title: The evolution of the mitochondrial genetic code in arthropods revisited.
abstract: A variant of the invertebrate mitochondrial genetic code was previously identified in arthropods (Abascal et al. 2006a, PLoS Biol 4:e127) in which, instead of translating the AGG codon as serine, as in other invertebrates, some arthropods translate AGG as lysine. Here, we revisit the evolution of the genetic code in arthropods taking into account that (1) the number of arthropod mitochondrial genomes sequenced has triplicated since the original findings were published; (2) the phylogeny of arthropods has been recently resolved with confidence for many groups; and (3) sophisticated probabilistic methods can be applied to analyze the evolution of the genetic code in arthropod mitochondria. According to our analyses, evolutionary shifts in the genetic code have been more common than previously inferred, with many taxonomic groups displaying two alternative codes. Ancestral character-state reconstruction using probabilistic methods confirmed that the arthropod ancestor most likely translated AGG as lysine. Point mutations at tRNA-Lys and tRNA-Ser correlated with the meaning of the AGG codon. In addition, we identified three variables (GC content, number of AGG codons, and taxonomic information) that best explain the use of each of the two alternative genetic codes.
authors.affiliation: Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain. abascal@mncn.csic.es
authors.forename: Federico
authors.initials: F
authors.lastname: Abascal
authors.forename: David
authors.initials: D
authors.lastname: Posada
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
mesh_terms: D000818:Animals; D001181:Arthropods / Q000145:classification / Q000235:genetics*; D001499:Bayes Theorem; D003062:Codon / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D012357:RNA, Transfer, Lys / Q000235:genetics; D012362:RNA, Transfer, Ser / Q000235:genetics
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial; D012357:RNA, Transfer, Lys; D012362:RNA, Transfer, Ser