Maintenance and loss of duplicated genes by dosage subfunctionalization

Molecular Biology and Evolution

Volumn 32, Issue 8, 2015, Pages 2141-2148

  Gout, Jean Francois ^a   Lynch, Michael ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Duplication; Expression level; Paramecium; Pseudogenization; Subfunctionalization; Whole genome duplication

Indexed keywords

GENE EXPRESSION; GENE LOSS; GENETIC DRIFT; MODEL; PARAMECIUM; SPECIES; YEAST; BIOLOGICAL MODEL; GENE DOSAGE; GENE DUPLICATION; GENETICS; GENOME;

GENE DOSAGE; GENE DUPLICATION; GENOME, PROTOZOAN; MODELS, GENETIC; PARAMECIUM;

EID: 84940111566     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv095     Document Type: Article

References (46)

1. Adams KL. 2007. Evolution of duplicate gene expression in polyploid and hybrid plants. J Hered. 98:136-141.
2. Arnaiz O, Cain S, Cohen J, Sperling L. 2007. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 35: D439-D444.
3. Arnaiz O, Sperling L. 2011. ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. Nucleic Acids Res. 39:D632-D636.
4. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Segurens B, Daubin V, Anthouard V, Aiach N, et al. 2006. Global trends of wholegenome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444:171-178.
5. Birchler JA, Veitia RA. 2012. Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A. 109:14746-14753.
6. Blanc G, Wolfe KH. 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16: 1679-1691.
7. Byrne KP, Wolfe KH. 2005. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15:1456-1461.
8. Davis JC, Petrov DA. 2005. Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet. 21:548-551.
9. Decatur WA, Hall JA, Smith JJ, Li W, Sower SA. 2013. Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropinreleasing hormone (GnRH). Gen Comp Endocrinol. 192:237-245.
10. Doyle JJ, Flagel LE, Paterson AH, Rapp RA, Soltis DE, Soltis PS,Wendel JF. 2008. Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet. 42:443-461.
11. Force A, Lynch M, Pickett FB, Amores A, Yan Y-I, Postlethwait J. 1999. The preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
12. Freeling M, Thomas BC. 2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res. 16:805-814.
13. Gout J-F, Duret L, Kahn D. 2009. Differential retention of metabolic genes following whole-genome duplication. Mol Biol Evol. 26: 1067-1072.
14. Gout J-F, Kahn D, Duret L. 2010. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet. 6:e1000944.
15. Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL. 2007. All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biol. 8:R209.
16. Holland PW, Garcia-Fernandez J, Williams NA, Sidow A. 1994. Gene duplications and the origins of vertebrate development. Development (Supplement):125-133.
17. Hughes T, Liberles DA. 2008. Whole-genome duplications in the ancestral vertebrate are detectable in the distribution of gene family sizes of tetrapod species. J Mol Evol. 67:343-357.
18. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
19. Jiao YN, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang HY, Soltis PS, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
20. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36.
21. Lynch M. 2007. The origins of genome architecture. Sunderland (MA): Sinauer Associates.
22. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science (Washington) 290:1151-1155.
23. Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. 2005. Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A. 102:5454-5459.
24. McGrath CL, Gout JF, Doak TG, Yanagi A, Lynch M. 2014. Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence. Genetics 197: 1417-1428.
25. McGrath CL, Gout JF, Johri P, Doak TG, Lynch M. 2014. Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Res. 24:1665-1675.
26. Metzger BP, Yuan DC, Gruber JD, Duveau F, Wittkopp PJ. 2015. Selection on noise constrains variation in a eukaryotic promoter. Nature Advance Access published March 16, 2015, doi:10.1038/ nature14244.
27. Meyer A, Van de Peer Y. 2005. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). Bioessays 27:937-945.
28. Mi H, Muruganujan A, Thomas PD. 2012. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 41:D377-D386.
29. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, ChowW, Kirkpatrick R, Butterfield YS, Young AC, Stott J, et al. 2006. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 16:796-803.
30. Ohno S. 1970. Evolution by gene duplication. Berlin (Germany): Springer-Verlag.
31. Panopoulou G, Poustka AJ. 2005. Timing and mechanism of ancient vertebrate genome duplications - the adventure of a hypothesis. Trends Genet. 21:559-567.
32. Papp B, Pal C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.
33. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10: 1890-1902.
34. Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu J-K, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064-1071.
35. Qian W, Liao BY, Chang AY, Zhang J. 2010. Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends Genet. 26:425-430.
36. Rastogi S, Liberles DA. 2005. Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol. 5:28.
37. Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH. 2007. Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci U S A. 104:8397-8402.
38. Seoighe C, Wolfe KH. 1999. Yeast genome evolution in the post-genome era. Curr Opin Microbiol. 2:548-554.
39. Simillion C, Vandepoele K, Van Montagu C, Zabeau M, Van de Peer Y. 2002. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 99:13627-13632.
40. Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3:Article3.
41. Sonneborn TM. 1975. The Paramecium aurelia complex of fourteen sibling species. Trans Am Microsc Soc. 94:155-178.
42. Sung W, Tucker AE, Doak TG, Choi E, Thomas WK, Lynch M. 2012. Extraordinary genome stability in the ciliate Paramecium tetraurelia. Proc Natl Acad Sci U S A. 109:19339-19344.
43. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28:511-515.
44. Wagner A. 2000. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc Natl Acad Sci U S A. 97:6579-6584.
45. Wolfe KH, Shields DC. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713.
46. Zhang JZ. 2003. Evolution by gene duplication: an update. Trends Ecol Evol. 18:292-298.