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 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholis argus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp 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, rRNA and tRNA 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 (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) 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 Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.

Cephalopoda are a class of Mollusca species found in all the world's oceans. They are an important model organism in neurobiology. Unfortunately, the lack of neuronal molecular sequences, such as ESTs, transcriptomic or genomic information, has limited the development of molecular neurobiology research in this unique model organism. With high-throughput Illumina Solexa sequencing technology, we have generated 59,859 high quality sequences from 12,918,391 paired-end reads. Using BLASTx/BLASTn, 12,227 contigs have blast hits in the Swissprot, NR protein database and NT nucleotide database with E-value cutoff 1e⁻⁵. The comparison between the Octopus vulgaris central nervous system (CNS) library and the Aplysia californica/Lymnaea stagnalis CNS ESTs library yielded 5.93%/13.45% of O. vulgaris sequences with significant matches (1e⁻⁵) using BLASTn/tBLASTx. Meanwhile the hit percentage of the recently published Schistocerca gregaria, Tilapia or Hirudo medicinalis CNS library to the O. vulgaris CNS library is 21.03%–46.19%. We constructed the Phylogenetic tree using two genes related to CNS function, Synaptotagmin-7 and Synaptophysin. Lastly, we demonstrated that O. vulgaris may have a vertebrate-like Blood-Brain Barrier based on bioinformatic analysis. This study provides a mass of molecular information that will contribute to further molecular biology research on O. vulgaris. In our presentation of the first CNS transcriptome analysis of O. vulgaris, we hope to accelerate the study of functional molecular neurobiology and comparative evolutionary biology.

The large yellow croaker, Larimichthys crocea, was once the most abundant and economically important marine fish in China. Thus far, it has also been the most successful mariculture fish species in China. However, its wild stock severely declined in the 1970s because of overexploitation, and therefore hatchery release has been carried out for stock enhancement since 2000. As a migratory fish, large yellow croaker was divided into three geographical stocks according to ambiguous morphological and biological characteristics in early documents. To investigate the identity of wild large yellow croaker populations and assess the influence of hatchery supplementation on wild populations, a total of 2,785 cultured individuals and 591 wild individuals were collected from 91 hatcheries and six wild populations along the coast of mainland China and analyzed using two mitochondrial genes [cytochrome oxidase I (COI) and cytochrome b (Cyt b)] and one nuclear gene (RyR3). The higher haplotype diversity and moderate nucleotide diversity of wild large yellow croaker indicated that overexploitation, which caused a sharp decrease in biomass, did not lead to a loss of genetic diversity. According to phylogenetic construction and network analysis, the absence of a significant population structure pattern revealed a single panmictic population of wild large yellow croaker with exception of a population collected from the Sansha Bay, which showed high genetic relatedness to the cultured population, suggesting significant genetic effects resulting from stock enhancement. Overall, our study suggests no genetic differentiation in the entire wild population of large yellow croaker, which means that we have great flexibility in mixing and matching farmed and wild populations. However, since the result showed that domestication, the relaxation of purifying selection, increased genetic loads, and maladapted farmed fish will be at a selective disadvantage when cultured juveniles are released in the wild, the effectiveness of stock enhancement and the negative impact of hatchery-wild fish hybridization on the wild population must be carefully evaluated in future.