Fig. 1
Four mitogenomic rearrangement variants in 13 bothids using the DMNL model. The letters a to f after the variant number I-IV represent the steps of DMNL process. a: Ancestral gene order in typical fish. The rRNA, protein-coding genes and CRs are indicated by boxes; the tRNA genes are indicated by columns, genes labeled above the columns are located on the H-strand, those below the columns on the L-strand. TAS is an acronym for the terminal associated sequences. b: Translocated position of tRNA-D prior to DMNL gene rearrangement in Type I, and that of tRNA-D posterior to DMNL gene rearrangement and the finally mitogenomic structure in Type II, III, and IV. c: The dimeric molecule formed by two monomers linked head-to-tail. The HSP, HSP′, LSP, and LSP′ indicate the H- and L- strand promoters of transcription. The TAS, TAS′, tRNA-L1, and tRNA-L1′ indicate the H- and L- strand terminations of transcription. The direction of transcription is shown by an arrow. d: Functional loss of LSP and HSP. Grey boxes indicate the degenerated genes controlled by non-functional HSP and LSP. The triangle marks the retention of tRNA-N rather than the expected tRNA-N′ gene. e: The translocation of tRNA-D posterior to DMNL gene rearrangement and the finally mitogenomic structure in Type I. f: The mitogenomic structure generated after degeneration of non-transcribed genes in the dimeric molecule. The path from A, II-C, II-D, II-F to I-E in Type I indicates the translocation of tRNA-D occurred after the DMNL process; the path from A, II-B′, II-C′, II-D′, II-F′ to II-B in Type II indicates the translocation of tRNA-D occurred before DMNL process; the difference between the steps of B′, C′, D′ and F′ with that of B, C, D and F is the location of tRNA-D. The broken line in IV-B2 indicates the omitted genes that are the same as those shown in IV-B1