Figure 2

Standard genetic code and naturally occurring variants. The standard genetic code and the naturally occurring variants studied in this work, written using the RNA alphabet and standard abbreviations for the amino acids ('St' indicates stop codon). Concerning the alternative genetic codes, we follow the naming scheme of the NCBI database (http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi, including the transl_table numbering). We give in a following only a very brief description of a given alternative genetic code's systematic range, a more detailed description with references can be found on the NCBI's web page. The standard genetic code is shown in black (3 stop codons), whereas the seven naturally occurring variants studied are shown using the following color scheme: (1, blue): 'The Echinoderm and Flatworm Mitochondrial Code' (NCBI transl_table=9), mitochondrial code of Asterozoa, Echinozoa, and Rhabditophora (4 differences, 2 stop codons) [48]; (2, orange): 'The Invertebrate Mitochondrial Code' (NCBI transl_table=5), mitochondrial code of Nematoda, Mollusca, Crustacea, and Insecta (4 differences, 2 stop codons) [48]; (3, magenta): 'The Ascidian Mitochondrial Code' (NCBI transl_table=13), mitochondrial code of Urochordata (4 differences, 2 stop codons) [48]; (4, green): 'The Vertebrate Mitochondrial Code' (NCBI transl_table=2), mitochondrial code of Vertebrata (4 differences, 4 stop codons) [49]; (5, cyan): 'The Yeast Mitochondrial Code' (NCBI transl_table=3), mitochondrial code of Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, and Kluyveromyces thermotolerans (6 differences, 2 stop codons) [50]; (6, yellow): 'The Ciliate, Dasycladacean and Hexamita Nuclear Code' (NCBI transl_table=6), nuclear code of Ciliata, Dasycladaceae, Diplomonadida (2 differences, 1 stop codon) [51]; (7, red): 'The Alternative Yeast Nuclear Code' (NCBI transl_table=12), nuclear code of Candida albicans (1 difference, 3 stop codons) [52]. The color scheme is as in Figs. 3 to 6.