دورية أكاديمية
أعرض في EDS

Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.

التفاصيل البيبلوغرافية
العنوان: Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.
المؤلفون: Tsangaras K; Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany., Siracusa MC; Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, California, United States of America., Nikolaidis N; Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, California, United States of America., Ishida Y; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America., Cui P; Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, California, United States of America., Vielgrader H; Zoo Vienna, Vienna, Austria., Helgen KM; National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America., Roca AL; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America., Greenwood AD; Department of Biological Science and Center for Applied Biotechnology Studies, California State University, Fullerton, California, United States of America.
المصدر: PloS one [PLoS One] 2014 Apr 21; Vol. 9 (4), pp. e95633. Date of Electronic Publication: 2014 Apr 21 (Print Publication: 2014).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science
مواضيع طبية MeSH: Evolution, Molecular*, Conserved Sequence/*genetics , Genome, Viral/*genetics , Nucleic Acid Hybridization/*genetics , Phascolarctidae/*virology , Retroviridae/*genetics, Animals ; Binding Sites ; Codon/genetics ; Models, Molecular ; Polymorphism, Genetic ; Protein Binding ; Protein Structure, Tertiary ; Proviruses/genetics ; Sequence Alignment ; Terminal Repeat Sequences/genetics ; Transcription Factors/metabolism ; Virus Integration/genetics
مستخلص: The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.
References: Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
EMBO Rep. 2010 Jan;11(1):28-31. (PMID: 20033091)
Viruses. 2012 Dec;4(12):3859-911. (PMID: 23342377)
Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448. (PMID: 20516186)
Mol Biol Evol. 2011 Oct;28(10):2731-9. (PMID: 21546353)
Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):E828-37. (PMID: 23401540)
Mol Biol Evol. 1986 Sep;3(5):418-26. (PMID: 3444411)
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):E746-52. (PMID: 21876176)
J Virol. 1998 Nov;72(11):9101-8. (PMID: 9765455)
J Virol. 2013 May;87(9):5081-8. (PMID: 23427161)
PLoS One. 2013 Apr 04;8(4):e59994. (PMID: 23593157)
BMC Res Notes. 2012 Jul 02;5:337. (PMID: 22748135)
Annu Rev Genet. 2004;38:645-79. (PMID: 15568989)
Mol Biol Evol. 2013 Feb;30(2):299-304. (PMID: 22983950)
Bioinformatics. 2000 Jun;16(6):566-7. (PMID: 10980157)
J Virol. 2000 May;74(9):4264-72. (PMID: 10756041)
PLoS One. 2009 May 25;4(5):e5683. (PMID: 19479085)
Methods Mol Biol. 2000;132:365-86. (PMID: 10547847)
J Gen Virol. 2005 Mar;86(Pt 3):783-787. (PMID: 15722540)
Methods Mol Biol. 2012;840:189-95. (PMID: 22237536)
PLoS One. 2008;3(11):e3602. (PMID: 18985148)
Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11547-52. (PMID: 23798387)
Front Oncol. 2013 Jul 10;3:179. (PMID: 23847767)
Biotechniques. 1994 Nov;17(5):858-60. (PMID: 7639844)
FEBS Lett. 2014 Jan 3;588(1):41-6. (PMID: 24239536)
Cell Mol Life Sci. 2008 Nov;65(21):3413-21. (PMID: 18818870)
Proc Natl Acad Sci U S A. 2007 Oct 30;104(44):17506-11. (PMID: 17959780)
PLoS One. 2010 Nov 16;5(11):e14004. (PMID: 21103372)
J Virol. 2012 Mar;86(6):3219-29. (PMID: 22205753)
Electrophoresis. 1999 Jun;20(8):1722-8. (PMID: 10435438)
Genome Res. 2011 Oct;21(10):1695-704. (PMID: 21880778)
Bioinformatics. 2006 Jan 15;22(2):195-201. (PMID: 16301204)
Nature. 2006 Jul 6;442(7098):79-81. (PMID: 16823453)
Bioinformatics. 2011 Aug 1;27(15):2153-5. (PMID: 21659319)
J Mol Diagn. 2011 May;13(3):325-33. (PMID: 21497292)
Aust Vet J. 2012 Oct;90(10):404-9. (PMID: 23004234)
J Virol. 2013 Sep;87(17):9943-8. (PMID: 23824806)
Mol Biol Evol. 2005 Mar;22(3):478-85. (PMID: 15509724)
Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3259-63. (PMID: 19221034)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Genome Res. 2012 Mar;22(3):568-76. (PMID: 22300766)
Science. 2009 Jul 17;325(5938):318-21. (PMID: 19608918)
Retrovirology. 2006 Feb 07;3:11. (PMID: 16460575)
Curr Biol. 2001 Nov 13;11(22):R914-6. (PMID: 11719237)
Bioinformatics. 2011 Feb 1;27(3):343-50. (PMID: 21134891)
Forensic Sci Int. 2003 Jan 9;131(1):59-64. (PMID: 12505472)
Methods Mol Biol. 2012;840:197-228. (PMID: 22237537)
Genome Biol. 2006;7(11):241. (PMID: 17118218)
BMC Genet. 2012 Oct 24;13:92. (PMID: 23095716)
J Virol. 2003 Oct;77(19):10504-14. (PMID: 12970435)
معلومات مُعتمدة: R01 GM092706 United States GM NIGMS NIH HHS; United States HHMI Howard Hughes Medical Institute; R01GM092706 United States GM NIGMS NIH HHS
المشرفين على المادة: 0 (Codon)
0 (Transcription Factors)
تواريخ الأحداث: Date Created: 20140423 Date Completed: 20150114 Latest Revision: 20211021
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC3994108
DOI: 10.1371/journal.pone.0095633
PMID: 24752422
قاعدة البيانات: MEDLINE
الوصف
تدمد:1932-6203
DOI:10.1371/journal.pone.0095633