Asymmetric and non-uniform evolution of recently duplicated human genes

Biology Direct

Volumn 5, Issue , 2010, Pages

  Panchin, Alexander Y ^a,b   Gelfand, Mikhail S ^a,b   Ramensky, Vasily E ^c   Artamonova, Irena I ^a,b,d  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^d VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DUPLICATE GENE; GENETIC SELECTION; GENETICS; HUMAN; MOLECULAR EVOLUTION;

EVOLUTION, MOLECULAR; GENES, DUPLICATE; HUMANS; SELECTION, GENETIC;

EID: 77956465856     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-5-54     Document Type: Article

References (55)

1. Ohta T. Role of gene duplication in evolution. Genome 1989, 31:304-310.
2. Conrad B, Antonarakis SE. Gene duplication: a drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet 2007, 8:17-35. 10.1146/annurev.genom.8.021307.110233, 17386002.
3. Canestro C, Catchen JM, Rodriguez-Mari A, Yokoi H, Postlethwait JH. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. PLoS Genet 2009, 5:e1000496. 10.1371/journal.pgen.1000496, 2682703, 19478994.
4. Ye C, Sun H, Guo W, Wei Y, Zhou Q. Molecular evolution of PKD2 gene family in mammals. Genetica 2009, 137:77-86. 10.1007/s10709-009-9352-4, 19184643.
5. Lane RP, Cutforth T, Young J, Athanasiou M, Friedman C, Rowen L, Evans G, Axel R, Hood L, Trask BJ. Genomic analysis of orthologous mouse and human olfactory receptor loci. Proc Natl Acad Sci USA 2001, 98:7390-7395. 10.1073/pnas.131215398, 34679, 11416212.
6. Artamonova II, Gelfand MS. Evolution of the exon-intron structure and alternative splicing of the MAGE-A family of cancer/testis antigens. J Mol Evol 2004, 59:620-631. 10.1007/s00239-004-2654-3, 15693618.
7. Shustrova EN, Artamonova II. The Evolutionary History of the SSX Family of Human C/T-Antigens. Molecular Biology 2009, 43:7.
8. Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15:1421-1430. 10.1101/gr.3992505, 1240085, 16204195.
9. Conant GC, Wagner A. Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans. Proc Biol Sci 2004, 271:89-96. 10.1098/rspb.2003.2560, 1691561, 15002776.
10. Davis JC, Petrov DA. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol 2004, 2:E55. 10.1371/journal.pbio.0020055, 368158, 15024414.
11. He X, Zhang J. Higher duplicability of less important genes in yeast genomes. Mol Biol Evol 2006, 23:144-151. 10.1093/molbev/msj015, 16151181.
12. Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155. 10.1126/science.290.5494.1151, 11073452.
13. Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624. 10.1038/nature02424, 15004568.
14. Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL. All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol 2007, 8:R209. 10.1186/gb-2007-8-10-r209, 2246283, 17916239.
15. Scannell DR, Wolfe KH. A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genome Res 2008, 18:137-147. 10.1101/gr.6341207, 2134778, 18025270.
16. Wagner A. Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 2002, 19:1760-1768.
17. Conant GC, Wagner A. Asymmetric sequence divergence of duplicate genes. Genome Res 2003, 13:2052-2058. 10.1101/gr.1252603, 403682, 12952876.
18. Koonin EV, Wolf YI, Jordan IK. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evolutionary Biology 2004, 4.
19. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biol 2002, 3:RESEARCH0008. 10.1186/gb-2002-3-2-research0008, 65685, 11864370.
20. Hughes T, Liberles DA. The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. J Mol Evol 2007, 65:574-588. 10.1007/s00239-007-9041-9, 17957399.
21. Zhang P, Gu Z, Li WH. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol 2003, 4:R56. 10.1186/gb-2003-4-9-r56, 193656, 12952535.
22. Cusack BP, Wolfe KH. Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Mol Biol Evol 2007, 24:679-686. 10.1093/molbev/msl199, 17179139.
23. Chain FJ, Ilieva D, Evans BJ. Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization. BMC Evol Biol 2008, 8:43. 10.1186/1471-2148-8-43, 2275784, 18261230.
24. Kim SH, Yi SV. Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae. Mol Biol Evol 2006, 23:1068-1075. 10.1093/molbev/msj115, 16510556.
25. Beissbarth T, Speed TP. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20:1464-1465. 10.1093/bioinformatics/bth088, 14962934.
26. Chung WY, Albert R, Albert I, Nekrutenko A, Makova KD. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC Bioinformatics 2006, 7:46. 10.1186/1471-2105-7-46, 1403810, 16441884.
27. UniGene. , http://www.ncbi.nlm.nih.gov/unigene
28. Sunyaev S, Kondrashov FA, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Hum Mol Genet 2003, 12:3325-3330. 10.1093/hmg/ddg359, 14570704.
29. Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 2008, 82:100-112. 10.1016/j.ajhg.2007.09.006, 2253956, 18179889.
30. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 2002, 30:3894-3900. 10.1093/nar/gkf493, 137415, 12202775.
31. Vizcaino JA, Cote R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L. A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 2009, 9:4276-4283. 10.1002/pmic.200900402, 19662629.
32. PRoteomics IDEntifications database (PRIDE). , http://www.ebi.ac.uk/pride/
33. Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol 1982, 158:573-597. 10.1016/0022-2836(82)90250-9, 6750137.
34. Pavlov MY, Watts RE, Tan Z, Cornish VW, Ehrenberg M, Forster AC. Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc Natl Acad Sci USA 2009, 106:50-54. 10.1073/pnas.0809211106, 2629218, 19104062.
35. Stoletzki N, Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol 2007, 24:374-381. 10.1093/molbev/msl166, 17101719.
36. Marais G, Duret L. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans. J Mol Evol 2001, 52:275-280.
37. Crombie T, Swaffield JC, Brown AJ. Protein folding within the cell is influenced by controlled rates of polypeptide elongation. J Mol Biol 1992, 228:7-12. 10.1016/0022-2836(92)90486-4, 1447795.
38. Willie E, Majewski J. Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet 2004, 20:534-538. 10.1016/j.tig.2004.08.014, 15475111.
39. Parmley JL, Hurst LD. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol 2007, 24:1600-1603. 10.1093/molbev/msm104, 17525472.
40. NCBI Reference Sequence (RefSeq). , http://www.ncbi.nlm.nih.gov/RefSeq/
41. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-65. 10.1093/nar/gkl842, 1716718, 17130148.
42. UCSC Genome Bioinformatics. , http://genome.ucsc.edu/
43. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 186604, 12045153.
44. RepeatMasker. , http://www.repeatmasker.org/
45. Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics 2004, Chapter 4. Unit 4 10.
46. Mega BLAST. , http://www.ncbi.nlm.nih.gov/blast/megablast.shtml
47. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7:203-214. 10.1089/10665270050081478, 10890397.
48. Align Sequences using ClustalW2. , http://www.ebi.ac.uk/Tools/clustalw2/index.html
49. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948. 10.1093/bioinformatics/btm404, 17846036.
50. Phylogenetic Analysis by Maximum Likelihood (PAML). , http://abacus.gene.ucl.ac.uk/software/paml.html
51. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591. 10.1093/molbev/msm088, 17483113.
52. Lynch M, Katju V. The altered evolutionary trajectories of gene duplicates. Trends Genet 2004, 20:544-549. 10.1016/j.tig.2004.09.001, 15475113.
53. Feller W. An introduction to probability theory and its applications 1970, New York; Chichester: Wiley, 3.
54. GOstat. , http://gostat.wehi.edu.au/
55. PolyPhen: prediction of functional effect of human nsSNPs. , http://genetics.bwh.harvard.edu/pph/