Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116?bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146?bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

The complete mitochondrial genome of the spotted steed, Hemibarbus maculatus (Teleostei, Cypriniformes)

The complete mitogenome sequence of the spotted steed (Hemibarbus maculatus) was determined using long PCR reactions. The genome is 16,611 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition of H. maculatus was similar to that of most other vertebrates. The base composition of H-strand in descending order is A (29.16%), C (27.41%), T (25.93%), and G (17.50%), with an AT content of 55.09%. The Kimura two-parameter distances between mitogenome sequences of H. maculatus and Hemibarbus labeo, Hemibarbus barbus, Hemibarbus longirostris, Hemibarbus mylodon were 2.09%, 2.35%, 12.77%, and 13.92%, respectively. The phylogenetic relationships among the five Hemibarbus species based on the whole mitogenome sequence data were (((H. barbus, H. labeo), H. maculatus), (H. longirostris, H. mylodon)).     

Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei)

The complete mitochondrial genome of Trypauchen vagina was determined first. The genome is 16,686 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of T. vagina is T 27.6%, C 27.6%, A 29.5%, and G 15.3%, with a slight A+T bias of 57.1%. In addition to the discrete and conserved sequence blocks, an incomplete tandem repeat unit is detected within the CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Mitochondrial genome of Silurus asotus (Teleostei: Siluriformes)

The complete mitogenome sequence of the Amur catfish Silurus asotus was determined using long PCRs. The genome was 16,528 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region; the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand is 30.5% A, 25.8% T, 28.0% C, and 15.8% G, with an AT content of 56.3%. The mtDNA sequence of S. asotus shared 93.6% and 90.6% sequence identity with that of Silurus meridionalis and Silurus glanis. This mitogenome sequence data would play an important role in silurid catfish phylogenetics and siluriform catfish systematics in general.     

Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes)

The complete mitogenome sequence of a vulnerable species Onychostoma lini was determined using polymerase chain reaction and directly sequenced with primer walking method. The complete mitogenome was 16,595?bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene order and composition of O. lini was similar to most other fishes. The descending order of the base composition on heavy strand was 31.6% A, 27.9% C, 24.6% T, and 15.9% G, with a relatively lower level of G and a slight AT bias of 56.2%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The complete mitogenome sequence of O. lini provides fundamental data for further conversation genetics and captive breeding studies on this species.     

The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)

The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.     

Complete mitochondrial genome of Chilo suppressalis (Walker) (Lepidoptera: Crambidae)

The complete sequence of the mitochondrial genome (mitogenome) of the rice stem borer Chilo suppressalis (Walker) (Lepidoptera: Crambidae) was determined to be 15,465 bp. It contains 13 protein-coding genes (PCGs), 22 tRNA genes, the large and small rRNA genes, and an A+T-rich region. The nucleotide composition of the mitogenome of C. suppressalis is highly A+T biased, accounting for 79.70% in whole mitogenome, 77.74% in PCGs, 84.70% in tRNAs, 81.20% in rRNAs and 94.19% in A+T-rich region, respectively. The PCGs have typical ATN start codons, except for cox1, which contains the unusual CGA. The C. suppressalis A+T-rich region contains a conserved structure combining the motif ATAGA and a 19-bp poly-T stretch, but absence of the 9-bp poly-A element upstream trnM.     

Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.     

The mitochondrial genome of the quiet-calling katydids, <Emphasis Type="Italic">Xizicus fascipes</Emphasis> (Orthoptera: Tettigoniidae: Meconematinae)

To help determine whether the typical arthropod arrangement was a synapomorphy for the whole Tettigoniidae, we sequenced the mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae). The 16,166-bp nucleotide sequences of X. fascipes mitogenome contains the typical gene content, gene order, base composition, and codon usage found in arthropod mitogenomes. As a whole, the X. fascipes mitogenome contains a lower A+T content (70.2%) found in the complete orthopteran mitogenomes determined to date. All protein-coding genes started with a typical ATN codon. Ten of the 13 protein-coding genes have a complete termination codon, but the remaining three genes (COIII, ND5 and ND4) terminate with incomplete T. All tRNAs have the typical clover-leaf structure of mitogenome tRNA, except for tRNA(Ser(AGN)), in which lengthened anticodon stem (9 bp) with a bulged nuleotide in the middle, an unusual T-stem (6 bp in constrast to the normal 5 bp), a mini DHU arm (2 bp) and no connector nucleotides. In the A+T-rich region, two (TA)n conserved blocks that were previously described in Ensifera and two 150-bp tandem repeats plus a partial copy of the composed at 61 bp of the beginning were present. Phylogenetic analysis found: i) the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and ii) Meconematinae was the most basal group among these five subfamilies.     

The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes)

The Chinese rare minnow, Gobiocypris rarus, which is endemic to China, is an attractive aquatic laboratory animal in China. In the present study, the complete mitogenome sequence of G. rarus has been determined using long polymerase chain reaction (PCR) method. It was 16,601 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, the gene composition and order of which are similar to most other vertebrates. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 29.5% A, 27.6% T, 25.7% C, and 17.2% G, with a slight AT bias of 57.1%. There are 10 regions of gene overlap totaling 27 bp and 13 intergenic spacer regions totaling 63 bp. The mitogenome sequence of G. rarus could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the whole mitogenomic data.     

The complete mitochondrial genome of silver croaker Argyrosomus argentatus (Perciforems; Sciaenidae): genome characterization and phylogenetic consideration

The complete mitochondrial genome sequence of the silver croaker, Argyrosomus argentatus, was obtained by using LA-PCR and sequencing. The mitogenome is 16485 bp in length, consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region like those found in other vertebrates, with the gene order similar to that of typical teleosts. Most of the genes of A. argentatus were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro)) genes were encoded on the L-strand. The reading frames of two pairs of genes overlapped: ATPase8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The origin of L-strand replication in A. argentatus was in a cluster of five tRNA genes (WANCY) and was 46 nucleotides in length. The conserved motif (5'-GCGGG-3') was found at the base of the stem within the tRNA(Cys) gene. Within the control region, we identified all of the conserved motifs except for CSB-F.     

Mitochondrial Genome of the Stonefly Kamimuria wangi (Plecoptera: Perlidae) and Phylogenetic Position of Plecoptera Based on Mitogenomes

This study determined the mitochondrial genome sequence of the stonefly, Kamimuria wangi. In order to investigate the relatedness of stonefly to other members of Neoptera, a phylogenetic analysis was undertaken based on 13 protein-coding genes of mitochondrial genomes in 13 representative insects. The mitochondrial genome of the stonefly is a circular molecule consisting of 16,179 nucleotides and contains the 37 genes typically found in other insects. A 10-bp poly-T stretch was observed in the A+T-rich region of the K. wangi mitochondrial genome. Downstream of the poly-T stretch, two regions were located with potential ability to form stem-loop structures; these were designated stem-loop 1 (positions 15848–15651) and stem-loop 2 (15965–15998). The arrangement of genes and nucleotide composition of the K. wangi mitogenome are similar to those in Pteronarcys princeps, suggesting a conserved genome evolution within the Plecoptera. Phylogenetic analysis using maximum likelihood and Bayesian inference of 13 protein-coding genes supported a novel relationship between the Plecoptera and Ephemeroptera. The results contradict the existence of a monophyletic Plectoptera and Plecoptera as sister taxa to Embiidina, and thus requires further analyses with additional mitogenome sampling at the base of the Neoptera.     

The complete nucleotide sequence of the mitochondrial genome of <Emphasis Type="Italic">Phthonandria atrilineata</Emphasis> (Lepidoptera: Geometridae)

Using long-polymerase chain reaction (Long-PCR) method, we determined the complete nucleotide sequence of the mitochondrial genome (mitogenome) of Phthonandria atrilineata. The complete mtDNA from P. atrilineata was 15,499 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The P. atrilineata genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. The nucleotide composition of P. atrilineata mitogenome was biased toward A + T nucleotides (81.02%), and the 13 PCGs show different A + T contents that range from 73.25% (cox1) to 92.12% (atp8). Phthonandria had the canonical set of 22 tRNA genes, that fold in the typical cloverleaf structure described for metazoan mt tRNAs, with the unique exception of trnS(AGN). The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, which confirmed that P. atrilineata is most closely related to the superfamily Bombycoidea.     

Complete mitochondrial genome of the jackknife clam Solen grandis (Veneroida, Solenidae)

The complete mitochondrial genome sequence of Solen grandis that lives in sub-tidal waters and being buried in muddy to fine sand substrates, is described in this paper. The mitogenome (16,794?bp) consists of 12 protein-coding genes (loss of ATPase subunit 8), 22 tRNA genes, 2 rRNA genes and 1 putative control region. It is the typical bivalve mitochondrial gene composition.     

社鼠（Niviventer confucianus）线粒体基因组全序列分析

社鼠（Niviventer confucianus）属于啮齿目（Rodentia）、鼠科（Muridae）、白腹鼠属（Niviventer）,关于该物种的分子系统学研究极少。为获取社鼠线粒体基因组全序列,提取其基因组总DNA,参照近缘物种线粒体基因组全序列设计34对特异性引物,利用PCR扩增全部片段后进行测序,之后对其基因组组成及结构特点进行了初步分析。结果表明,社鼠线粒体基因组全序列长16 281 bp（GenBank收录号：KJ152220）,包含22个tRNA基因、13个蛋白质编码基因、2个rRNA基因和1个非编码控制区;基因组核苷酸组成为34.0%A、28.6%T、24.9%C、12.5%G。将所得序列与社鼠近缘物种（川西白腹鼠、小家鼠、褐家鼠）的线粒体全基因组进行比较,结果显示,四个物种的线粒体基因组虽然在基因组大小、部分tRNA二级结构、部分蛋白质编码基因的起始或终止密码子及控制区长度和碱基组成上有差异,但基因组结构和序列特征方面都具有较高的相似性。四个物种线粒体全基因组间的遗传距离显示,社鼠与川西白腹鼠距离最近,而与小家鼠距离最远。该研究为利用线粒体全基因组信息进行啮齿类分子系统学研究提供了有价值的资料。     

Complete mitochondrial genome of the red drum, Sciaenops ocellatus (Perciformes, Sciaenidae): absence of the typical conserved motif in the origin of the light-strand replication

In this study, the complete mitochondrial genome of the red drum Sciaenops ocellatus was determined first. The genome was 16,500?bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication); the gene composition and order of which were similar to most other vertebrates. The overall base composition of the heavy strand was T 25.5%, C 30.7%, A 27.5%, and G 16.3%, with a slight AT bias of 53%. Within the control region, the discrete and conserved sequence blocks were identified. Motif 5'-ACCGG-3' rather than 5'-GCCGG-3' was detected in the origin of light-strand replication (O(L)) of red drum, which is rare in the mitogenomes of Sciaenidae species. These results would play an important role in elucidating sequence-function relationships of the O(L).     

Complete mitochondrial genome of the boreal digging frog Kaloula borealis (Anura, Microhylidae)

We sequenced the complete mitochondrial genome from the boreal digging frog Kaloula borealis. The genome sequence was 17,173 bp in size, and the gene order and contents were identical to those of previously reported amphibian mitochondrial genomes. Of 13 protein-coding genes (PCGs), 5 genes (CO2, ATPase 6, CO3, ND3, and ND4) had incomplete stop codons. Also ND1 gene used GTG as a start codon, while CO1 and ND5 genes used AGG as a stop codon. The base composition of K. borealis mitogenome showed a strong anti-G bias (6.11%) on the 3rd position of PCGs.     

Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae

The monophyly and phylogenetic relationships of Pseudosciaeniae have long been controversial. Here we describe the mitochondrial genome (mitogenome) sequence of Collichthys niveatus. It is a circular double-stranded DNA molecule of 16,450 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes as well as a non-coding control region. The mitogenome of C. niveatus shared common features with those of other bony fishes in terms of gene arrangement, base composition, and tRNA structures. The C. niveatus mitogenome exhibited pronounced strand-specific asymmetry in nucleotide composition, which was also reflected in the codon usage of genes oriented in opposite directions. Contrary to the typical structure of the control region, the central conserved blocks (CSB-D, -E, and -F) could not be detected in C. niveatus mitogenome. Phylogenetic analysis based on whole mitogenome sequences provided strong support for the monophyly of Pseudosciaeniae, and sister-group relationships of C. niveatus + Collichthys lucidus and Larimichthys crocea + Larimichthys polyactis, which was consistent with the traditional taxonomy. Unexpected divergence was found in two C. niveatus mitogenomes and several hypotheses were proposed to explain this observation including misidentification and introgressive hybridization between C. niveatus and L. polyactis, and polyphyletic origin of C. niveatus. We considered species misidentification to be the main hypothesis. However, additional data is essential to test these proposed hypotheses.     

Mitochondrial genome of <Emphasis Type="Italic">Pteronotus personatus</Emphasis> (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations

We described the complete mitochondrial genome (mitogenome) of the Wagner’s mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.