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Article: Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage

TitleDifferential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage
Authors
Issue Date2005
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/
Citation
Bmc Genetics, 2005, v. 6 How to Cite?
AbstractBackground: Bacterial genomes differ dramatically in AT%. We have developed a model to show that the genomic AT% in rapidly replicating bacterial species can be used as an index of the availability of nucleotides A and T for DNA replication in cellular medium. This index is then used to (1) study the evolution and adaptation of the bacteriophage genomic AT% in response to the differential nucleotide availability of the host and (2) test the prediction that double-stranded DNA (dsDNA) phage should exhibit better adaptation than single-stranded DNA (ssDNA) phage because the rate of spontaneous deamination, which leads to C→T or C→U mutations depending on whether C is methylated or not, is about 100-fold greater in ssDNA than in dsDNA. Results: We retrieved 79 dsDNA phage and 27 ssDNA phage genomes together with their host genomic sequences. The dsDNA phages have their genomic AT% better adapted to the host genomic AT% than ssDNA phage. The poorer adaptation of the ssDNA phage can be partially accounted for by the C→T(U) mutations mediated by the spontaneous deamination. For ssDNA phage, the genomic A% is more strongly correlated with their host genomic AT% than the genomic T%. Conclusion: A significant fraction of variation in the genomic AT% in the dsDNA phage, and that in the genomic A% and T% of the ssDNA phage, can be explained by the difference in selection and mutation between them. © 2005 Xia and Yuen; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/53439
ISSN
2015 Impact Factor: 2.152
2015 SCImago Journal Rankings: 1.185
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorXia, Xen_HK
dc.contributor.authorYuen, KYen_HK
dc.date.accessioned2009-04-03T07:19:47Z-
dc.date.available2009-04-03T07:19:47Z-
dc.date.issued2005en_HK
dc.identifier.citationBmc Genetics, 2005, v. 6en_HK
dc.identifier.issn1471-2156en_HK
dc.identifier.urihttp://hdl.handle.net/10722/53439-
dc.description.abstractBackground: Bacterial genomes differ dramatically in AT%. We have developed a model to show that the genomic AT% in rapidly replicating bacterial species can be used as an index of the availability of nucleotides A and T for DNA replication in cellular medium. This index is then used to (1) study the evolution and adaptation of the bacteriophage genomic AT% in response to the differential nucleotide availability of the host and (2) test the prediction that double-stranded DNA (dsDNA) phage should exhibit better adaptation than single-stranded DNA (ssDNA) phage because the rate of spontaneous deamination, which leads to C→T or C→U mutations depending on whether C is methylated or not, is about 100-fold greater in ssDNA than in dsDNA. Results: We retrieved 79 dsDNA phage and 27 ssDNA phage genomes together with their host genomic sequences. The dsDNA phages have their genomic AT% better adapted to the host genomic AT% than ssDNA phage. The poorer adaptation of the ssDNA phage can be partially accounted for by the C→T(U) mutations mediated by the spontaneous deamination. For ssDNA phage, the genomic A% is more strongly correlated with their host genomic AT% than the genomic T%. Conclusion: A significant fraction of variation in the genomic AT% in the dsDNA phage, and that in the genomic A% and T% of the ssDNA phage, can be explained by the difference in selection and mutation between them. © 2005 Xia and Yuen; licensee BioMed Central Ltd.en_HK
dc.languageengen_HK
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/en_HK
dc.relation.ispartofBMC Geneticsen_HK
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.rightsB M C Genetics. Copyright © BioMed Central Ltd.en_HK
dc.subject.meshBacteriophages - geneticsen_HK
dc.subject.meshBase Compositionen_HK
dc.subject.meshGenome, Viral - geneticsen_HK
dc.subject.meshMutationen_HK
dc.subject.meshSelection (Genetics)en_HK
dc.titleDifferential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentageen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1471-2156&volume=6&issue=1&spage=20&epage=&date=2005&atitle=Differential+selection+and+mutation+between+dsDNA+and+ssDNA+phages+shape+the+evolution+of+their+genomic+AT+percentageen_HK
dc.identifier.emailYuen, KY:kyyuen@hkucc.hku.hken_HK
dc.identifier.authorityYuen, KY=rp00366en_HK
dc.description.naturepublished_or_final_versionen_HK
dc.identifier.doi10.1186/1471-2156-6-20en_HK
dc.identifier.pmid15823202en_HK
dc.identifier.pmcidPMC1087484-
dc.identifier.scopuseid_2-s2.0-25444483877en_HK
dc.identifier.hkuros100313-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-25444483877&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume6en_HK
dc.identifier.isiWOS:000228696000001-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridXia, X=7402179513en_HK
dc.identifier.scopusauthoridYuen, KY=36078079100en_HK
dc.identifier.citeulike10715701-

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