This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.
1. Wichmann S, Ardern Z. Optimality in the standard genetic code is robust with respect to comparison code sets. Bio Systems. 2019 November;2019;185:104023. doi:10.10.1016/j.biosystems.2019.104023WichmannSArdernZ.Optimality in the standard genetic code is robust with respect to comparison code sets..2019November;2019;185:104023. doi:10.1016/j.biosys-tems.2019.104023Open DOISearch in Google Scholar
2. Barrell BG, Air GM, Hutchison CA 3rd. Overlapping genes in bacteriophage phiX174. Nature. 1976;264(5581):34-41. doi:10.1038/264034a0BarrellBGAirGMHutchisonCA3rd.Overlapping genes in bacteriophage phiX174..1976;264(5581):34-41. doi:10.1038/264034a0Open DOISearch in Google Scholar
3. Firth AE, Brierley I. Non-canonical translation in RNA viruses. J Gen Virol. 2012;93(Pt 7):1385-1409. doi:10.1099/vir.0.042499-0FirthAEBrierleyI.Non-canonical translation in RNA viruses..2012;93(Pt 7):1385-1409. doi:10.1099/vir.0.042499-0Open DOISearch in Google Scholar
4. Cassan E, Arigon-Chifolleau AM, Mesnard JM, Gross A, Gascuel O. Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic. Proc Natl Acad Sci USA. 2016;113(41):11537-11542. doi:10.1073/pnas.1605739113CassanEArigon-ChifolleauAMMesnardJMGrossAGascuelO.Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic..2016;113(41):11537-11542. doi:10.1073/pnas.1605739113Open DOISearch in Google Scholar
5. Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, Pazgier M, Ray K, Latinovic OS, Romerio F. The HIV-1 antisense protein ASP is a transmembrane protein of the cell surface and an integral protein of the viral envelope. J Virol. 2019;93(21):e00574-19. doi:10.1128/JVI.00574-19AfframYZapataJCGholizadehZTolbertWDZhouWIglesias-UsselMDPazgierMRayKLatinovicOSRomerioF.The HIV-1 antisense protein ASP is a transmembrane protein of the cell surface and an integral protein of the viral envelope..2019;93(21):e00574-19. doi:10.1128/JVI.00574-19Open DOISearch in Google Scholar
6. Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo CH, Ludwig C, Kolokotronis SO, Wei X. Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic. Elife. 2020;9:e59633. doi:10.7554/eLife.59633NelsonCWArdernZGoldbergTLMengCKuoCHLudwigCKolokotronisSOWeiX.Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic..2020;9:e59633. doi:10.7554/eLife.59633Open DOISearch in Google Scholar
7. Firth AE. A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a. J Gen Virol. 2020;101(10):1085-1089. doi:10.1099/jgv.0.001469FirthAE.A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a..2020;101(10):1085-1089. doi:10.1099/jgv.0.001469Open DOISearch in Google Scholar
8. Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K. Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection. iScience. 2022;25(2):103844. doi:10.1016/j.isci.2022.103844KreitmeierMArdernZAbeleMLudwigCSchererSNeuhausK.Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection..2022;25(2):103844. doi:10.1016/j.isci.2022.103844Open DOISearch in Google Scholar
9. Zehentner B, Ardern Z, Kreitmeier M, Scherer S, Neuhaus K. Evidence for numerous embedded antisense overlapping genes in diverse E. coli strains. bioRxiv. 2020. Available from: https://doi.org/10.1101/2020.11.18.388249ZehentnerBArdernZKreitmeierMSchererSNeuhausK.Evidence for numerous embedded antisense overlapping genes in diverse E. coli strains..2020. Available from: https://doi.org/10.1101/2020.11.18.388249Open DOISearch in Google Scholar
10. Ardern Z, Neuhaus K, Scherer S. Are Antisense Proteins in Prokaryotes Functional?. Front Mol Biosci. 2020;7:187. doi:10.3389/fmolb.2020.00187ArdernZNeuhausKSchererS.Are Antisense Proteins in Prokaryotes Functional?..2020;7:187. doi:10.3389/fmolb.2020.00187Open DOISearch in Google Scholar
11. Meydan S, Vázquez-Laslop N, Mankin Alexander S. Genes within genes in bacterial genomes. Microbiology Spectrum. 2018;6(4). Available from: https://doi.org/10.1128/microbiolspec.RWR-0020-2018MeydanSVázquez-LaslopNMankin AlexanderS.Genes within genes in bacterial genomes..2018;6(4). Available from: https://doi.org/10.1128/microbiolspec.RWR-0020-2018Open DOISearch in Google Scholar
12. Hücker SM, Vanderhaeghen S, Abellan-Schneyder I, Scherer S, Neuhaus K. The novel anaerobiosis-responsive overlapping gene ano is overlapping antisense to the annotated gene ECs2385 of Escherichia coli O157:H7 Sakai. Front Microbiol. 2018;9:931. doi:10.3389/fmicb.2018.00931HückerSMVanderhaeghenSAbellan-SchneyderISchererSNeuhausK.The novel anaerobiosis-responsive overlapping gene ano is overlapping antisense to the annotated gene ECs2385 of Escherichia coli O157:H7 Sakai..2018;9:931. doi:10.3389/fmicb.2018.00931Open DOISearch in Google Scholar
13. Vanderhaeghen S, Zehentner B, Scherer S, Neuhaus K, Ardern Z. The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Sci Rep. 2018;8(1):17875. doi:10.1038/s41598-018-35756-yVanderhaeghenSZehentnerBSchererSNeuhausKArdernZ.The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase..2018;8(1):17875. doi:10.1038/s41598-018-35756-yOpen DOISearch in Google Scholar
14. Gelsinger DR, Dallon E, Reddy R, Mohammad F, Buskirk AR, DiRuggiero J. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res. 2020;48(10):5201-5216. doi:10.1093/nar/gkaa304GelsingerDRDallonEReddyRMohammadFBuskirkARDiRuggieroJ.Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution..2020;48(10):5201-5216. doi:10.1093/nar/gkaa304Open DOISearch in Google Scholar
15. Loughran G, Zhdanov AV, Mikhaylova MS, Andreev DE. Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF. 2020;117(40):24936-24946. Available from: https://doi.org/10.1073/pnas.2001433117LoughranGZhdanovAVMikhaylovaMSAndreevDE..2020;117(40):24936-24946. Available from: https://doi.org/10.1073/pnas.2001433117Open DOISearch in Google Scholar
16. Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet. 2020;21(1):25. doi:10.1186/s12863-020-0828-7KhanYAJungreisIWrightJCMudgeJMChoudharyJSFirthAEKellisM.Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon..2020;21(1):25. doi:10.1186/s12863-020-0828-7Open DOISearch in Google Scholar
17. Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Gonzalez JM, Magrane M, Martinez T, Schulz JF, Yang YT, Alba MM, et al. A community-driven roadmap to advance research on translated open reading frames detected by Ribo-Seq. bioRxiv. 2021. Available from: https://doi.org/10.1101/2021.06.10.447896MudgeJMRuiz-OreraJPrensnerJRBrunetMAGonzalezJMMagraneMMartinezTSchulzJFYangYTAlbaMM.A community-driven roadmap to advance research on translated open reading frames detected by Ribo-Seq..2021. Available from: https://doi.org/10.1101/2021.06.10.447896Open DOISearch in Google Scholar
18. Cao X, Khitun A, Luo Y, Na Z, Phoodokmai T, Sappakhaw K, Olatunji E, Uttamapinant C, Slavoff SA. Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24. Nat Commun. 2021;12(1):508. doi:10.1038/s41467-020-20841-6CaoXKhitunALuoYNaZPhoodokmaiTSappakhawKOlatunjiEUttamapinantCSlavoffSA.Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24..2021;12(1):508. doi:10.1038/s41467-020-20841-6Open DOISearch in Google Scholar
19. Wright BW, Yi Z, Weissman JS, Chen J. The dark proteome: translation from noncanonical open reading frames. Trends Cell Biol. 2022;32(3):243-258. doi:10.1016/j.tcb.2021.10.010WrightBWYiZWeissmanJSChenJ.The dark proteome: translation from noncanonical open reading frames..2022;32(3):243-258. doi:10.1016/j.tcb.2021.10.010Open DOISearch in Google Scholar
20. Szekely M. Triple overlapping genes. Nature. 1978;272(5653): 492.SzekelyM.Triple overlapping genes..1978;272(5653):492.Search in Google Scholar
21. Siegel AF, Fitch WM. Degeneracy when DNA codes for overlapping genes. Mathematical Biosciences. 1980;49(1):1-16. Available from: https://doi.org/10.1016/0025-5564(80)90107-8SiegelAFFitchWM.Degeneracy when DNA codes for overlapping genes..1980;49(1):1-16. Available from: https://doi.org/10.1016/0025-5564(80)90107-8Open DOISearch in Google Scholar
22. Smith TF, Waterman MS. Overlapping genes and information theory. J Theoret Biol. 1981;91(2):379-380.SmithTFWatermanMS.Overlapping genes and information theory..1981;91(2):379-380.Search in Google Scholar
23. Yockey HP. Rebuttal of ‘overlapping genes and information theory.’ J Theoret Biol. 1981;91(2):381-382.YockeyHP.Rebuttal of ‘overlapping genes and information theory.’.1981;91(2):381-382.Search in Google Scholar
24. Miyata T, Yasunaga T. Evolution of overlapping genes. Nature. 1978;272(5653):532-535.MiyataTYasunagaT.Evolution of overlapping genes..1978;272(5653):532-535.Search in Google Scholar
25. Yockey HP. Do overlapping genes violate molecular biology and the theory of evolution? J Theoret Biol. 1979;80(1):21-26.YockeyHP.Do overlapping genes violate molecular biology and the theory of evolution?.1979;80(1):21-26.Search in Google Scholar
26. Kolata GB. Overlapping genes: more than anomalies? Science. 1977;196(4295):1187-1188.KolataGB.Overlapping genes: more than anomalies?.1977;196(4295):1187-1188.Search in Google Scholar
27. Wright BW, Molloy MP, Jaschke PR. Overlapping genes in natural and engineered genomes. Nat Rev Genet. 2022;23(3): 154-168. doi:10.1038/s41576-021-00417-wWrightBWMolloyMPJaschkePR.Overlapping genes in natural and engineered genomes..2022;23(3):154-168. doi:10.1038/s41576-021-00417-wOpen DOISearch in Google Scholar
28. Brandes N, Linial M. Gene overlapping and size constraints in the viral world. Biol Direct. 2016 May;11:26.BrandesNLinialM.Gene overlapping and size constraints in the viral world..2016May;11:26.Search in Google Scholar
29. Vakirlis N, Carvunis AR, McLysaght A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. Elife. 2020;9:e53500. doi:10.7554/eLife.53500VakirlisNCarvunisARMcLysaghtA.Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes..2020;9:e53500. doi:10.7554/eLife.53500Open DOISearch in Google Scholar
30. Keese PK, Gibbs A. Origins of genes: “big bang” or continuous creation?. Proc Natl Acad Sci USA. 1992;89(20):9489-9493. doi:10.1073/pnas.89.20.9489KeesePKGibbsA.Origins of genes: “big bang” or continuous creation?..1992;89(20):9489-9493.doi:10.1073/pnas.89.20.9489Open DOISearch in Google Scholar
31. Ohno S. Evolution by gene duplication. Berlin: Springer; 1970.OhnoS..Berlin:Springer;1970.Search in Google Scholar
32. Carter CW. Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins. Cur Opin Struct Biol. 2021;68:142-148.CarterCW.Simultaneous codon usage, the origin of the proteome, and the emergence of de-novo proteins..2021;68:142-148.Search in Google Scholar
33. Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodeled gene families in the escherichia coli pangenome. Mol Biol Evol. 2022;39(1):msab329. Available from: https://doi.org/10.1093/molbev/msab329WatsonAKLopezPBaptesteE.Hundreds of out-of-frame remodeled gene families in the escherichia coli pangenome..2022;39(1):msab329. Available from: https://doi.org/10.1093/molbev/msab329Open DOISearch in Google Scholar
34. Biba D, Klink G, Bazykin GA. Pairs of mutually compensatory frameshifting mutations contribute to protein evolution. Mol Biol Evol. 2022;39(3):msac031. Available from: https://doi.org/10.1093/molbev/msac031BibaDKlinkGBazykinGA.Pairs of mutually compensatory frameshifting mutations contribute to protein evolution..2022;39(3):msac031. Available from: https://doi.org/10.1093/molbev/msac031Open DOISearch in Google Scholar
35. Bartonek L, Braun D, Zagrovic B. Frameshifting preserves key physicochemical properties of proteins. Proc Natl Acad Sci USA. 2020;117(11):5907-5912.BartonekLBraunDZagrovicB.Frameshifting preserves key physicochemical properties of proteins..2020;117(11):5907-5912.Search in Google Scholar
36. Xu H, Zhang J. On the origin of frameshift-robustness of the standard genetic code. Mol Biol Evol. 2021a;38(10):4301-4309. doi:10.1093/molbev/msab1642021aXuHZhangJ.On the origin of frameshift-robustness of the standard genetic code..2021a;38(10):4301-4309. doi:10.1093/molbev/msab1642021aOpen DOISearch in Google Scholar
37. Blalock JE, Smith EM. Hydropathic anti-complementarity of amino acids based on the genetic code. Biochem Biophys Res Comm. 1984;121(1):203-207.BlalockJESmithEM.Hydropathic anti-complementarity of amino acids based on the genetic code..1984;121(1):203-207.Search in Google Scholar
38. Zull JE, Smith SK. Is genetic code redundancy related to retention of structural information in both DNA strands? Trends Biochem Sci. 1990;15(7):257-261.ZullJESmithSK.Is genetic code redundancy related to retention of structural information in both DNA strands?.1990;15(7):257-261.Search in Google Scholar
39. Konecny J, Eckert M, Schöniger M, Hofacker GL. Neutral adaptation of the genetic code to double-strand coding. J Mol Evol. 1993;36(5):407-416.KonecnyJEckertMSchönigerMHofackerGL.Neutral adaptation of the genetic code to double-strand coding..1993;36(5):407-416.Search in Google Scholar
40. Blalock JE. Complementarity of peptides specified by ‘sense’ and ‘antisense’ strands of DNA. Trends Biotechnol. 1990;8(6): 140-144.BlalockJE.Complementarity of peptides specified by ‘sense’ and ‘antisense’ strands of DNA..1990;8(6):140-144.Search in Google Scholar
41. Willis S, Masel J. Gene birth contributes to structural disorder encoded by overlapping genes. genetics. 2018;210(1):303-313. doi:10.1534/genetics.118.301249WillisSMaselJ.Gene birth contributes to structural disorder encoded by overlapping genes..2018;210(1):303-313. doi:10.1534/genetics.118.301249Open DOISearch in Google Scholar
42. Wei X, Zhang J. A simple method for estimating the strength of natural selection on overlapping genes. Genome Biol Evol. 2015;7(10): 381-390. Available from: https://doi.org/10.1093/gbe/evu294WeiXZhangJ.A simple method for estimating the strength of natural selection on overlapping genes..2015;7(10):381-390. Available from: https://doi.org/10.1093/gbe/evu294Open DOISearch in Google Scholar
43. Osawa S. Evolution of the genetic code. Oxford: Oxford University Press; 1995.OsawaS..Oxford:Oxford University Press;1995.Search in Google Scholar
44. Freeland SJ, Knight RD, Landweber LF, Hurst LD. Early fixation of an optimal genetic code. Mol Biol Evol. 2000;17(4):511-518. doi:10.1093/oxfordjournals.molbev.a026331FreelandSJKnightRDLandweberLFHurstLD.Early fixation of an optimal genetic code..2000;17(4):511-518. doi:10.1093/oxfordjournals.molbev.a026331Open DOISearch in Google Scholar
45. Freeland SJ, Hurst LD. The genetic code is one in a million. J Mol Evol. 1998;47(3):238-248.FreelandSJHurstLD.The genetic code is one in a million..1998;47(3):238-248.Search in Google Scholar
46. Itzkovitz S, Alon U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 2007;17(4):405-412.ItzkovitzSAlonU.The genetic code is nearly optimal for allowing additional information within protein-coding sequences..2007;17(4):405-412.Search in Google Scholar
47. Ilardo M, Meringer M, Freeland S, Rasulev B, Cleaves HJ 2nd. Extraordinarily adaptive properties of the genetically encoded amino acids. Sci Rep. 2015;5:9414. doi:10.1038/srep09414IlardoMMeringerMFreelandSRasulevBCleavesHJ2nd.Extraordinarily adaptive properties of the genetically encoded amino acids..2015;5:9414. doi:10.1038/srep09414Open DOISearch in Google Scholar
48. Ilardo M, Bose R, Meringer M, Rasulev B, Grefenstette N, Stephenson J, Freeland S, Gillams RJ, Butch CJ, Cleaves HJ 3rd. Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Sci Reports. 2019;9(12468). Available from: https://doi.org/10.1038/s41598-019-47574-xIlardoMBoseRMeringerMRasulevBGrefenstetteNStephensonJFreelandSGillamsRJButchCJCleavesHJ3rd.Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets..2019;9(12468). Available from: https://doi.org/10.1038/s41598-019-47574-xOpen DOISearch in Google Scholar
49. Mayer-Bacon C, Freeland SJ. A broader context for understanding amino acid alphabet optimality. J Theo Biol. 2021 July;520:110661.Mayer-BaconCFreelandSJ.A broader context for understanding amino acid alphabet optimality..2021July;520:110661.Search in Google Scholar
50. Freeland SJ. The Darwinian genetic code: An adaptation for adapting? Genet Program Evolvable Mach. 2002;3(2):113-127. Available from: https://doi.org/10.1023/A:1015527808424FreelandSJ.The Darwinian genetic code: An adaptation for adapting?.2002;3(2):113-127. Available from: https://doi.org/10.1023/A:1015527808424Open DOISearch in Google Scholar
51. Zhu W, Freeland SJ. The standard genetic code enhances adaptive evolution of proteins. J Theoret Biol. 2006;239(1):63-70.ZhuWFreelandSJ.The standard genetic code enhances adaptive evolution of proteins..2006;239(1):63-70.Search in Google Scholar
52. Firnberg E, Ostermeier M. The genetic code constrains yet facilitates Darwinian evolution. Nucleic Acids Res. 2013;41(15): 7420-7428.FirnbergEOstermeierM.The genetic code constrains yet facilitates Darwinian evolution..2013;41(15):7420-7428.Search in Google Scholar
53. Tripathi S, Deem MW. The standard genetic code facilitates exploration of the space of functional nucleotide sequences. J Mol Evol. 2018;86(6):325-339.TripathiSDeemMW.The standard genetic code facilitates exploration of the space of functional nucleotide sequences..2018;86(6):325-339.Search in Google Scholar
54. Richter H, Engelbrecht A, editors. Recent advances in the theory and application of fitness landscapes. Berlin: Springer; 2014.RichterHEngelbrechtA, editors..Berlin:Springer;2014.Search in Google Scholar
55. de Visser JA, Krug J. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet. 2014;15(7):480-490. doi:10.1038/nrg3744de VisserJAKrugJ.Empirical fitness landscapes and the predictability of evolution..2014;15(7):480-490. doi:10.1038/nrg3744Open DOISearch in Google Scholar
56. Payne JL, Wagner A. The causes of evolvability and their evolution. Nat Rev Genet. 2019;20(1):24-38.PayneJLWagnerA.The causes of evolvability and their evolution..2019;20(1):24-38.Search in Google Scholar
57. Chen JZ, Fowler DM, Tokuriki N. Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape. Nat Ecol Evol. 2022;6(4):427-438. doi:10.1038/s41559-022-01675-5ChenJZFowlerDMTokurikiN.Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape..2022;6(4):427-438. doi:10.1038/s41559-022-01675-5Open DOISearch in Google Scholar
58. Tenaillon O. The utility of Fisher’s geometric model in evolutionary genetics. Annu Rev Ecol Evol Syst. 2014;45:179-201. doi:10.1146/annurev-ecolsys-120213-091846TenaillonO.The utility of Fisher’s geometric model in evolutionary genetics..2014;45:179-201. doi:10.1146/annurev-ecolsys-120213-091846Open DOISearch in Google Scholar
59. Fisher RA. The genetical theory of natural selection. Oxford: Clarendon Press; 1930. Available from: https://doi.org/10.5962/bhl.title.27468FisherRA..Oxford:Clarendon Press;1930. Available from: https://doi.org/10.5962/bhl.title.27468Open DOISearch in Google Scholar
60. Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC. On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol. 1966;31:723-736. doi:10.1101/sqb.1966.031.01.093WoeseCRDugreDHDugreSAKondoMSaxingerWC.On the fundamental nature and evolution of the genetic code..1966;31:723-736. doi:10.1101/sqb.1966.031.01.093Open DOISearch in Google Scholar
61. Buhrman H, van der Gulik PT, Kelk SM, Koolen WM, Stougie L. Some mathematical refinements concerning error minimization in the genetic code. IEEE/ACM Trans Comput Biol Bioinform. 2011;8(5):1358-1372. doi:10.1109/TCBB.2011.40BuhrmanHvan der GulikPTKelkSMKoolenWMStougieL.Some mathematical refinements concerning error minimization in the genetic code..2011;8(5):1358-1372. doi:10.1109/TCBB.2011.40Open DOISearch in Google Scholar
62. Lèbre S, Gascuel O. The combinatorics of overlapping genes. J Theoret Biol. 2017 February;415:90-101.LèbreSGascuelO.The combinatorics of overlapping genes..2017February;415:90-101.Search in Google Scholar
63. Shenhav L, Zeevi D. Resource conservation manifests in the genetic code. Science. 2020;370(6517): 683–687.ShenhavLZeeviD.Resource conservation manifests in the genetic code..2020;370(6517):683–687.Search in Google Scholar
64. Rozhoňová H, Payne JL. Little evidence the standard genetic code is optimized for resource conservation. Mol Biol Evol. 2021;38(11):5127-5133.RozhoňováHPayneJL.Little evidence the standard genetic code is optimized for resource conservation..2021;38(11):5127-5133.Search in Google Scholar
65. Xu H, Zhang J. Is the genetic code optimized for resource conservation? Mol Biol Evol. 2021b;38(11):5122-5126.XuHZhangJ.Is the genetic code optimized for resource conservation?.2021b;38(11):5122-5126.Search in Google Scholar
66. Massey SE. A neutral origin for error minimization in the genetic code. J Mol Evol. 2008;67(5):510-516.MasseySE.A neutral origin for error minimization in the genetic code..2008;67(5):510-516.Search in Google Scholar
67. Massey SE. The neutral emergence of error minimized genetic codes superior to the standard genetic code. J Theoret Biol. 2016 November;408:237-242.MasseySE.The neutral emergence of error minimized genetic codes superior to the standard genetic code..2016November;408:237-242.Search in Google Scholar
68. Di Giulio M. A non-neutral origin for error minimization in the origin of the genetic code. J Mol Evol. 2018;86(9):593-597.Di GiulioM.A non-neutral origin for error minimization in the origin of the genetic code..2018;86(9):593-597.Search in Google Scholar
69. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218-223. doi:10.1126/science.1168978IngoliaNTGhaemmaghamiSNewmanJRWeissmanJS.Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling..2009;324(5924):218-223. doi:10.1126/science.1168978Open DOISearch in Google Scholar
70. Finkel Y, Mizrahi O, Nachshon A, Weingarten-Gabbay S, Morgenstern D, Yahalom-Ronen Y, Tamir H, Achdout H, Stein D, Israeli O, et al. The coding capacity of SARS-CoV-2. Nature. 2021;589(7840):125-130. doi:10.1038/s41586-020-2739-1FinkelYMizrahiONachshonAWeingarten-GabbaySMorgensternDYahalom-RonenYTamirHAchdoutHSteinDIsraeliO.The coding capacity of SARS-CoV-2..2021;589(7840):125-130. doi:10.1038/s41586-020-2739-1Open DOISearch in Google Scholar
71. Firth AE. Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses. Nucleic Acids Res. 2014;42(20):12425-12439.FirthAE.Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses..2014;42(20):12425-12439.Search in Google Scholar
72. Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC. FRESCo: finding regions of excess synonymous constraint in diverse viruses. Genome Biol. 2015;16(1):38. doi:10.1186/s13059-015-0603-7SealfonRSLinMFJungreisIWolfMYKellisMSabetiPC.FRESCo: finding regions of excess synonymous constraint in diverse viruses..2015;16(1):38. doi:10.1186/s13059-015-0603-7Open DOISearch in Google Scholar
73. Schlub TE, Buchmann JP, Holmes EC. A simple method to detect candidate overlapping genes in viruses using single genome sequences. Mol Biol Evol. 2018;35(10):2572-2581.SchlubTEBuchmannJPHolmesEC.A simple method to detect candidate overlapping genes in viruses using single genome sequences..2018;35(10):2572-2581.Search in Google Scholar
74. Nelson CW, Ardern Z, Wei X. OLGenie: Estimating natural selection to predict functional overlapping genes. Mol Biol Evol. 2020;37(8):2440-2449. doi:10.1093/molbev/msaa087NelsonCWArdernZWeiX.OLGenie: Estimating natural selection to predict functional overlapping genes..2020;37(8):2440-2449.doi:10.1093/molbev/msaa087Open DOISearch in Google Scholar
75. Louis AA. Contingency, convergence and hyper-astronomical numbers in biological evolution. Stud Hist Philos Biol Biomed Sci. 2016;58:107-116. doi:10.1016/j.shpsc.2015.12.014LouisAA.Contingency, convergence and hyper-astronomical numbers in biological evolution..2016;58:107-116. doi:10.1016/j.shpsc.2015.12.014Open DOISearch in Google Scholar
76. Keefe AD, Szostak JW. Functional proteins from a random-sequence library. Nature. 2001;410(6829):715-718.KeefeADSzostakJW.Functional proteins from a random-sequence library..2001;410(6829):715-718.Search in Google Scholar
77. Çakir U, Gabed N, Brunet M, Roucou X, Kryvoruchko I. Mosaic translation hypothesis: Chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability [published online ahead of print, 2021 Nov 7]. FEBS J. 2021;10.1111/febs.16269. doi:10.1111/febs.16269ÇakirUGabedNBrunetMRoucouXKryvoruchkoI.Mosaic translation hypothesis: Chimeric polypeptides produced via multiple ribosomal frameshifting as a basis for adaptability [published online ahead of print, 2021 Nov 7]..2021;10.1111/febs.16269. doi:10.1111/febs.16269Open DOISearch in Google Scholar
78. Kosinski LJ, Masel J. Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences. Mol Biol Evol. 2020;37(6):1761-1774.KosinskiLJMaselJ.Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences..2020;37(6):1761-1774.Search in Google Scholar
79. Fernandes JD, Faust TB, Strauli NB, Smith C, Crosby DC, Nakamura RL, Hernandez RD, Frankel AD. Functional segregation of overlapping genes in HIV. Cell. 2016;167(7):1762-1773. e12. doi:10.1016/j.cell.2016.11.031FernandesJDFaustTBStrauliNBSmithCCrosbyDCNakamuraRLHernandezRDFrankelAD.Functional segregation of overlapping genes in HIV..2016;167(7):1762-1773.e12. doi:10.1016/j.cell.2016.11.031Open DOISearch in Google Scholar
80. Safari M, Jayaraman B, Yang S, Smith C, Fernandes JD, Frankel AD. Functional and structural segregation of overlapping helices in HIV-1. Elife. 2022;11:e72482. doi:10.7554/eLife.72482SafariMJayaramanBYangSSmithCFernandesJDFrankelAD.Functional and structural segregation of overlapping helices in HIV-1..2022;11:e72482. doi:10.7554/eLife.72482Open DOISearch in Google Scholar
81. Dingle K, Ghaddar F, Šulc P, Louis AA. Phenotype bias determines how natural RNA structures occupy the morphospace of all possible shapes. Mol Biol Evol. 2022;39(1):msab280. Available from: https://doi.org/10.1093/molbev/msab280.DingleKGhaddarFŠulcPLouisAA.Phenotype bias determines how natural RNA structures occupy the morphospace of all possible shapes..2022;39(1):msab280. Available from: https://doi.org/10.1093/molbev/msab280.Open DOISearch in Google Scholar
82. Schulz L, Sendker FL, Hochberg GKA. Non-adaptive complexity and biochemical function. Curr Opin Structur Biol. 2022 April;73:102339.SchulzLSendkerFLHochbergGKA.Non-adaptive complexity and biochemical function..2022April;73:102339.Search in Google Scholar
83. Gould SJ, Lewontin RC. The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Concept Iss Evol Biol. 1979;205:79.GouldSJLewontinRC.The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme..1979;205:79.Search in Google Scholar
84. Morris SC. Life’s solution: Inevitable humans in a lonely universe. Cambridge: Cambridge University Press; 2003. Available from: https://doi.org/10.1017/CBO9780511535499MorrisSC..Cambridge:Cambridge University Press;2003. Available from: https://doi.org/10.1017/CBO9780511535499Open DOISearch in Google Scholar