Overview of the organization of the circular mt DNA of R. similis. The arrow indicates direction of transcription. Genes and non-coding regions are indicated: in white, the protein-coding and rRNA genes, in gray, the tRNA genes called by their amino acid symbol (S1: Ser-AGN, S2: Ser-UCN, L1: Leu-CUN, L2: Leu-UUR). Bold and italic numbers indicate non-coding and overlapping nucleotides between neighboring genes, respectively. The pattern-filled part represents the large non-coding region, divided in five regions as explained in the text. The repeat region of 302 bp is filled with large checkers and the 26 bp repeat region is filled with small checkers. The black lines at the inner periphery of the ring represent EST sequences, with UAG stop codons indicated by little black triangles. The colored bar code-like circles represent the nucleotide content of the coding strand, differing intensities corresponding to different content (red: thymine, blue: adenine, green: guanine, purple: cytosine). The positions of secondary structures depicted in figure 4 are indicated by light-gray balks perpendicular to the circle. The predicted origins of replication for the heavy (OriH) and light strand (OriL) are indicated (see figure 5).