Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements.

作者: King Jordan , John F. McDonald

DOI: 10.1007/978-94-011-4156-7_2

关键词: Phylogenetic treeBiologyGenomeGenomicsGeneticsRetrotransposonWhole genome sequencingMolecular evolutionNonsynonymous substitutionComparative genomics

摘要: The availability of the complete genome sequence Saccharomyces cerevisiae provides unique opportunity to study an entire genomic complement retrotransposons from evolutionary perspective. There are five families yeast retrotransposons, Ty1-Ty5. We have conducted a series comparative analyses within and among S. Ty in effort document forces that shaped element variation. Our results indicate elements vary little terms both size sequence. Furthermore, intra-element 5′-3′ long terminal repeat (LTR) comparisons almost all recently transposed. For each family, solo LTR sequences generated by recombination far outnumber full length insertions. Taken together, these suggest rapid turnover elements. closely related Ty1 Ty2 most numerous genome. Phylogenetic analysis insertions reveals reverse transcriptase mediated between has number hybrid Ty1/2 These similar structures with chimeric LTRs TYB (pol) genes. Analysis levels nonsynonymous (Ka) synonymous (Ks) nucleotide variation indicates coding regions been subject strong negative (purifying) selection. Distribution Ka Ks on Ty1, phytogenies evidence selection internal external branches. This pattern suggests majority represent active or lineages is consistent high level turnover. dynamics cerevisae uncovered our discussed respect interaction their host

参考文章(31)
John F. McDonald, Lilya V. Matyunina, Susanne Wilson, I. King Jordan, Nathan J. Bowen, Wolfgang J. Miller, LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica. ,vol. 100, pp. 3- 13 ,(1997) , 10.1023/A:1018392117410
J D Boeke, D Eichinger, D Castrillon, G R Fink, The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Molecular and Cellular Biology. ,vol. 8, pp. 1432- 1442 ,(1988) , 10.1128/MCB.8.4.1432
Jin M. Kim, Swathi Vanguri, Jef D. Boeke, Abram Gabriel, Daniel F. Voytas, Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence Genome Research. ,vol. 8, pp. 464- 478 ,(1998) , 10.1101/GR.8.5.464
Gerald R. Fink, Jef D. Boeke, David J. Garfinkel, The mechanism and consequences of retrotransposition Trends in Genetics. ,vol. 2, pp. 118- 123 ,(1986) , 10.1016/0168-9525(86)90200-3
Robert D Fleischmann, Mark D Adams, Owen White, Rebecca A Clayton, Ewen F Kirkness, Anthony R Kerlavage, Carol J Bult, Jean-Francois Tomb, Brian A Dougherty, Joseph M Merrick, Keith McKenney, Granger Sutton, Will FitzHugh, Chris Fields, Jeannine D Gocayne, John Scott, Robert Shirley, Li-lng Liu, Anna Glodek, Jenny M Kelley, Janice F Weidman, Cheryl A Phillips, Tracy Spriggs, Eva Hedblom, Matthew D Cotton, Teresa R Utterback, Michael C Hanna, David T Nguyen, Deborah M Saudek, Rhonda C Brandon, Leah D Fine, Janice L Fritchman, Joyce L Fuhrmann, NSM Geoghagen, Cheryl L Gnehm, Lisa A McDonald, Keith V Small, Claire M Fraser, Hamilton O Smith, J Craig Venter, Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. ,vol. 269, pp. 496- 512 ,(1995) , 10.1126/SCIENCE.7542800
L. V. Matyunina, I. K. Jordan, J. F. McDonald, Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 93, pp. 7097- 7102 ,(1996) , 10.1073/PNAS.93.14.7097
D. E. L. Promislow, I. K. Jordan, J. E. McDonald, Genomic demography: a life-history analysis of transposable element evolution Proceedings of The Royal Society B: Biological Sciences. ,vol. 266, pp. 1555- 1560 ,(1999) , 10.1098/RSPB.1999.0815
Eugene Koonin, Roman Tatusov, Michael Galperin, Mikhail Rozanov, David Lipman, A Genomic Perspective on Protein Families Science. ,vol. 278, pp. 631- 637 ,(1997) , 10.1126/SCIENCE.278.5338.631
Dmitri A. Petrov, Daniel L. Hartl, Trash DNA is what gets thrown away: high rate of DNA loss in Drosophila. Gene. ,vol. 205, pp. 279- 289 ,(1997) , 10.1016/S0378-1119(97)00516-7
I. King Jordan, John F. McDonald, The Role of Interelement Selection in Saccharomyces cerevisiae Ty Element Evolution Journal of Molecular Evolution. ,vol. 49, pp. 352- 357 ,(1999) , 10.1007/PL00006558