Molecular evolution of synonymous codon usage in Populus

BMC Evolutionary Biology

Volumn 8, Issue 1, 2008, Pages

  Ingvarsson, Pär K ^a  

^a UMEÅ UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; ASPEN; CODON USAGE; CONTROLLED STUDY; DNA BASE COMPOSITION; GENE EXPRESSION; GENE MUTATION; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PHYLOGENY; SPECIES DIVERSITY; BIOLOGICAL MODEL; BIOLOGY; CODON; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETICS; MUTATION; PLANT GENOME; POPULATION GENETICS; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

NES; POPULUS; POPULUS DELTOIDES; POPULUS TREMULA;

PLANT DNA;

BASE COMPOSITION; CODON; COMPUTATIONAL BIOLOGY; DNA, PLANT; EVOLUTION, MOLECULAR; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETICS, POPULATION; GENOME, PLANT; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; PHYLOGENY; POLYMORPHISM, GENETIC; POPULUS; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 56649091351     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-8-307     Document Type: Article

References (42)

1. Translational selection and molecular evolution. H Akashi A Eyre-Walker, Curr Opin Genet Dev 1998 8 688 693 10.1016/S0959-437X(98)80038-5 9914211
2. Gene expression and molecular evolution. H Akashi, Curr Opin Genet Dev 2001 11 660 666 10.1016/S0959-437X(00)00250-1 11682310
3. Evolution of synonymous codon usage in metazoans. L Duret, Curr Opin Genet Dev 2002 12 640 649 10.1016/S0959-437X(02)00353-2 12433576
4. Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes. S Subramanian, Genetics 2008 178 2429 2432 18430960 10.1534/genetics.107.086405
5. The population and evolutionary genetics of codon bias. M Kreitman M Antezana, Evolutionary genetics: from molecules to morphology Cambridge, U.K.: Cambridge University Press, Singh KS, Krimbas CB, 2000 82 101
6. The Selection-Mutation-Drift Theory Of Synonymous Codon Usage. M Bulmer, Genetics 1991 129 897 907 1752426
7. A population genetic model for the evolution of synonymous codon usage: patterns and predictions. GAT McVean B Charlesworth, Genet Res 1999 74 145 158 10.1017/S0016672399003912
8. Molecular Evolution Between Drosophila melanogaster and D. simulans: Reduced Codon Bias, Faster Rates of Amino Acid Substitution, and Larger Proteins in D. melanogaster. H Akashi, Genetics 1996 144 1297 1307 http://www.genetics. org/cgi/content/abstract/144/3/1297 8913769
9. Molecular evolution in the Drosophila melanogaster species subgroup: Frequent parameter fluctuations on the timescale of molecular divergence. H Akashi WY Ko SF Piao A John P Goel CF Lin AP Vitins, Genetics 2006 172 1711 1726 16387879 10.1534/genetics.105.049676
10. Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila. R Nielsen VLB DuMont MJ Hubisz CF Aquadro, Mol Biol Evol 2007 24 228 235 http://mbe.oxfordjournals.org/cgi/content/abstract/24/1/228 10.1093/molbev/msl146 17041152
11. Reduced selection for codon usage bias in Drosophila miranda. D Bachtrog, J Mol Evol 2007 64 586 590 10.1007/s00239-006-0257-x 17457633
12. Patterns of molecular variation and evolution in Drosophila americana and its relatives. X Maside B Charlesworth, Genetics 2007 176 2293 2305 17507679 10.1534/genetics.107.071191
13. Breeding systems and genome evolution. D Charlesworth SI Wright, Curr Opin Genet Dev 2001 11 685 690 10.1016/S0959-437X(00)00254-9 11682314
14. Patterns of Molecular Evolution in Caenorhabditis Preclude Ancient Origins of Selfing. AD Cutter JD Wasmuth NL Washington, Genetics 2008 178 2093 2104 http://www.genetics.org/cgi/content/abstract/178/4/2093 18430935 10.1534/genetics.107.085787
15. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. PK Ingvarsson, Mol Biol Evol 2007 24 836 844 10.1093/molbev/msl212 17204548
16. The evolution of biased codon and amino acid usage in nematode genomes. AD Cutter JD Wasmuth ML Blaxter, Mol Biol Evol 2006 23 2303 2315 10.1093/molbev/msl097 16936139
17. Identification of Ortholog Groups for Eukaryotic Genomes. L Li CJ Stoeckert DS Roos, Genome Res 2003 13 2178 2189 12952885 10.1101/gr.1224503
18. Systematics and evolution of Populus. JE Eckenwalder, Biology of Populus and its implications for managements and conservation Ottawa, Canada: NRC Research Press, Stettler RF, Bradshaw HD, Heilman PE, Hinckley TM, 1996 7 32
19. Molecular phylogeny of Salicaceae and closely related Flacourtiaceae: evidence from 5.8S, ITS1 and ITS2 or the rDNA. E Leskinen C Alström- Rapaport, Pl Syst Evol 1999 215 209 227 10.1007/BF00984656
20. Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast trnT-trnF region and nuclear rDNA. M Hamzeh S Dayanandan, Am J Bot 2004 91 1398 1408 10.3732/ajb.91.9.1398
21. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. DA Pollard VN Iyer AM Moses MB Eisen, PLoS Genet 2006 2 e173 17132051 10.1371/journal.pgen.0020173
22. Simple methods for testing molecular clock hypothesis. F Tajima, Genetics 1993 135 599 607 8244016
23. Codon-substitution models for heterogeneous selection pressure at amino acid sites. ZH Yang R Nielsen N Goldman AMK Pedersen, Genetics 2000 155 431 449 10790415
24. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. WSW Wong ZH Yang N Goldman R Nielsen, Genetics 2004 168 1041 1051 15514074 10.1534/genetics.104.031153
25. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. GA McVean J Vieira, Genetics 2001 157 245 257 11139506
26. Statistical significance for genome-wide studies. JD Storey R Tibshirani, Proc Natl Acad Sci USA 2003 100 9440 9445 12883005 10.1073/pnas.1530509100
27. Patterns of mutation and selection at synonymous sites in Drosophila. ND Singh VL Bauer DuMont MJ Hubisz R Nielsen CF Aquadro, Mol Biol Evol 2007 2687 2697 10.1093/molbev/msm196 18000010
28. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, Arabidopsis. L Duret D Mouchiroud, Proc Natl Acad Sci USA 1999 96 4482 4487 10200288 10.1073/pnas.96.8.4482
29. Microarray and EST database estimates of mRNA expression levels differ: The protein length versus expression curve for C. elegans. E Munoz L Bogarad M Deem, BMC Genomics 2004 5 30 15134588 10.1186/1471-2164-5-30
30. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. SI Wright CBK Yau M Looseley BC Meyers, Mol Biol Evol 2004 21 1719 1726 10.1093/molbev/msh191 15201397
31. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length and number of protein-protein interactions. B Lemos BR Bettencourt CD Meiklejohn DL Hartl, Mol Biol Evol 2005 22 1345 1354 10.1093/molbev/msi122 15746013
32. Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. PK Ingvarsson, Genetics 2008 180 329 340 10.1534/genetics.108.090431 18716330
33. The genome of Black cottonwood Populus trichocarpa (Torr. & Gray). G Tuskan S DiFazio S Jansson J Bohlman, Science 2006 313 1596 1604 10.1126/science.1128691 16973872
34. Rates and patterns of molecular evolution in inbred and outbred Arabidopsis. SI Wright B Lauga D Charlesworth, Mol Biol Evol 2002 19 1407 1420 12200469
35. PlantGDB, plant genome database and analysis tools. Q Dong SD Schlueter V Brendel, Nucl Acids Res 2004 32 D354 D359 14681433 10.1093/nar/gkh046
36. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. T Schiex J Gouzy A Moisan Y de Oliveira, Nucl Acids Res 2003 31 3738 3741 12824407 10.1093/nar/gkg610
37. R: a language for data analysis and graphics. R Ihaka R Gentleman, J Comp Graph Stat 1996 5 299 314 10.2307/1390807
38. Codon usage and tRNA content in unicellular and multicellular organisms. T Ikemura, Mol Biol Evol 1985 2 13 34 3916708
39. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucl Acids Res 1994 22 4673 4680 7984417 10.1093/nar/22.22.4673
40. PAML: a program package for phylogenetic analysis by maximum likelihood. Z Yang, CABIOS 1997 13 555 556 9367129
41. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: Implications for the correlation between the synonymous substitution rate and codon usage bias. N Bierne A Eyre-Walker, Genetics 2003 165 1587 1597 14668405
42. Codon-Based Model Of Nucleotide Substitution For Protein-Coding DNA-Sequences. N Goldman ZH Yang, Mol Biol Evol 1994 11 725 736 7968486