioMed Central Ltd.</description.abstract>
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Author Affiliations
  1. The University of Hong Kong
  2. Centre for Health Protection
  3. Prince of Wales Hospital Hong Kong
  4. Chinese University of Hong Kong