Phylogenetic distribution of trans-spliced and permuted tRNAs in Archaea. Trans-spliced tRNAs were identified in A. pernix, T. aggregans, S. marinus, and S. marinus in this study, in N. equitans by Randau and colleagues [4,5], and in C. maquilingensis by Fujishima and colleagues  (highlighted in gray). Permuted tRNAs were found in T. pendens in this study (yellow), and are most similar to the permuted tRNAs found in Cyanidioschyzon merolae, a eukaryotic algal species that is not included in the tree but would be a distant outgroup to the archaea shown here. The phylogenetic tree was generated based on the concatenation of 23S and 16S ribosomal RNAs. Sequences were aligned using ClustalW . Alignments were manually adjusted using Jalview  to remove introns. The maximum likelihood tree was computed using PhyML  with general time-reversible model of sequence evolution. Numbers at nodes represent non-parametric bootstrap values computed by PhyML  with 1,000 replications of the original dataset.
Chan et al. Genome Biology 2011 12:R38 doi:10.1186/gb-2011-12-4-r38