Skip to main content
SpringerLink
Log in

The Phenomenon of Evolutionary “De Novo Generation” of Genes

  • REVIEWS
  • Published:
Russian Journal of Developmental Biology Aims and scope Submit manuscript

Abstract

Evolutionary biologists have always been interested in the origin and evolution of new genes. The most obvious mechanisms of their formation are various types of chromosomal and intergenic rearrangements, suggesting the use of existing genes as the source material. The possibility of the origin of a fully functional gene from noncoding DNA, i.e., de novo, was not rejected but it was practically considered as impossible until recently. Nevertheless, in 1996, after analysis of the yeast Saccharomyces cerevisiae genome, the first experimental evidence of the possibility of de novo gene formation was obtained. Ten years later, genes that do not have homologs, presumably having originated de novo, were found in Drosophila. The relatively high probability of the occurrence of genes de novo, estimated in bioinformatics studies, raised the interest in this topic and made the search for genes of this type relevant. Recently, the number of works devoted to the problem of the emergence of de novo genes in different organisms, including humans, is constantly growing, demystifying this phenomenon. Nevertheless, there are still many questions that require theoretical and practical research. This review is devoted to the problem of finding and characterizing genes that have arisen de novo, as well as to the proposed mechanisms of their occurrence.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

REFERENCES

  1. Abdulrehman, D., Monteiro, P.T., Teixeira, M.C., et al., YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface, Nucleic Acids Res., 2011, vol. 39, pp. D136–D140.

    Article  CAS  PubMed  Google Scholar 

  2. Abrusán, G., Integration of new genes into cellular networks, and their structural maturation, Genetics, 2013, vol. 195, no. 4, pp. 1407–1417.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Altschul, S.F., Gish, W., Miller, W., et al., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410.

    Article  CAS  PubMed  Google Scholar 

  4. Altschul, S.F., Madden, T.L., Schaffer, A.A., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, vol. 25, no. 17, pp. 3389–3402.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Andersson, D.I., Jerlström-Hultqvist, J., and Nasvall, J., Evolution of new functions de novo and from preexisting genes, Cold Spring Harb. Perspect. Biol., 2015, vol. 7, no. 6, art. a017996.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Ángyán, A.F., Perczel, A., and Gáspári, Z., Estimating intrinsic structural preferences of de novo emerging random-sequence proteins: is aggregation the main bottleneck?, FEBS Lett., 2012, vol. 586, no. 16, pp. 2468–2472.

    Article  PubMed  Google Scholar 

  7. Basile, W., Sachenkova, O., Light, S., et al., High GC content causes orphan proteins to be intrinsically disordered, PLoS Comp. Biol., 2017, vol. 13, no. 3, art. e1005375.

    Article  Google Scholar 

  8. Begun, D.J., Lindfors, H.A., Thompson, M.E., et al., Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags, Genetics, 2006, vol. 172, pp. 1675–1681.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Begun, D.J., Lindfors, H.A., Kern, A.D., et al., Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade, Genetics, 2007, vol. 176, pp. 1131–1137.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bekpen, C., Xie, C., and Tautz, D., Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences, BMC Evol. Biol., 2018, vol. 18.

  11. Bitard-Feildel, T., Heberlein, M., Bornberg-Bauer, E., et al., Detection of orphan domains in Drosophila using “hydrophobic cluster analysis,” Biochimie, 2015, vol. 119, pp. 244–253.

    Article  CAS  PubMed  Google Scholar 

  12. Cai, J., Zhao, R., Jiang, H., et al., De novo origination of a new protein-coding gene in Saccharomyces cerevisiae, Genetics, 2008, vol. 179, no. 1, pp. 487–496.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Carelli, F.N., Liechti, A., Halbert, J., et al., Repurposing of promoters and enhancers during mammalian evolution, Nat. Commun., 2018, vol. 9, no. 1, p. 4066.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Carvunis, A.-R., Rolland, T., Wapinski, I., et al., Proto-genes and de novo gene birth, Nature, 2012, vol. 487, pp. 370–374.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Casola, C., From de novo to “de nono:” the majority of novel protein-coding genes identified with phylostratigraphy are old genes or recent duplicates, Genome Biol. Evol., 2018, vol. 10, no. 11, pp. 2906–2918.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Chen, S., Zhang, Y.E., and Long, M., New genes in Drosophila quickly become essential, Science, 2010, vol. 330, pp. 1682–1685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Chen, S., Krinsky, B.H., and Long, M., New genes as drivers of phenotypic evolution, Nat. Rev. Genet., 2013, vol. 14, no. 9, pp. 645–660.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Clark, N.L., Aagaard, J.E., and Swanson, W.J., Evolution of reproductive proteins from animals and plants, Reproduction, 2006, vol. 131, no. 1, pp. 11–22.

    Article  CAS  PubMed  Google Scholar 

  19. Clark, M.B., Amaral, P.P., Schlesinger, F.J., et al., The reality of pervasive transcription, PLoS Biol., 2011, vol. 9, no. 7, art. e1000625.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Costanzo, M., Baryshnikova, A., Bellay, J., et al., The genetic landscape of a cell, Science, 2010, vol. 327, no. 5964, pp. 425–431.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Domazet-Lošo, T. and Tautz, D., A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns, Nature, 2010, vol. 468, no. 7325, pp. 815–818.

    Article  PubMed  Google Scholar 

  22. Domazet-Lošo, T., Brajković, J., and Tautz, D., A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages, Trends Genet., 2007, vol. 23, no. 11, pp. 533–539.

    Article  PubMed  Google Scholar 

  23. Donoghue, M.T., Keshavaiah, C., Swamidatta, S.H., et al., Evolutionary origins of brassicaceae specific genes in Arabidopsis thaliana, BMC Evol. Biol., 2011, vol. 11, no. 1, p. 47.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Doolittle, W.F., Brunet, T.D.P., Linquist, S., et al., Distinguishing between “function” and “effect” in genome biology, Genome Biol. Evol., 2014, vol. 6, no. 5, pp. 1234–1237.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Dowling, D., Schmitz, J.F., and Bornberg-Bauer, E., Stochastic gain and loss of novel transcribed open reading frames in the human lineage, Genome Biol. Evol., 2020, vol. 12, no. 11, pp. 2183–2195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Dujon, B., The yeast genome project: what did we learn?, Trends Genet., 1996, vol. 12, no. 7, pp. 263–270.

    Article  CAS  PubMed  Google Scholar 

  27. Ekman, D. and Elofsson, A., Identifying and quantifying orphan protein sequences in fungi, J. Mol. Biol., 2010, vol. 396, no. 2, pp. 396–405.

    Article  CAS  PubMed  Google Scholar 

  28. Elhaik, E., Sabath, N., and Graur, D., The “inverse relationship between evolutionary rate and age of mammalian genes” is an artifact of increased genetic distance with rate of evolution and time of divergence, Mol. Biol. Evol., 2006, vol. 23, no. 1, pp. 1–3.

    Article  CAS  PubMed  Google Scholar 

  29. Espinar, L., Tamarit, M.A.S., Domingo, J., and Carey, L.B., Promoter architecture determines cotranslational regulation of mRNA, Genome Res., 2018, vol. 28, no. 4, pp. 509–518.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gehrmann, T. and Reinders, M.J.T., Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level, Bioinformatics, 2015, vol. 31, no. 21, pp. 3437–3444.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Ghiurcuta, C.G. and Moret, B.M.E., Evaluating synteny for improved comparative studies, Bioinformatics, 2014, vol. 30, no. 12, pp. i9–i18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Grasse, P.-P., Evolution of Living Organisms, London: Academic, 1977.

    Google Scholar 

  33. Guerzoni, D. and McLysaght, A., De novo genes arise at a slow but steady rate along the primate lineage and have been subject to incomplete lineage sorting, Genome Biol. Evol., 2016, vol. 8, no. 4, pp. 1222–1232.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Guo, W.-J., Li, P., Ling, J., et al., Significant comparative characteristics between orphan and nonorphan genes in the rice (Oryza sativa L.) genome, Comp. Func. Genomics, 2007, vol. 2007, p. 21676.

    Google Scholar 

  35. Haberle, V. and Stark, A., Eukaryotic core promoters and the functional basis of transcription initiation, Nat. Rev. Mol., 2018, vol. 19, no. 10, pp. 621–637.

    Article  CAS  Google Scholar 

  36. Haldane, J.B.S., The part played by recurrent mutation in evolution, Am. Nat., 1933, vol. 67, no. 708, pp. 5–19.

    Article  Google Scholar 

  37. He, B., Chen, C., Teng, L., et al., Global view of enhancer-promoter interactome in human cells, Proc. Natl. Acad. Sci. U. S. A., 2014, vol. 111, no. 21, pp. E2191–E2199.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Heames, B., Schmitz, J., and Bornberg-Bauer, E., A continuum of evolving de novo genes drives protein-coding novelty in Drosophila, J. Mol. Evol., 2020, vol. 88, no. 4, pp. 382–398.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Heinen, T.J.A.J., Staubach, F., Häming, D., et al., Emergence of a new gene from an intergenic region, Curr. Biol., 2009, vol. 19, no. 18, pp. 1527–1531.

    Article  CAS  PubMed  Google Scholar 

  40. Husnik, F. and McCutcheon, J.P., Functional horizontal gene transfer from bacteria to eukaryotes, Nat. Rev. Microbiol., 2018, vol. 16, no. 2, pp. 67–79.

    Article  CAS  PubMed  Google Scholar 

  41. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R.S., et al., Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling, Science, 2009, vol. 324, no. 5924, pp. 218–223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ingolia, N.T., Brar, G.A., Stern-Ginossar, N., et al., Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes, Cell Rep., 2014, vol. 8, no. 5, pp. 1365–1379.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Jacob, F., Evolution and tinkering, Science, 1977, vol. 196, pp. 1161–1166.

    Article  CAS  PubMed  Google Scholar 

  44. Kaessmann, H., Origins, evolution, and phenotypic impact of new genes, Genome Res., 2010, vol. 20, no. 10, pp. 1313–1326.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kang, M., Ren, M., Li, Y., Fu, Y., et al., Exosome-mediated transfer of lncRNA PART1 induces gefitinib resistance in esophageal squamous cell carcinoma via functioning as a competing endogenous RNA, J. Exp. Clin. Cancer Res., 2018, vol. 37.

  46. Kapranov, P., Willingham, A.T., and Gingeras, T.R., Genome-wide transcription and the implications for genomic organization, Nat. Rev. Genet., 2007, vol. 8, no. 6, pp. 413–423.

    Article  CAS  PubMed  Google Scholar 

  47. Kellis, M., Wold, B., Snyder, M.P., et al., Defining functional DNA elements in the human genome, Proc. Natl. Acad. Sci. U. S. A., 2014, vol. 111, no. 17, pp. 6131–6138.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kim, T.-K., Hemberg, M., Gray, J.M., et al., Widespread transcription at neuronal activity-regulated enhancers, Nature, 2010, vol. 465, pp. 182–187.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Knowles, D.G. and McLysaght, A., Recent de novo origin of human protein-coding genes, Genome Res., 2009, vol. 19, no. 10, pp. 1752–1759.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Kozlov, A.P., Expression of evolutionarily novel genes in tumors, Infect. Agents Cancer, 2016, vol. 11, no. 34.

  51. Kröger, H., Donner, I., and Skiello, G., Influence of a new virostatic compound on the induction of enzymes in rat liver, Arzneimittelforschung, 1975, vol. 25, no. 9, pp. 1426–1429.

    PubMed  Google Scholar 

  52. Lercher, M.J., Urrutia, A.O., Pavlíček, A., et al., A unification of mosaic structures in the human genome, Hum. Mol. Genet., 2003, vol. 12, no. 19, pp. 2411–2415.

    Article  CAS  PubMed  Google Scholar 

  53. Levine, M.T., Jones, C.D., Kern, A.D., et al., Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression, Proc. Natl. Acad. Sci. U. S. A., 2006, vol. 103, no. 26, pp. 9935–9939.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Li, L., Foster, C.M., Gan, Q., et al., Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves, Plant J., 2009, vol. 58, no. 3, pp. 485–498.

    Article  CAS  PubMed  Google Scholar 

  55. Li, D., Dong, Y., Jiang, Y., et al., A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand, Cell Res., 2010, vol. 20, no. 4, pp. 408–420.

    Article  CAS  PubMed  Google Scholar 

  56. Li, C.-Y., Zhang, Y., Wang, Z., et al., A human-specific de novo protein-coding gene associated with human brain functions, PLoS Comput. Biol., 2010, vol. 6, no. 3, art. e1000734.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Li, D., Yan, Z., Lu, L., et al., Pleiotropy of the de novo-originated gene MDF1, Sci. Rep., 2014, vol. 4, no. 1, p. 7280.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Li, W., Notani, D., and Rosenfeld, M.G., Enhancers as non-coding RNA transcription units: recent insights and future perspectives, Nat. Rev. Genet., 2016, vol. 17, no. 4, pp. 207–223.

    Article  CAS  PubMed  Google Scholar 

  59. Li, Z.-W., Chen, X., Wu, Q., et al., On the origin of de novo genes in Arabidopsis thaliana populations, Genome Biol. Evol., 2016, vol. 8, no. 7, pp. 2190–2202.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lin, B., White, J.T., Ferguson, C., et al., PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12, Cancer Res., 2000, vol. 60, no. 4, pp. 858–863.

    CAS  PubMed  Google Scholar 

  61. Liu, D., Hunt, M., and Tsai, I.J., Inferring synteny between genome assemblies: a systematic evaluation, BMC Bioinformatics, 2018, vol. 19, no. 1, p. 26.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Luis Villanueva-Cañas, J., Ruiz-Orera, J., Agea, M.I., et al., New genes and functional innovation in mammals, Genome Biol. Evol., 2017, vol. 9, no. 7, pp. 1886–1900.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Majic, P. and Payne, J.L., Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks, Mol. Biol. Evol., 2020, vol. 37, no. 4, pp. 1165–1178.

    Article  CAS  PubMed  Google Scholar 

  64. McLysaght, A. and Guerzoni, D., New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation, Philos. Trans. R. Soc., B, 2015, vol. 370, no. 1678, p. 20140332.

  65. McLysaght, A. and Hurst, L.D., Open questions in the study of de novo genes: what, how and why, Nat. Rev. Genet., 2016, vol. 17, no. 9, pp. 567–578.

    Article  CAS  PubMed  Google Scholar 

  66. Moyers, B.A. and Zhang, J., Phylostratigraphic bias creates spurious patterns of genome evolution, Mol. Biol. Evol., 2015, vol. 32, no. 1, pp. 258–267.

    Article  CAS  PubMed  Google Scholar 

  67. Moyers, B.A. and Zhang, J., Evaluating phylostratigraphic evidence for widespread de novo gene birth in genome evolution, Mol. Biol. Evol., 2016, vol. 33, no. 5, pp. 1245–1256.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Mukherjee, S., Panda, A., and Ghosh, T.C., Elucidating evolutionary features and functional implications of orphan genes in leishmania major, Infect. Genet. Evol., 2015, vol. 32, pp. 330–337.

    Article  CAS  PubMed  Google Scholar 

  69. Muller, H.J., The origination of chromatin deficiencies as minute deletions subject to insertion elsewhere, Genetics, 1935, vol. 17, no. 3, pp. 237–252.

    Google Scholar 

  70. Murphy, D.N. and McLysaght, A., De novo origin of protein-coding genes in murine rodents, PLoS One, 2012, vol. 7, no. 11, art. e48650.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Neme, R. and Tautz, D., Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution, BMC Genomics, 2013, vol. 14, no. 1, p. 117.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Neme, R. and Tautz, D., Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence, eLife, 2016, vol. 5, art. e09977.

    Article  PubMed  PubMed Central  Google Scholar 

  73. Nielly-Thibault, L. and Landry, C.R., Differences between the raw material and the products of de novo gene birth can result from mutational biases, Genetics, 2019, vol. 212, no. 4, pp. 1353–1366.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Nishida, H., Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae, Biosci. Biotechnol. Biochem., 2006, vol. 70, no. 11, pp. 2646–2652.

    Article  CAS  PubMed  Google Scholar 

  75. Ohno, S., Evolution by Gene Duplication, Berlin: Springer-Verlag, 1970.

    Book  Google Scholar 

  76. Ohno, S., Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence, Proc. Natl. Acad. Sci. U. S. A., 1984, vol. 81, no. 8, pp. 2421–2425.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Ohno, S., Wolf, U., and Atkin, N.B., Evolution from fish to mammals by gene duplication, Hereditas, 1968, vol. 59, no. 1, pp. 169–187.

    Article  CAS  PubMed  Google Scholar 

  78. Oss, S.B.V. and Carvunis, A.-R., De novo gene birth, PLoS Genet., 2019, vol. 15, no. 5, art. e1008160.

    Article  PubMed  PubMed Central  Google Scholar 

  79. Palmieri, N., Kosiol., C., and Schlötterer, C., The life cycle of Drosophila orphan genes, eLife, 2014, vol. 3, art. e01311.

    Article  PubMed  PubMed Central  Google Scholar 

  80. Papamichos, S.I., Margaritis, D., and Kotsianidis, I., Adaptive evolution coupled with retrotransposon exaptation allowed for the generation of a human-protein-specific coding gene that promotes cancer cell proliferation and metastasis in both haematological malignancies and solid tumours: the extraordinary case of MYEOV gene, Science (Washington, D.C.), 2015, vol. 2015, p. 984706.

    Book  Google Scholar 

  81. Pertea, M., Shumate, A., Pertea, G., et al., Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise, bioRxiv, 2018, p. 332825.

  82. Potter, S.C., Luciani, A., Eddy, S.R., et al., HMMER web server: 2018 update, Nucleic Acids Res., 2018, vol. 46, pp. W200–W204.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Rancurel, C., Khosravi, M., Dunker, A.K., et al., Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation, J. Virol., 2009, vol. 83, pp. 10719–10736.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Ranz, J.M., Casals, F., and Ruiz, A., How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila, Genome Res., 2001, vol. 11, pp. 230–239.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Reinhardt, J.A., Wanjiru, B.M., Brant, A.T., et al., De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences, PLoS Genet., 2013, vol. 9, р. e1003860.

  86. Ruiz-Orera, J., Messeguer, X., Subirana, J.A., et al., Long non-coding RNAs as a source of new peptides, eLife, 2014, vol. 3, art. e1003860.

    Article  Google Scholar 

  87. Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., et al., Origins of de novo genes in human and chimpanzee, PLoS Genet., 2015, vol. 11, art. e1005721.

    Article  PubMed  PubMed Central  Google Scholar 

  88. Samusik, N., Krukovskaya, L., Meln, I., Shilov, E., and Kozlov, A.P., PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer, PLoS One, 2013, vol. 8, no. 2, art. e56162.

  89. De Santa, F., Barozzi, I., Mietton, F., et al., A large fraction of extragenic RNA pol II transcription sites overlap enhancers, PLoS Biol., 2010, vol. 8, no. 5, р. e1000384.

  90. Schlötterer, C., Genes from scratch—the evolutionary fate of de novo genes, Trends Genet., 2015, vol. 31, no. 4, pp. 215–219.

    Article  PubMed  PubMed Central  Google Scholar 

  91. Schmidt, E.E., Transcriptional promiscuity in testes, Curr. Biol., 1996, vol. 6, no. 7, pp. 768–769.

    Article  CAS  PubMed  Google Scholar 

  92. Schmitz, J.F., Ullrich, K.K., and Bornberg-Bauer, E., Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover, Nat. Ecol. Evol., 2018, vol. 2, no. 10, pp. 1626–1632.

    Article  PubMed  Google Scholar 

  93. Schmitz, J.F., Chain, F.J.J., and Bornberg-Bauer, E., Evolution of novel genes in three-spanned stickleback populations, Heredity, 2020, vol. 125, pp. 50–59.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Stark, C., Breitkreutz, B.-J., Chatr-aryamontri, A., et al., The bioGRID interaction database: 2011 update, Nucleic Acids Res., 2011, vol. 39, pp. D698–D704.

    Article  CAS  PubMed  Google Scholar 

  95. Swanson, W.J. and Vacquier, V.D., The rapid evolution of reproductive proteins, Nat. Rev. Genet., 2002, vol. 3, no. 2, pp. 137–144.

    Article  CAS  PubMed  Google Scholar 

  96. Tautz, D. and Domazet-Lošo, T., The evolutionary origin of orphan genes, Nat. Rev. Genet., 2011, vol. 12, no. 10, pp. 692–702.

    Article  CAS  PubMed  Google Scholar 

  97. Toll-Riera, M., Bosch, N., Bellora, N., et al., Origin of primate orphan genes: a comparative genomics approach, Mol. Biol. Evol., 2009, vol. 26, no. 3, pp. 603–612.

    Article  CAS  PubMed  Google Scholar 

  98. Tretyachenko, V., Vymětal, J., Bednárová, L., et al., Random protein sequences can form defined secondary structures and are well-tolerated in vivo, Sci. Rep., 2017, vol. 7, no. 1, p. 15449.

    Article  PubMed  PubMed Central  Google Scholar 

  99. Vakirlis, N., Hebert, A.S., Opulente, D.A., et al., Molecular portrait of de novo genes in yeasts, Mol. Biol. Evol., 2018, vol. 35, no. 3, pp. 631–645.

    Article  CAS  PubMed  Google Scholar 

  100. Vakirlis, N., Carvunis, A.-R., and McLysaght, A., Synteny-based analyses indicate that sequence divergence is not the main source of orphan gene eLife, 2020, vol. 9, art. e53500.

    Article  PubMed  PubMed Central  Google Scholar 

  101. Wang, J., Zhuang, J., Iyer, S., et al., Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Genome Res., 2012, vol. 22, no. 9, pp. 1798–1812.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Weisman, C.M., Murray, A.W., and Eddy, S.R., Many, but not all, lineage-specific genes can be explained by homology detection failure, PLoS Biol., 2020, vol. 18, no. 11, art. e3000862.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Werner, M.S., Sieriebriennikov, B., Prabh, N., et al., Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation, Genome Res., 2018, vol. 28, no. 11, pp. 1675–1687.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Wilson, B.A. and Masel, J., Putatively noncoding transcripts show extensive association with ribosomes, Genome Biol. Evol., 2011, vol. 3, pp. 1245–1252.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Wilson, B.A., Foy, S.G., Neme, R., et al., Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth, Nat. Ecol. Evol., 2017, vol. 1, no. 6, p. 0146.

  106. Wu, D.-D., Irwin, D.M., and Zhang, Y.-P., De novo origin of human protein-coding genes, PLoS Genet., 2011, vol. 7, no. 11, art. e1002379.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Wu, X. and Sharp, P.A., Divergent transcription: a driving force for new gene origination?, Cell, 2013, vol. 155, no. 5, pp. 990–996.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Xie, C., Bekpen, C., Kunzel, S., et al., Studying the dawn of de novo gene emergence in mice reveals fast integration of new genes into functional networks, bioRxiv, 2019, p. 510214.

  109. Zhang, J.-Y. and Zhou, Q., On the regulatory evolution of new genes throughout their life history, Mol. Biol. Evol., 2019, vol. 36, no. 1, pp. 15–27.

    Article  CAS  PubMed  Google Scholar 

  110. Zhang, Y.E., Landback, P., Vibranovski, M.D., and Long, M., Accelerated recruitment of new brain development genes into the human genome, PLoS Biol., 2011, vol. 9, no. 10, art. e1001179.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Zhang, L., Ren, Y., Yang, T., et al., Rapid evolution of protein diversity by de novo origination in Oryza, Nat. Ecol., 2019, vol. 3, no. 4, pp. 679–690.

    Article  Google Scholar 

  112. Zhang, W., Gao, Y., Long, M., and Shen, B., Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans, Sci. China Life Sci., 2019, vol. 62, pp. 579–593.

    Article  PubMed  Google Scholar 

  113. Zhao, L., Saelao, P., Jones, C.D., et al., Origin and spread of de novo genes in Drosophila melanogaster populations, Science, 2014, vol. 343, no. 6172, pp. 769–772.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Zhou, Q., Zhang, G., Zhang, Y., et al., On the origin of new genes in Drosophila, Genet. Res., 2008, vol. 18, no. 9, pp. 1446–1455.

    CAS  Google Scholar 

  115. Zhuang, X., Yang, C., Murphy, K.R., et al., Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids, Proc. Natl. Acad. Sci. U. S. A., 2019, vol. 116, no. 10, pp. 4400–4405.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

The work was performed with the financial support of the Russian Foundation for Basic Research (project no. 20-04-00272а) and within the framework of State Assignment of Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 2021, no. 0088-2021-0007 “Molecular Genetic Mechanisms of Regulation of Cell Differentiation and Morphogenesis.”

Author information

Authors and Affiliations

  1. Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334, Moscow, Russia

    R. O. Cherezov, Ju. E. Vorontsova & O. B. Simonova

Authors
  1. R. O. Cherezov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ju. E. Vorontsova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. O. B. Simonova
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Cherezov R.O. analyzed international literature and wrote the main text of the article. Vorontsova Ju.E. participated in the editing of the text of the article and discussion about it. Simonova O.B. initiated the writing of this review and edited the text.

Corresponding author

Correspondence to O. B. Simonova.

Ethics declarations

COMPLIANCE WITH ETHICAL STANDARDS

The authors declare that they have no conflicts of interests. This paper does not contain any studies involving animals or human participants performed by the authors.

GLOSSARY

Outgroup is a group that is phylogenetically distant from the studied group of sister taxa, originating from a common ancestor, serves as a comparison point for the studied group of taxa.

ncRNA is a noncoding RNA.

Orthologs are homologous genes in different types of organisms, that is, genes that have a common evolutionary origin, a similar structure, and perform a similar function.

ORF is an Open Reading Frame, a section of the gene encoding a protein.

Synteny is the location of genetic loci on the same chromosome, regardless of whether they are linked according to the analysis of linked inheritance.

Synteny blocks are conservative sections of the compared genomes in which the order of arrangement of the studied elements is preserved.

Hidden Markov models are statistical models that are used for recognizing genes, modeling their structure, modeling sequence families, etc.

BLAST (Basic Local Alignment Search Tool) is software that allows you to find areas of similarity between sequences of proteins or nucleotides.

CS-BLAST (Context-Specific BLAST) is software that extends the sensitivity of BLAST to search for similar amino acid sequences.

PSI-BLAST (Position-Specific Iterated BLAST) is a software that extends the capabilities of BLAST to search for similar amino acid sequences, allowing the user to find drastically phylogenetically distant homologous proteins.

k-mers are parts of nucleotide sequences of a certain length (k).

Additional information

Translated by A. Ermakov

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cherezov, R.O., Vorontsova, J.E. & Simonova, O.B. The Phenomenon of Evolutionary “De Novo Generation” of Genes. Russ J Dev Biol 52, 390–400 (2021). https://doi.org/10.1134/S1062360421060035

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1062360421060035

Keywords:

Search

Navigation