The proposed mechanism of the rearrangement of the ancestral gene order to that of S. latus mitogenome. Protein-coding genes and CRs are indicated by boxes, and tRNA genes are indicated by columns. Genes labeled above the diagram are encoded by the H-strand and the others by the L-strand. OH indicates the origin of replication for the H-strand; the direction of replication is shown by arrows. Consecutive numbers (1–38) indicate the gene order. The dark boxes indicate the control regions (CRs) and noncoding region (NC). (A) The ancestral mitogenome with 37 genes and one CR. (B) The ancestral CR was duplicated to CRI and CRII, and then CRI translocated to the position between tRNA-Q and tRNA-M. A mitochondrial replication event (RP1) was initiated at OH1. (C) After RP1 passed through OH2, replication2 (RP2) began at OH2. Both replications terminated close to OH1 (namely, the 5′ end of the nascent strand of RP1). (D) Double replications led to the duplication of one CR and 29 genes. One of each copied gene pair was lost randomly. Dark gray boxes indicate the degenerated genes. (E) The gene order after the loss of several genes and CRs. (F) The gene order of S. latus mitogenome that was formed after CR and tRNA-C-Y duplicated and translocated to the position between tRNA-L2 and tRNA-P.