Genomes and Genes
Summary: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
- Cusack B, Wolfe K. Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. Mol Biol Evol. 2007;24:679-86 pubmed..Finally, we demonstrate that the faster sequence evolution of retrogenes correlates with the profound alteration of their expression pattern that is precipitated by retrotransposition. ..
- Ha M, Kim E, Chen Z. Duplicate genes increase expression diversity in closely related species and allopolyploids. Proc Natl Acad Sci U S A. 2009;106:2295-300 pubmed publisher..or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely related species ..
- Bruggmann R, Bharti A, Gundlach H, Lai J, Young S, Pontaroli A, et al. Uneven chromosome contraction and expansion in the maize genome. Genome Res. 2006;16:1241-51 pubmed..In addition, no differences in methylation of single genes and tandemly repeated gene copies have been detected. These results, therefore, provide new insights into the diploidization of polyploid species. ..
- Papp B, Pal C, Hurst L. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature. 2004;429:661-4 pubmed..Instead their presence is better explained by selection for high enzymatic flux. ..
- Lynch M. Genomics. Gene duplication and evolution. Science. 2002;297:945-7 pubmed
- Schmidt T, Doan J, Goodman M, Grossman L. Retention of a duplicate gene through changes in subcellular targeting: an electron transport protein homologue localizes to the golgi. J Mol Evol. 2003;57:222-8 pubmed..Noncomplementary null mutations could also uncover an alternate localization, which is the more likely case for pCOX7AR. ..
- Musso G, Zhang Z, Emili A. Retention of protein complex membership by ancient duplicated gene products in budding yeast. Trends Genet. 2007;23:266-9 pubmed..These results highlight the value of protein complex membership in studying functional divergence among gene duplicates. ..
- Park C, Makova K. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biol. 2009;10:R10 pubmed publisherGene expression divergence is one manifestation of functional differences between duplicate genes. Although rapid accumulation of expression divergence between duplicate gene copies has been observed, the driving mechanisms behind this ..
- Horton A, Mahadevan N, Ruvinsky I, Gibson Brown J. Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. J Exp Zool B Mol Dev Evol. 2003;299:41-53 pubmed
- Li W, Yang J, Gu X. Expression divergence between duplicate genes. Trends Genet. 2005;21:602-7 pubmedA general picture of the role of expression divergence in the evolution of duplicate genes is emerging, thanks to the availability of completely sequenced genomes and functional genomic data, such as microarray data...
- Zhang P, Gu Z, Li W. Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol. 2003;4:R56 pubmedFollowing gene duplication, two duplicate genes may experience relaxed functional constraints or acquire different mutations, and may also diverge in function...
- Alvarez I, Wendel J. Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol. 2003;29:417-34 pubmed..It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes. ..
- Dehal P, Boore J. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3:e314 pubmed..Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage...
- Adams K, Wendel J. Novel patterns of gene expression in polyploid plants. Trends Genet. 2005;21:539-43 pubmedGenome doubling, or polyploidy, is a major factor accounting for duplicate genes found in most eukaryotic genomes...
- Davis J, Petrov D. Do disparate mechanisms of duplication add similar genes to the genome?. Trends Genet. 2005;21:548-51 pubmed..Our results demonstrate that genes duplicated by WGD and SSD are similarly biased with respect to codon bias and evolutionary rate, although differing significantly in their functional constituency. ..
- Castillo Davis C, Hartl D, Achaz G. cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 2004;14:1530-6 pubmed..of protein coding sequences, or whether these changes differ among orthologs (species homologs) and paralogs (duplicate genes)...
- Dean E, Davis J, Davis R, Petrov D. Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet. 2008;4:e1000113 pubmed publisher..We argue that duplicate genes do not often evolve to behave like singleton genes even after very long periods of time.
- Scanlon M, Chen K, McKnight CC I. The narrow sheath duplicate genes: sectors of dual aneuploidy reveal ancestrally conserved gene functions during maize leaf development. Genetics. 2000;155:1379-89 pubmed..The data suggest that the narrow sheath duplicate genes may perform ancestrally conserved, redundant functions in the development of a lateral domain in the maize ..
- He X, Zhang J. Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?. Genetics. 2006;172:1363-7 pubmed..However, duplicate genes rapidly diverge in expression patterns after duplication, making functional compensation less probable for ..
- Chapman B, Bowers J, Feltus F, Paterson A. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A. 2006;103:2730-5 pubmed
- Rizzon C, Ponger L, Gaut B. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Comput Biol. 2006;2:e115 pubmed..Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance. ..
- Hurles M. Gene duplication: the genomic trade in spare parts. PLoS Biol. 2004;2:E206 pubmed
- Lynch M, Katju V. The altered evolutionary trajectories of gene duplicates. Trends Genet. 2004;20:544-9 pubmed..However, the mutational events and population-genetic mechanisms that lead to the short-term preservation of duplicate genes are not necessarily the same as those exhibited by well-established paralogs en route to the origin of new ..
- Leach L, Zhang Z, Lu C, Kearsey M, Luo Z. The role of cis-regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes. Mol Biol Evol. 2007;24:2556-65 pubmedExpression divergence of duplicate genes is widely believed to be important for their retention and evolution of new function, although the mechanism that determines their expression divergence remains unclear...
- Uechi T, Maeda N, Tanaka T, Kenmochi N. Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes. Nucleic Acids Res. 2002;30:5369-75 pubmed..Although the role of the autosomal RP genes remains unclear, they may have evolved to compensate for the reduced dosage of X-linked RP genes. ..
- Friedman R, Hughes A. Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse. Mol Biol Evol. 2004;21:1008-13 pubmed
- Rodin S, Riggs A. Epigenetic silencing may aid evolution by gene duplication. J Mol Evol. 2003;56:718-29 pubmed
- Qian J, Luscombe N, Gerstein M. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol. 2001;313:673-81 pubmed..e. larger b). Clearly, the power law indicates a preference to duplicate genes that encode for molecular parts which are already common...
- Katju V, Lynch M. On the formation of novel genes by duplication in the Caenorhabditis elegans genome. Mol Biol Evol. 2006;23:1056-67 pubmed..Finally, both intron loss and gain contribute to the differential distribution of introns between two copies...
- Komili S, Farny N, Roth F, Silver P. Functional specificity among ribosomal proteins regulates gene expression. Cell. 2007;131:557-71 pubmed..Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes and support the existence of a ribosomal code. ..
- Marques A, Vinckenbosch N, Brawand D, Kaessmann H. Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biol. 2008;9:R54 pubmed publisher..as a model organism, we investigate a previously little considered mode for the functional diversification of duplicate genes: subcellular adaptation of encoded proteins...
- Sjödin P, Hedman H, Kruskopf Osterberg M, Gustafsson S, Lagercrantz U, Lascoux M. Polymorphism and divergence at three duplicate genes in Brassica nigra. J Mol Evol. 2008;66:581-90 pubmed publisher..nigra combined with a decrease in A. thaliana. In conclusion, a complex scenario involving both demography and selection seems to have shaped the pattern of polymorphism at the three genes. ..
- Rogers R, Bedford T, Hartl D. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics. 2009;181:313-22 pubmed publisherHistorically, duplicate genes have been regarded as a major source of novel genetic material...
- Hittinger C, Carroll S. Gene duplication and the adaptive evolution of a classic genetic switch. Nature. 2007;449:677-81 pubmed
- Takechi M, Kawamura S. Temporal and spatial changes in the expression pattern of multiple red and green subtype opsin genes during zebrafish development. J Exp Biol. 2005;208:1337-45 pubmed..These results provide the framework for subsequent studies of opsin gene regulation and for probing functional rationale of the developmental changes by using the power of zebrafish genetics. ..
- Blanc G, Wolfe K. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004;16:1679-91 pubmed..Together, these results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids. ..
- Castillo Davis C, Bedford T, Hartl D. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. Mol Biol Evol. 2004;21:1422-7 pubmed..falciparum and the rodent malaria P. y. yoelii in both orthologous and duplicate genes. Specifically, we test the hypothesis that intron gain/loss and protein evolution is accelerated in duplicate ..
- Gu Z, Steinmetz L, Gu X, Scharfe C, Davis R, Li W. Role of duplicate genes in genetic robustness against null mutations. Nature. 2003;421:63-6 pubmed..The first is the existence of duplicate genes: that is, the loss of function in one copy can be compensated by the other copy or copies...
- Shiu S, Byrnes J, Pan R, Zhang P, Li W. Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A. 2006;103:2232-6 pubmedThe question of how duplicate genes are retained in a population remains controversial...
- DeLuna A, Springer M, Kirschner M, Kishony R. Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS Biol. 2010;8:e1000347 pubmed publisherMany duplicate genes maintain functional overlap despite divergence over long evolutionary time scales. Deleting one member of a paralogous pair often has no phenotypic effect, unless its paralog is also deleted...
- Zou C, Lehti Shiu M, Thomashow M, Shiu S. Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet. 2009;5:e1000581 pubmed publisher..Finally, duplicate genes that lost most or all of the ancestral responses are more likely to have gained responses to other stresses...
- Makova K, Li W. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res. 2003;13:1638-45 pubmed..The divergence of gene expression between human duplicate genes is rapid, probably faster than that between yeast duplicates in terms of generations...
- Zhao Z, Sheps J, Ling V, Fang L, Baillie D. Expression analysis of ABC transporters reveals differential functions of tandemly duplicated genes in Caenorhabditis elegans. J Mol Biol. 2004;344:409-17 pubmed..Finally, our observations suggest that it is possible for coding sequences to function as a regulatory region for a neighbouring gene. ..
- Zhang J, Zhang Y, Rosenberg H. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet. 2002;30:411-5 pubmed publisher..Our findings demonstrate the contribution of gene duplication to organismal adaptation and show the power of combining sequence analysis and functional assays in delineating the molecular basis of adaptive evolution...
- Conant G, Wagner A. GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Res. 2002;30:3378-86 pubmed..unm.edu/~compbio/software/GenomeHistory) that identifies all pairs of duplicate genes in a genome and then determines the degree of synonymous and non-synonymous divergence between each duplicate ..
- Escriva H, Manzon L, Youson J, Laudet V. Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol Biol Evol. 2002;19:1440-50 pubmed..Thus, the complexity of all the paralogy groups present in vertebrates should be explained by the contribution of genome duplications (2R hypothesis), extra gene duplications, and gene losses. ..
- Xue C, Fu Y. Preservation of duplicate genes by originalization. Genetica. 2009;136:69-78 pubmed publisher..in some natural populations, such as yeast Saccharomyces cerevisiae, a considerable proportion of the duplicate genes originated from ancient whole genomic duplication (WGD) is preserved till now, which cannot be sufficiently ..
- Ranson H, Claudianos C, Ortelli F, Abgrall C, Hemingway J, Sharakhova M, et al. Evolution of supergene families associated with insecticide resistance. Science. 2002;298:179-81 pubmed..The analyses also provide the means for identifying previously unknown molecules involved in fundamental biological processes such as development. ..
- Walsh B. Population-genetic models of the fates of duplicate genes. Genetica. 2003;118:279-94 pubmed..All three of these fates are critical to the expansion and diversification of gene families. ..
- Conant G, Wagner A. Asymmetric sequence divergence of duplicate genes. Genome Res. 2003;13:2052-8 pubmed..The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons. ..
- Cronn R, Adams K. Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP. Biotechniques. 2003;34:726-30, 732, 734 pubmed..Most significantly, the method yields quantitative estimates of transcript ratios in template pools that range from equimolar to approximately 100:1. ..
- Qian W, Liao B, Chang A, Zhang J. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 2010;26:425-30 pubmed publisherAlthough evolutionary theories predict functional divergence between duplicate genes, many old duplicates still maintain a high degree of functional similarity and are synthetically lethal or sick, an observation that has puzzled many ..