Figure 1.
Gene maps for mitochondrial genomes.
Genes encoded on the heavy and light strand are shown outside and inside the circle, respectively. The inner grey ring indicates the GC content. This genome map was constructed via OrganellarGenomeDRAW [81] with manual modifications. (A) The mt gemone organization of Aethaloperca rogaa, Anyperodon leucogrammicus, Cephalopholis sonnerati, Cromileptes altivelis, Epinephelus akaara, E. areolatus, E. awoara, E. bruneus, E. coioides, E. epistictus, E. fuscoguttatus, E. lanceolatus, E. moara, E. trimaculatus, Hyporthodus octofasciatus, H. septemfasciatus, Plectropomus areolatus, P. leopardus, and Triso dermopterus. (B) The mt gemone organization of genera Variola, V. albimarginata and V. louti. (C) The mt gemone organization of Cephalopholis argus.
Figure 2.
Phylogenetic tree of 22 groupers in family Epinephelidae and 29 representatives from other families in suborder Percoidei.
A species from the suborder Labrodei family Labridae, Pseudolabrus sieboldi, was selected as outgroup. Congruent tree topology was inferred from partitioned Maximum likelihood and Bayesian analyses using the concatenated nucleotide sequences of 12 mitochondrial protein-coding genes (excluding ND6). The Bayesian posterior probability values (top) and bootstrap values (bottom) are labeled at branch nodes. Branch length information from the Bayesian tree is shown. NCBI RefSeq or GenBank accession number of each species was listed on the right of the species name. Clade A indicates the derived epinephelid clade whose ATP6 start codon is not ATG but CTG or TTG, different from most other teleosts and basal groupers.
Figure 3.
Schematic structures of mitochondrial control regions.
ETAS, extended termination associated sequences; CCD, central conserved domain; CBSs, conserved sequence blocks. This figure does not show the structure for the CR of Cephalopholis argus.
Figure 4.
Sequence variations among mitochondrial genes.
Genes were ranked by their sequence identity percentages from low to high (left to right). (A) Sequence identities of 22 tRNA genes. (B) NT% (dark grey) and deduced AA% (light grey) of 13 protein-coding genes. Genes were ranked by the AA%.
Figure 5.
Average Ka /Ks ratios of 13 protein-coding genes.
Ka /Ks is the ratio of non-synonymous substitutions rate (Ka) to synonymous substitutions substitution rate (Ks).