Population diversity of orfan genes in escherichia coli

Genome Biology and Evolution

Volumn 4, Issue 11, 2012, Pages 1176-1187

  Yu, Guoqin ^a   Stoltzfus, Arlin ^a,b  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Evolution; Lineage specific genes; Negative selection; ORFan; Population genetics; Positive selection

Indexed keywords

ESCHERICHIA COLI; SHIGELLA;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; ESCHERICHIA COLI; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; OPEN READING FRAME; PHYLOGENY; PSEUDOGENE; SHIGELLA; SPECIES DIFFERENTIATION;

ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENETIC SPECIATION; GENETIC VARIATION; GENOME, BACTERIAL; OPEN READING FRAMES; PHYLOGENY; PSEUDOGENES; SHIGELLA;

EID: 84876015046     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs081     Document Type: Article

References (41)

1. Awano T, et al. 2006. A frame shift mutation in canine TPP1 (the ortholog of human CLN2) in a juvenile dachshund with neuronal ceroid lipofuscinosis. Mol Genet Metabol. 89:254-260.
2. Benson MD, et al. 2001. A new human hereditary amyloidosis: the result of a stop-codon mutation in the apolipoprotein AII gene. Genomics 72:272-277.
3. Cai JJ, Petrov DA. 2010. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol. 2: 393-409.
4. Cai J, Zhao RP, Jiang HF, Wang W. 2008. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179: 487-496.
5. Charlebois RL, Clarke GD, Beiko RG, St. Jean A. 2003. Characterization of species-specific genes using a flexible, Web-based querying system. FEMS Microbiol Lett. 225:213-220.
6. Chen SD, Zhang YE, Long MY. 2010. New genes in Drosophila quickly become essential. Science 330:1682-1685.
7. Chothia C. 1992. Proteins. One thousand families for the molecular biologist. Nature 357:543-544.
8. Cortez D, Forterre P, Gribaldo S. 2009. A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biol. 10:R65.
9. Daubin V, Lerat E, Perriere G. 2003. The source of laterally transferred genes in bacterial genomes. Genome Biol. 4: R57.
10. Daubin V, Ochman H. 2004. Bacterial genomes as new gene homes: the genealogy of ORFans in E coli. Genome Res. 14: 1036-1042.
11. Domazet-Loso T, Tautz D. 2003. An evolutionary analysis of orphan genes in Drosophila. Genome Res. 13:2213-2219.
12. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
13. Felsenstein J. 1995. PHYLIP (Phylogenetic inference package). Seattle: Department of Genetics, University of Washington.
14. Hahn Y, Lee B. 2005. Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences. Bioinformatics 21:I186-I194.
15. Hey J, Wakeley J. 1997. A coalescent estimator of the population recombination rate. Genetics 145:833-846.
16. Hurst L. 2002. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18:486-489.
17. Khalturin K, et al. 2008. A novel gene family controls species-specific morphological traits in hydra. PLoS Biol. 6:2436-2449.
18. Klimke W, et al. 2009. The national center for biotechnology information's protein clusters database. Nucleic Acids Res. 37: D216-D223.
19. Knowles DG, McLysaght A. 2009. Recent de novo origin of human protein-coding genes. Genome Res. 19:1752-1759.
20. Kryazhimskiy S, Plotkin JB. 2008. The population genetics of dN/dS. PLoS Genet. 4:e1000304.
21. KuoMC, Chou LF, Chang HY. 2008. Evolution of exceptionally large genes in prokaryotes. J Mol Evol. 66:333-349.
22. Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 44:383-397.
23. Logsdon JM Jr, Doolittle WF. 1997. Origin of antifreeze protein genes: a cool tale in molecular evolution. Proc Natl Acad Sci U S A. 94: 3485-3487.
24. Long M. 2001. Evolution of novel genes. Curr Opin Genet Dev. 11: 673-680.
25. Long M, et al. 2003. Origin of new genes: evidence fromexperimental and computational analyses. Genetica 118:171-182.
26. Moore DS, McCabe GP. 2002. Introduction to the practice of statistics. New York: W.H. Freeman.
27. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
28. Nei M, Gojobori T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 3:418-426.
29. Ochman H. 2002. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 18: 335-337.
30. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
31. Ohno S. 1984. Birth of a unique enzyme froman alternative reading frame of the preexisted, internally repetitious coding sequence. Proc Natl Acad Sci U S A. 81:2421-2425.
32. Rancurel C, Khosravi M, Dunker AK, Romero PR, Karlin D. 2009. Overlapping genes produce proteinswith unusual sequence properties and offer insight into de novo protein creation. J Virol. 83: 10719-10736.
33. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
34. Toll-Riera M, et al. 2009. Origin of primate orphan genes: a comparative genomics approach. Mol Biol Evol. 26:603-612.
35. Touchon M, et al. 2009. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoSGenet. 5:e1000344.
36. Wang W, Yu H, Long M. 2004. Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat Genet. 36:523-527.
37. Wang W, et al. 2005. Origin and evolution of new exons in rodents. Genome Res. 15:1258-1264.
38. Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, Field D. 2005. Orphans as taxonomically restricted and ecologically important genes. Microbiology 151:2499-2501.
39. Wu D, et al. 2009. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056-1060.
40. Yin Y, Fischer D. 2006. On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer. BMC Evol Biol. 6:63.
41. Yin Y, Fischer D. 2008. Identification and investigation of ORFans in the viral world. BMC Genom. 9:24.