publication . Article . Other literature type . 2010

Transposases are the most abundant, most ubiquitous genes in nature

Mya Breitbart; Robert Edwards; Ramy K. Aziz;
Open Access
  • Published: 09 Mar 2010
  • Publisher: Oxford University Press (OUP)
Abstract
Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature. The unbiased determination of the most successful genes requires access to sequence data from a wide range of phylogenetic taxa and ecosystems, which has finally become achievable thanks to the deluge of genomic and metagenomic sequences. Here, we analyzed 10 million protein-encoding genes and gene tags in sequenced bacterial, archaeal, eukaryotic and viral genomes and metagenomes, and our analysis demonstrates that genes encoding transposases are the most prevalent genes in nature. The finding that these genes, classically considered as selfish...
Subjects
free text keywords: Survey and Summary, Genetics, Biology, Evolutionary biology, Genome, Housekeeping gene, Minimal genome, Metagenomics, Genomics, Gene, Selfish Genes, Phylogenetic tree
Funded by
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850356
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850206
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
101 references, page 1 of 7

Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. 1859

Huxley, JS. Evolution: The Modern Synthesis. 1942

Dawkins, R. The Selfish Gene. 1976

Edgell, DR, Fast, NM, Doolittle, WF. Selfish DNA: the best defense is a good offense. Curr. Biol.. 1996; 6: 385-388 [OpenAIRE] [PubMed]

Doolittle, WF, Sapienza, C. Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980; 284: 601-603 [OpenAIRE] [PubMed]

Orgel, LE, Crick, FH. Selfish DNA: the ultimate parasite. Nature. 1980; 284: 604-607 [OpenAIRE] [PubMed]

Drummond, DA, Wilke, CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008; 134: 341-352 [OpenAIRE] [PubMed]

Koonin, EV. Darwinian evolution in the light of genomics. Nucleic Acids Res.. 2009; 37: 1011-1034 [OpenAIRE] [PubMed]

Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol.. 2002; 3: REVIEWS0003 [OpenAIRE] [PubMed]

Wu, D, Hugenholtz, P, Mavromatis, K, Pukall, R, Dalin, E, Ivanova, NN, Kunin, V, Goodwin, L, Wu, M, Tindall, BJ. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature. 2009; 462: 1056-1060 [OpenAIRE] [PubMed]

Dhingra, A, Portis, A.R., Daniell, H. Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants. Proc. Natl Acad. Sci. USA. 2004; 101: 6315-6320 [OpenAIRE] [PubMed]

Kristensen, DM, Mushegian, AR, Dolja, VV, Koonin, EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol.. 2010; 18: 11-19 [OpenAIRE] [PubMed]

Overbeek, R, Begley, T, Butler, RM, Choudhuri, JV, Chuang, HY, Cohoon, M, de Crecy-Lagard, V, Diaz, N, Disz, T, Edwards, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res.. 2005; 33: 5691-5702 [OpenAIRE] [PubMed]

Aziz, RK, Bartels, D, Best, AA, DeJongh, M, Disz, T, Edwards, RA, Formsma, K, Gerdes, S, Glass, EM, Kubal, M. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9: 75 [OpenAIRE] [PubMed]

Meyer, F, Paarmann, D, D'Souza, M, Olson, R, Glass, EM, Kubal, M, Paczian, T, Rodriguez, A, Stevens, R, Wilke, A. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9: 386 [OpenAIRE] [PubMed]

101 references, page 1 of 7
Abstract
Genes, like organisms, struggle for existence, and the most successful genes persist and widely disseminate in nature. The unbiased determination of the most successful genes requires access to sequence data from a wide range of phylogenetic taxa and ecosystems, which has finally become achievable thanks to the deluge of genomic and metagenomic sequences. Here, we analyzed 10 million protein-encoding genes and gene tags in sequenced bacterial, archaeal, eukaryotic and viral genomes and metagenomes, and our analysis demonstrates that genes encoding transposases are the most prevalent genes in nature. The finding that these genes, classically considered as selfish...
Subjects
free text keywords: Survey and Summary, Genetics, Biology, Evolutionary biology, Genome, Housekeeping gene, Minimal genome, Metagenomics, Genomics, Gene, Selfish Genes, Phylogenetic tree
Funded by
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850356
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
,
NSF| Collaborative Research: PHANTOME: PHage ANnotation TOols and MEthods
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0850206
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
101 references, page 1 of 7

Darwin, C. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. 1859

Huxley, JS. Evolution: The Modern Synthesis. 1942

Dawkins, R. The Selfish Gene. 1976

Edgell, DR, Fast, NM, Doolittle, WF. Selfish DNA: the best defense is a good offense. Curr. Biol.. 1996; 6: 385-388 [OpenAIRE] [PubMed]

Doolittle, WF, Sapienza, C. Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980; 284: 601-603 [OpenAIRE] [PubMed]

Orgel, LE, Crick, FH. Selfish DNA: the ultimate parasite. Nature. 1980; 284: 604-607 [OpenAIRE] [PubMed]

Drummond, DA, Wilke, CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008; 134: 341-352 [OpenAIRE] [PubMed]

Koonin, EV. Darwinian evolution in the light of genomics. Nucleic Acids Res.. 2009; 37: 1011-1034 [OpenAIRE] [PubMed]

Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol.. 2002; 3: REVIEWS0003 [OpenAIRE] [PubMed]

Wu, D, Hugenholtz, P, Mavromatis, K, Pukall, R, Dalin, E, Ivanova, NN, Kunin, V, Goodwin, L, Wu, M, Tindall, BJ. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature. 2009; 462: 1056-1060 [OpenAIRE] [PubMed]

Dhingra, A, Portis, A.R., Daniell, H. Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants. Proc. Natl Acad. Sci. USA. 2004; 101: 6315-6320 [OpenAIRE] [PubMed]

Kristensen, DM, Mushegian, AR, Dolja, VV, Koonin, EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol.. 2010; 18: 11-19 [OpenAIRE] [PubMed]

Overbeek, R, Begley, T, Butler, RM, Choudhuri, JV, Chuang, HY, Cohoon, M, de Crecy-Lagard, V, Diaz, N, Disz, T, Edwards, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res.. 2005; 33: 5691-5702 [OpenAIRE] [PubMed]

Aziz, RK, Bartels, D, Best, AA, DeJongh, M, Disz, T, Edwards, RA, Formsma, K, Gerdes, S, Glass, EM, Kubal, M. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9: 75 [OpenAIRE] [PubMed]

Meyer, F, Paarmann, D, D'Souza, M, Olson, R, Glass, EM, Kubal, M, Paczian, T, Rodriguez, A, Stevens, R, Wilke, A. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008; 9: 386 [OpenAIRE] [PubMed]

101 references, page 1 of 7
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