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Article: Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage
Title | Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage |
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Authors | |
Issue Date | 2005 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/ |
Citation | Bmc Genetics, 2005, v. 6 How to Cite? |
Abstract | Background: 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 Identifier | http://hdl.handle.net/10722/53439 |
ISSN | 2022 Impact Factor: 2.9 2020 SCImago Journal Rankings: 0.856 |
PubMed Central ID | |
ISI Accession Number ID | |
References |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Xia, X | en_HK |
dc.contributor.author | Yuen, KY | en_HK |
dc.date.accessioned | 2009-04-03T07:19:47Z | - |
dc.date.available | 2009-04-03T07:19:47Z | - |
dc.date.issued | 2005 | en_HK |
dc.identifier.citation | Bmc Genetics, 2005, v. 6 | en_HK |
dc.identifier.issn | 1471-2156 | en_HK |
dc.identifier.uri | http://hdl.handle.net/10722/53439 | - |
dc.description.abstract | Background: 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.language | eng | en_HK |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/ | en_HK |
dc.relation.ispartof | BMC Genetics | en_HK |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.rights | B M C Genetics. Copyright © BioMed Central Ltd. | en_HK |
dc.subject.mesh | Bacteriophages - genetics | en_HK |
dc.subject.mesh | Base Composition | en_HK |
dc.subject.mesh | Genome, Viral - genetics | en_HK |
dc.subject.mesh | Mutation | en_HK |
dc.subject.mesh | Selection (Genetics) | en_HK |
dc.title | Differential selection and mutation between dsDNA and ssDNA phages shape the evolution of their genomic AT percentage | en_HK |
dc.type | Article | en_HK |
dc.identifier.openurl | http://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+percentage | en_HK |
dc.identifier.email | Yuen, KY:kyyuen@hkucc.hku.hk | en_HK |
dc.identifier.authority | Yuen, KY=rp00366 | en_HK |
dc.description.nature | published_or_final_version | en_HK |
dc.identifier.doi | 10.1186/1471-2156-6-20 | en_HK |
dc.identifier.pmid | 15823202 | en_HK |
dc.identifier.pmcid | PMC1087484 | - |
dc.identifier.scopus | eid_2-s2.0-25444483877 | en_HK |
dc.identifier.hkuros | 100313 | - |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-25444483877&selection=ref&src=s&origin=recordpage | en_HK |
dc.identifier.volume | 6 | en_HK |
dc.identifier.isi | WOS:000228696000001 | - |
dc.publisher.place | United Kingdom | en_HK |
dc.identifier.scopusauthorid | Xia, X=7402179513 | en_HK |
dc.identifier.scopusauthorid | Yuen, KY=36078079100 | en_HK |
dc.identifier.citeulike | 10715701 | - |
dc.identifier.issnl | 1471-2156 | - |