Schematic structures of mitochondrial control regions.

<p>ETAS, extended termination associated sequences; CCD, central conserved domain; CBSs, conserved sequence blocks. This figure does not show the structure for the CR of <i>Cephalopholis argus</i>.</p

A Comprehensive Description and Evolutionary Analysis of 22 Grouper (Perciformes, Epinephelidae) Mitochondrial Genomes with Emphasis on Two Novel Genome Organizations

<div><p>Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 <i>tRNAs</i>, two <i>rRNAs</i>, and a non-coding control region. Differing from this, members of genus <i>Variola</i> have an extra <i>tRNA-Ile</i> between <i>tRNA-Val</i> and <i>16S rRNA</i>. Evidence suggests that this evolved from <i>tRNA-Val</i> via a duplication event due to slipped strand mispairing during replication. Additionally, <i>Cephalopholis</i><i>argus</i> has an extra <i>tRNA-Asp</i> in the midst of the control region, likely resulting from long-range duplication of the canonical <i>tRNA-Asp</i> through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes’ control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, <i>rRNA</i> and <i>tRNA</i> are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (<i>COI, II, III</i>) are the most conserved, while NADH dehydrogenase subunit 6 (<i>ND6</i>) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus <i>Hyporthodus</i>, and the combination of the monotypic genera <i>Anyperodon</i> and <i>Cromileptes</i> to genus <i>Epinephelus</i>, and <i>Aethaloperca</i> to genus <i>Cephalopholis</i><i>.</i></p> </div

Phylogenetic tree of 22 groupers in family Epinephelidae and 29 representatives from other families in suborder Percoidei.

<p>A species from the suborder Labrodei family Labridae, <i>Pseudolabrus sieboldi</i>, 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 <i>ND6</i>). 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 <i>ATP6</i> start codon is not ATG but CTG or TTG, different from most other teleosts and basal groupers.</p

Gene maps for mitochondrial genomes.

<p>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 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073561#B81" target="_blank">81</a>] with manual modifications. (A) The mt gemone organization of <i>Aethaloperca rogaa</i>, <i>Anyperodon leucogrammicus</i>, <i>Cephalopholis sonnerati</i>, <i>Cromileptes altivelis</i>, <i>Epinephelus akaara</i>, <i>E</i>. <i>areolatus</i>, <i>E</i>. <i>awoara</i>, <i>E</i>. <i>bruneus</i>, <i>E</i>. <i>coioides</i>, <i>E</i>. <i>epistictus</i>, <i>E</i>. <i>fuscoguttatus</i>, <i>E</i>. <i>lanceolatus</i>, <i>E</i>. <i>moara</i>, <i>E</i>. <i>trimaculatus</i>, <i>Hyporthodus octofasciatus</i>, <i>H</i>. <i>septemfasciatus</i>, <i>Plectropomus areolatus</i>, <i>P</i>. <i>leopardus</i>, and <i>Triso dermopterus</i>. (B) The mt gemone organization of genera <i>Variola, V</i>. <i>albimarginata</i> and <i>V</i>. <i>louti</i>. (C) The mt gemone organization of <i>Cephalopholis argus</i>.</p

Sequence variations among mitochondrial genes.

<p>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%.</p

Fundulus notatus raw data

Excel file containing the raw data (morphometric measurements as well as data on population, drainage, habitat, age, and sex)