Fig. 1

Linearized representation of the typical vertebrate gene order (circled t) and rearranged gene orders observed in fishes. All protein-coding genes are encoded on the H-strand with the exception of ND6 (underlined), which is encoded on the L-strand. Transfer RNA (tRNA) genes are designated by single-letter amino acid codes, and those encoded on the H- and L-strands are presented above and below the gene map, respectively. Capitalized A–G denote mt genome regions involved in major gene rearrangements. Coloured shadings (circled a-d) indicate fish groups that share the same unique gene order at least in part, and are related to Fig. 10. Numerals in front of the species name are the same as those in Additional file 1. 12S and 16S, 12S and 16S ribosomal RNA genes, respectively; ATPase 6 and 8, ATPase subunit 6 and 8 genes, respectively; COI–III, cytochrome c oxidase subunits I–III genes, respectively; CR, putative control region; Cyt b, cytochrome b gene; L1, L2, S1, and S2, tRNA Leu (UUR), tRNA Leu (CUN), tRNA Ser (UCN), and tRNA Ser (AGY) genes, respectively; NC, noncoding sequences of ≥50 bp; ND1–6 and 4 L, NADH dehydrogenase subunit 1–6 and 4 L genes, respectively