Liqin Liu

Phylogenetic analysis of the complete mitochondrial genome of Anguilla japonica (Anguilliformes, Anguillidae)

Abstract The Japanese eel (Anguilla japonica), which was listed as Endangered (EN) under the International Union for the Conservation of Nature due to the declines in its abundance, overfishing, and its narrow range distribution. To better protect this species, we described the complete mitogenome of A. japonica in this study. The mitogenome is 16717bp in length and contains 13PCGs, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and a putative control region (CR) and one origin of replication on the light-strand (OL). Moreover, the 13 PCGs encode 3813 amino acids in total, all the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COI uses AGG and two PCGs (COII and ND4) use an incomplete stop codon T. A phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Anguilla, which could be a useful basis for conservation of this species.

The complete mitochondrial genome of Chaetodon octofasciatus (Perciformes: Chaetodontidae) and phylogenetic studies of Percoidea

Abstract The complete mitochondrial genome of this species was first determined in this study, which is 16,485 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(28.2%), A(28.3%), T(27.4%), and G(16.1%). Moreover, the 13 PCGs encode 3796 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND3 ends with TAG, and three protein-coding genes (COII, ND4, and Cytb) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Percoidea, which could be a useful basis for management of this species.

The complete mitochondrial genome of Epinephelus Chlorostigma (Serranidae; Epinephelus) with phylogenetic consideration of Epinephelus

Abstract The complete mitochondrial genome of Epinephelus chlorostigma has been determined. It contains a typically conserved structure including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region, and the whole sequence was 16,894 bp in length. The overall base composition is A 28.70%, C 27.99%, G 16.28%, T 27.03%. Except ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Phylogenetic tree was constructed based on 12 protein-coding genes sequences of 18 Epinephelus species, four species belong to Cephalopholis as outgroup, the result showed that E. chlorostigma is most closely related to Epinephelus areolatus. We sequenced the complete mitochondrial genome of E. chlorostigma to enrich the resource of molecular markers for examination of phylogenetic relationships in Epinephelus.

Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda)

Abstract Octopus minor is an economically important resource commonly found in Chinese coastal waters. The nuclear gene (RD and ODH) approach of investigation has not reported in this species. Rhodopsin (RD) and octopine dehydrogenase (ODH) genes were used to elaborate the genetic structure collected from eight localities ranging from the northern to the southern coast of China. In total, 118 individuals for the RD gene and 108 for the ODH were sequenced. Overall (RD and ODH) genes resulted in high (0.741±0.032; 0.805±0.038) haplotype and low nucleotide (0.01261±0.00165; 0.00747±0.00086) diversity. Molecular variance displayed higher values among the populations and lower values within the population where the fixation index FST denoted 0.880 and 0.584 in RD and ODH genes respectively. The Dongshan population clustered separately in a phylogenetic tree as in the haplotype networking assessment. The current data suggests that the Dongshan population needs separate management.

Phylogenetic analysis of the complete mitochondrial genome of Hyporhamphus limbatus (Beloniformes; hemiramphidae)

Abstract The first complete mitochondrial (mt) genome of Hyporhamphus limbatus is reported herein, the gene composition and arrangement in H. limbatus mitogenome were identical to those of most vertebrates, which is 16,508 bp in length and contains 13 PCGs, two rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and a putative control region (CR) and one origin of replication on the light-strand (OL). Two start codon patterns and three stop codon patterns were found in protein-coding genes. Only the tRNA-Ser(AGY) could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. A phylogenetic tree based on the neighbour-joining method was constructed to provide relationship within Beloniformes, which could be a useful basis for management of this species.

The complete mitochondrial genome of Hyporhamphus quoyi (Beloniformes; Hemiramphidae)

Abstract The complete mitogenome of Hyporhamphus quoyi was sequenced, which is a closed double-stranded circular molecule of 16,511 bp, and we analyzed the main features in terms of the genome organization, gene arrangement and codon usage. The overall base composition includes A(27.4%), T(26.0%), C(30.4%) and G(16.2%). Moreover, the 13 protein-coding genes (PCGs) encode 3804 amino acids in total, 12 of which use the initiation codon ATG except COI uses GTG, most of them have a complete stop codon, whereas Cytb ends with the incomplete stop codon represented as a single T. The phylogenetic tree based on the neighbor-Joining method was conducted to provide relationship within Beloniformes, based on 12 PCGs encoded by the heavy strand, the NJ tree demonstrated that H. quoyi has a closest relationship with Hyporhamphus intermedius, which could be a useful basis for propagation of this species.

The complete mitochondrial genome of Lagocephalus sceleratus (Tetraodontiformes; Tetraodontidae) and phylogenetic studies of Tetraodontidae

Abstract The complete mitochondrial genome sequence of Lagocephalus sceleratus was determined. The complete mitochondrial genome was 16,444 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding region (the control region and the origin of light strand replication). The overall base composition was A 27.59%, C 31.43%, G 17.12%, T 23.85%. All protein-coding genes started with an ATG initiation codon, except COI used GTG. With the exception of ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. Additionally, the phylogenetic relationship of 37 Tetraodontidae species based on the complete genome was analyzed, and the result showed that L. sceleratus was clustered with other Lagocephalus species. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Tetraodontidae.

The complete mitochondrial genome of Hemiramphus far (Beloniformes; Hemiramphidae) and phylogenetic studies of Beloniformes

Abstract The complete mitochondrial genome of this species was first determined in this study, which is 16,544 bp in length, the overall base composition includes C(27.0%), A(30.7%), T(27.1%) and G(15.2%). Moreover, the 13 protein-coding genes (PCGs) encode 3801 amino acids in total, 12 of which use the initiation codon ATG except COI uses GTG, most of them have TAA or TAG as the stop codon, whereas four protein-coding genes (COII, COIII, ND4 and Cytb) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the neighbour-joining method was constructed to provide relationship within Beloniformes, the result supported that H. far was clustered with Hyporhamphus dussumieri.

The complete mitochondrial genome of Sardinella lemuru (Clupeinae, Clupeidae, Clupeoidei) and phylogenetic studies of Clupeoidei

Abstract The complete mitochondrial genome of Sardinella lemuru was sequenced using PCR amplification and primer walking sequence method. The complete mitochondrial genome of S. lemuru was 16,616 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The overall base composition was A 25.04%, C 29.36%, G 20.40%, T 25.20%. In this study, the gene arrangement was consistent with other Sardinella mitochondrial genomes. Additionally, the phylogenetic relationships of 23 Clupeoidei species based on the complete genome was analyzed, and the result showed that S. lemuru firstly clustered with other two Sardinella species, S. albella and S. maderensis. These results would be useful for the investigation of phylogenetic relationship, taxonomic classification and phylogeography of the Clupeoidei.

The complete mitochondrial genome of Hyporhamphus dussumieri (Beloniformes; hemiramphidae) and phylogenetic studies of Beloniformes

Abstract The Hyporhamphus dussumieri is a kind of minor commercial fishes, usually marketed fresh and dried salted. However, to date, there is a limited genetic resource available for this species. In this study, we assembled the whole mitochondrial genome of this species yielding a 16,542 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes C(28.3%), A(28.9%), T(27.1%), and G(15.7%). Moreover, the 13 PCGs encode 3800 amino acids in total. The result of the phylogenetic tree supports H. dussumieri has a closest relationship with Hemiramphus far.