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

TitleA cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
Authors
KeywordsProkaryota
Issue Date2012
PublisherBioMed Central Ltd.. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/
Citation
Bmc Research Notes, 2012, v. 5 How to Cite?
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.
Persistent Identifierhttp://hdl.handle.net/10722/146040
ISSN
2015 SCImago Journal Rankings: 0.702
PubMed Central ID
References

 

DC FieldValueLanguage
dc.contributor.authorJiang, Jen_HK
dc.contributor.authorLi, Jen_HK
dc.contributor.authorKwan, Hen_HK
dc.contributor.authorAu, Cen_HK
dc.contributor.authorWan Law, Pen_HK
dc.contributor.authorLi, Len_HK
dc.contributor.authorKam, Ken_HK
dc.contributor.authorLun Ling, Jen_HK
dc.contributor.authorLeung, FCen_HK
dc.date.accessioned2012-03-27T09:07:34Z-
dc.date.available2012-03-27T09:07:34Z-
dc.date.issued2012en_HK
dc.identifier.citationBmc Research Notes, 2012, v. 5en_HK
dc.identifier.issn1756-0500en_HK
dc.identifier.urihttp://hdl.handle.net/10722/146040-
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.en_HK
dc.languageengen_US
dc.publisherBioMed Central Ltd.. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/ en_HK
dc.relation.ispartofBMC Research Notesen_HK
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 simulationen_HK
dc.typeArticleen_HK
dc.identifier.emailLeung, FC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FC=rp00731en_HK
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/1756-0500-5-80en_HK
dc.identifier.pmid22289569-
dc.identifier.pmcidPMC3296665-
dc.identifier.scopuseid_2-s2.0-84862812240en_HK
dc.identifier.hkuros199089en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-84862812240&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume5en_HK
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridJiang, J=37085887400en_HK
dc.identifier.scopusauthoridLi, J=54881403300en_HK
dc.identifier.scopusauthoridKwan, H=7103369047en_HK
dc.identifier.scopusauthoridAu, C=55439019800en_HK
dc.identifier.scopusauthoridWan Law, P=55261414200en_HK
dc.identifier.scopusauthoridLi, L=54585407200en_HK
dc.identifier.scopusauthoridKam, K=7005354965en_HK
dc.identifier.scopusauthoridLun Ling, J=55261173000en_HK
dc.identifier.scopusauthoridLeung, FC=7103078633en_HK
dc.identifier.citeulike10294559-

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