Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Bu, Lijing ^a   Bergthorsson, Ulfar ^a   Katju, Vaishali ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABUNDANCE; CONSERVATION GENETICS; DIVERGENCE; FREQUENCY ANALYSIS; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; OBSERVATIONAL METHOD; SELECTION; YEAST;

SACCHAROMYCES CEREVISIAE;

ARTICLE; BIOLOGY; CODON; DUPLICATE GENE; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MUTATION RATE; SACCHAROMYCES CEREVISIAE; SYNTENY;

CODON; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENES, DUPLICATE; GENETIC VARIATION; MUTATION RATE; SACCHAROMYCES CEREVISIAE; SELECTION, GENETIC; SYNTENY;

EID: 80053345415     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-279     Document Type: Article

References (45)

1. The part played by recurrent mutation in evolution. Haldane JBS, Am Nat 1933 67 679 682
2. Ohno S, Evolution by Gene Duplication Springer-Verlag 1970
3. Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Hughes MK, Hughes AL, Mol Biol Evol 1993 10 1360 1369 8277859 (Pubitemid 23352616)
4. Duplicated genes evolve independently after polyploid formation in cotton. Cronn RC, Small RL, Wendel JF, Proc Natl Acad Sci USA 1999 96 14406 14411 10.1073/pnas.96.25.14406 10588718 (Pubitemid 30000663)
5. Evolutionary rate of duplicate genes in fish and mammals. Robinson-Rechavi M, Laudet V, Mol Biol Evol 2001 18 681 683 11264421 (Pubitemid 32268022)
6. Selection in the evolution of gene duplications. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV, Genome Biol 2002 3 ESEARCH0008 11864370
7. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Zhang L, Vision TJ, Gaut BS, Mol Biol Evol 2002 19 1464 1473 12200474 (Pubitemid 36752771)
8. The altered evolutionary trajectories of gene duplicates. Lynch M, Katju V, Trends Genet 2004 20 544 549 10.1016/j.tig.2004.09.001 15475113 (Pubitemid 39314561)
9. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. Van de Peer Y, Taylor J, Braasch I, Meyer A, J Mol Evol 2001 53 436 446 10.1007/s002390010233 11675603 (Pubitemid 32889551)
10. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Nembaware V, Crum K, Kelso J, Seoighe C, Genome Res 2002 12 1370 1376 10.1101/gr.270902 12213774
11. Asymmetric sequence divergence of duplicate genes. Conant GC, Wagner A, Genome Res 2003 13 2052 2058 10.1101/gr.1252603 12952876 (Pubitemid 37161762)
12. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisae. Kellis M, Birren BW, Lander ES, Nature 2004 428 617 624 10.1038/nature02424 15004568 (Pubitemid 38524797)
13. Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae. Kim S-O, Yi SV, Mol Biol Evol 2006 23 1068 1075 10.1093/molbev/msj115 16510556 (Pubitemid 43726072)
14. The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Katju V, Lynch M, Genetics 2003 165 1793 1803 14704166 (Pubitemid 38040270)
15. On the formation of novel genes by duplication in the Caenorhabditis elegans genome. Katju V, Lynch M, Mol Biol Evol 2006 23 1056 1067 10.1093/molbev/msj114 16500928 (Pubitemid 43726071)
16. Not born equal: increased asymmetry in relocated and retrotransposed rodent gene duplicates. Cusack BP, Wolfe KH, Mol Biol Evol 2007 24 679 686 17179139 (Pubitemid 46355795)
17. Adaptive evolution of young gene duplicates in mammals. Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW, Genome Res 2009 19 859 867 10.1101/gr.085951.108 19411603
18. Molecular evidence for an ancient duplication of the entire yeast genome. Wolfe KH, Shields DC, Nature 1997 387 708 713 10.1038/42711 9192896 (Pubitemid 27270611)
19. The Codon Adaptation Index-a measure of directional synonymous codon usage bias and its potential applications. Sharp PM, Li WH, Nucl Acids Res 1987 11 1281 1295
20. Selection in the evolution of gene duplications. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV, Genome Biol 2002 3 0008.1
21. Asymmetric functional divergence of duplicate genes in yeast. Wagner A, Mol Biol Evol 2002 19 1760 1768 12270902
22. Different evolutionary patterns between young gene duplicates in the human genome. Zhang P, Gu Z, Li W-H, Genome Biol 2003 4 56 10.1186/gb-2003-4-9- r56 12952535
23. A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Scannell DR, Wolfe KH, Genome Res 2008 18 137 147 18025270
24. Asymmetric and non-uniform evolution of recently duplicated human genes. Panchin AY, Gelfand MS, Ramensky VE, Artamanova IE, Biol Dir 2010 5 54 10.1186/1745-6150-5-54
25. Correlation between sequence conservation and the genomic context after gene duplication. Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B, Nucl Acids Res 2005 33 6164 6171 10.1093/nar/gki913 16257980 (Pubitemid 41742554)
26. After the duplication: gene loss and adaptation in Saccharomyces genomes. Cliften P, Fulton RS, Wilson RK, Johnston M, Genetics 2006 172 863 872 16322519 (Pubitemid 43345424)
27. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH, Nature 2006 440 341 345 10.1038/nature04562 16541074
28. Evidence of en bloc duplication in vertebrate genomes. Abi-Rached L, Gilles A, Shiina T, Pontarotti P, Inoko H, Nat Genetics 2002 31 100 105 10.1038/ng855
29. Why highly expressed proteins evolve slowly. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH, Proc Natl Acad Sci USA 2005 102 14338 14343 10.1073/pnas.0504070102 16176987 (Pubitemid 41429699)
30. A single determinant dominates the rate of yeast protein evolution. Drummond DA, Raval A, Wilke CO, Mol Biol Evol 2006 23 327 337 16237209 (Pubitemid 43100047)
31. Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans. Katju V, Farslow JC, Bergthorsson U, Genome Biol 2009 10 75 10.1186/gb-2009-10-7-r75 19594930
32. GenomeHistory: a software tool and its application to fully sequenced genomes. Conant GC, Wagner A, Nucl Acids Res 2002 30 3378 3386 10.1093/nar/gkf449 12140322 (Pubitemid 34845934)
33. Robustness-it's not where you think it is. Wolfe K, Nat Genet 2000 25 3 4 10.1038/75560 10802639 (Pubitemid 30257022)
34. Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Wong S, Butler G, Wolfe KH, Proc Natl Acad Sci USA 2002 99 9272 9277 10.1073/pnas.142101099 12093907 (Pubitemid 34764603)
35. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pöhlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P, Science 2004 304 304 307 10.1126/science.1095781 15001715 (Pubitemid 38452185)
36. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Byrne KP, Wolfe KH, Genome Res 2005 15 1456 1461 10.1101/gr.3672305 16169922 (Pubitemid 41400914)
37. Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. Gordon JL, Byrne KP, Wolfe KH, PLoS Genet 2009 5 1000485 10.1371/journal.pgen.1000485 19436716
38. A new method of inference of ancestral nucleotide and amino acid sequences. Yang Z, Kumar S, Nei M, Genetics 1995 141 1641 1650 8601501
39. Probabilistic reconstruction of ancestral protein sequences. Koshi JM, Goldstein RA, J Mol Evol 1996 42 313 320 10.1007/BF02198858 8919883 (Pubitemid 26102499)
40. Yang Z, Computational Molecular Evolution Oxford University Press, Oxford, England 2006
41. Simple methods for testing the molecular evolutionary clock hypothesis. Tajima F, Genetics 1993 135 599 607 8244016 (Pubitemid 23307610)
42. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Tamura K, Dudley J, Nei M, Kumar S, Mol Biol Evol 2007 24 1596 1599 10.1093/molbev/msm092 17488738 (Pubitemid 47236692)
43. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC, Jahn D, Nucl Acids Res 2005 33 526 W531 10.1093/nar/gki376 15980527 (Pubitemid 44529976)
44. Codon adaptation index as a measure of dominating codon bias. Carbone A, Zinovyev A, Képès F, Bioinformatics 2003 19 2005 2015 10.1093/bioinformatics/btg272 14594704 (Pubitemid 37408151)
45. Quantification of the yeast transcriptome by single-molecule sequencing. Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky S, Milos P, Causey M, Nat Biotech 2009 27 652 658 10.1038/nbt.1551