title: Two perspectives on the origin of the standard genetic code.
abstract: The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.
authors.affiliation: Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246, India, supratim.sen@iiserkol.ac.in.
authors.forename: Supratim
authors.initials: S
authors.lastname: Sengupta
authors.forename: Neha
authors.initials: N
authors.lastname: Aggarwal
authors.forename: Ashutosh Vishwa
authors.initials: AV
authors.lastname: Bandhu
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000378:metabolism; D003062:Codon / Q000737:chemistry* / Q000378:metabolism; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005796:Genes; D005815:Genetic Code; D008957:Models, Genetic; D000069497:Origin of Life; D011336:Probability; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D012345:RNA, Transfer, Amino Acid-Specific / Q000737:chemistry* / Q000378:metabolism; D012641:Selection, Genetic
chemical_list: D000596:Amino Acids; D003062:Codon; D012333:RNA, Messenger; D012345:RNA, Transfer, Amino Acid-Specific; D000604:Amino Acyl-tRNA Synthetases