Complete Mitochondrial DNA Sequence Research Articles

The complete mitochondrial genome sequence of Oceanic whitetip shark, Carcharhinus longimanus (Carcharhiniformes: Carcharhinidae)

The complete mitochondrial DNA sequence of Carcharhinus longimanus was determined and analyzed. The complete mtDNA genome sequence of C. longimanus was 16,706 bp in length. It contained 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 2 non-conding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of C. longimanus can provide a useful data for further studies on molecular systematics, stock evaluation, taxonomic status and conservation genetics.

The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae)

Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae), is a monotypic genus species only found in the Qinghai–Tibet plateau of China. Due to human disturbance and related environmental change since the 1950s, the population of P. extremus declined rapidly. As a result, it was listed in the China Red Data Book of Endangered Animal and the China’s Protected Species Priority List. There exist very limited researches done on P. extremus. The poor understanding of this species limits the effective protection on this species. Here, we determined the complete mitochondrial DNA sequence of P. extremus. The results show that the mitogenome is 16,651 bp in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: control region (D–loop) and origin of light-strand replication (OL). These baseline mitogenomic data provided by this study will facilitate the studies on P. extremus in genetics, developmental biology and conservation biology in the future.

The complete mitochondrial genome of the hybrid of Siniperca chuatsi (♀) × Siniperca kneri (♂)

In this study, we reported the complete mitochondrial DNA sequence of the hybrid of Siniperca chuatsi (♀)×Siniperca kneri (♂). The total length of the mitochondrial genome is 16,493 bp, with the base composition of 28.61% A, 29.21% C, 16.21% G, and 25.97% T. It contains 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a major non-coding control region (D-loop region). The composition and order of these genes are identical to most of other vertebrates. All the protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid of Siniperca chuatsi (♀) × Siniperca kneri (♂) provides an important data set for the study in genetic mechanism.

Mitochondrial tRNAArg T10454C variant may not influence the clinical expression of deafness associated 12S rRNA A1555G mutation

In this study, we examined the “pathogenic” role of the T10454C mutation in mitochondrial tRNAArg gene in deafness expression as increasing reports provided an active role of this mutation in clinical manifestation of deafness associated 12S rRNA A1555G mutation. For this purpose, we reanalyzed the complete mitochondrial DNA (mtDNA) sequence data containing the T10454C mutation. Moreover, we analyzed the reported “polymorphisms” of mtDNA in the proband using the phylogentic approach. To our surprise, other mutations which occurred at protein-coding genes played more important roles in resulting mitochondrial dysfunctions by using the bioinformatic tool. In addition, evolutionary conservation analysis of the T10454C mutation indicated that this mutation was not conserved between different species. To our knowledge, this is the first report that the T10454C variant may not modulate the phenotypic expression of the deafness associated A1555G mutation.

The complete mitochondrial genome of the hybrid of Siniperca chuatsi (♀) × Siniperca scherzeri (♂)

In this study, we determined the complete mitochondrial DNA sequence of the hybrid of Siniperca chuatsi (♀) × Siniperca scherzeri (♂). The total length of the hybrid mitogenome is 16,497 bp, with the base composition of 28.61% A, 29.16% C, 16.23% G, and 26.00% T. It contains 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region. The composition and order of these genes are identical to most of other vertebrates. All the protein-coding genes start with ATG, except for COX1 with the initiation codon GTG. Three types of stop codons are used by the coding genes, including complete stop codons (TAA and TAG) and an incomplete stop codon (T). Three conserved domains were observed in the control region. The complete mitogenome of the hybrid of S. chuatsi (♀) × S. scherzeri (♂) could contribute to a better solution of the study in mitochondrial inheritance mechanism.

The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes)

AbtractPaecilomyces hepiali, belonging to the Eurotiales order Ascomycota, is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. Here, we report the complete mitochondrial DNA sequences of P. hepiali for the first time. The genome is 24,245 bp in length, encoding 15 protein-coding genes (PCGs), 2 rRNA genes, 25 tRNA genes and 3 homing endonucleases. The overall AT composition is 73.37% and the average AT content of PCG, rRNA, tRNA and non-coding region are 74.21%, 66.07%, 62.83% and 75.96%, respectively. Phylogenetic analysis with eight Ascomycota species and thirteen Basidiomycota species revealed that P. hepiali is was more closely related to Cordyceps bassiana, Cordycep smilitaris and Cordyceps brongniartii. It is confirmed that P. hepiali is a derivative of Cordyceps sinensis. This study provided valuable information on the gene contents of the mitochondrial genome and would facilitate the study of function and evolution of P. hepiali.

The complete mitochondrial genome of snubnose pompano Trachinotus blochii (Teleostei, Carangidae)

The complete mitochondrial genome of Trachinotus blochii was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,558 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 29.21% for A, 15.74% for G, 26.49% for T, 28.56% for C, respectively, with a high A + T content (55.70%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The complete mitochondrial genome sequence of T. blochii can provide a basic data for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. blochii resource.

The mitochondrial genome of the red alga Kappaphycus striatus (“Green Sacol” variety): Complete nucleotide sequence, genome structure and organization, and comparative analysis

The complete mitochondrial (mt) DNA sequence of the rhodophyte Kappaphycus striatus (“Green Sacol” variety) was determined. The mtDNA is circular, 25,242 bases long (A+T content: 69.94%), and contains 50 densely packed genes comprising 93.22% of the mitochondrial genome, with genes encoded on both strands. Through comparative analysis, the overall sequence, genome structure, and organization of K. striatus mtDNA were seen to be highly similar with other fully sequenced mitochondrial genomes of the class Florideophyceae. On the other hand, certain degrees of genome rearrangements and greater sequence dissimilarities were observed for the mtDNAs of other evolutionarily distant red algae, such as those from the class Bangiophyceae and Cyanidiophyceae, compared to that of K. striatus. Furthermore, a trend was observed wherein the red algal mtDNAs tend to encode lesser number of protein-coding genes, albeit not necessarily shorter, as the organism becomes more morphologically complex. This trend is supported by the phylogenetic tree inferred from the concatenated amino acid sequences of the deduced protein products of cytochrome c oxidase subunit genes (cox1, 2, and 3).

Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs

Selection in genomic regions is prevalent in mammals; however, the effects of selection on the mitogenome are not clearly understood. We determined the complete mitochondrial DNA (mtDNA) sequences from six wild Tibetan pigs from the Tibetan plateau and four domestic pig breeds from the lowland of neighboring southwest China. Nucleotide diversity analysis using the sliding window method showed that the nucleotide diversity of wild Tibetan pigs in most regions of the mitogenome was higher than that of domestic pigs. The 12 s ribosomal RNA showed relatively lower nucleotide diversity in Tibetan pigs, suggesting purifying selection of these genes during high-altitude adaptation. More non-synonymous nucleotide substitutions in the ATP6 were found in wild Tibetan pigs, indicating adaptive selection in Tibetan pigs. The results suggested distinct impacts of natural selection and artificial selection upon the mitogenome, especially the mitochondrial signatures of adaptive evolution in wild Tibetan pigs under natural selection.

The complete mitochondrial genome of the Megalobrama skolkovii (Cyprinidae: Cultrinae)

The complete mitochondrial DNA (mtDNA) sequence of Megalobrama skolkovii was first presented in this study. The mitochondrial genome is 16,620 bp in length, including 13 protein-coding genes, 2 ribosomal RNA gens (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA) and a control region (D-loop), with the gene identical to that of typical vertebrates. The overall base composition of the light strand are 31.23% A, 24.73% T, 16.16% G and 27.88% C. Two copies of tandem repeat sequence was found in the control region.

A novel model of double replications and random loss accounts for rearrangements in the Mitogenome of Samariscus latus (Teleostei: Pleuronectiformes).

BackgroundAlthough more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements.ResultsIn the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained.ConclusionsWe propose a “Double Replications and Random Loss” model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-352) contains supplementary material, which is available to authorized users.

Complete mitochondrial genome of Florida pompano Trachinotus carolinus (Teleostei, Carangidae)

The complete mitochondrial genome sequence of Florida pompano Trachinotus carolinus was determined by the overlapped polymerase chain reaction. The complete mitochondrial DNA sequence is 16,544 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 28.68% for A, 16.27% for G, 26.00% for T, 29.06% for C, respectively, with a high A+T content (54.68%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The sequence data of T. carolinus can provide useful information for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. carolinus resource.

Complete mitogenome of the ixodid tick Ixodes pavlovskyi (Acari: Ixodida)

Here, we present complete mitochondrial DNA sequence of Ixodes pavlovskyi Pom., 1946 for the first time. The mitogenome is 14,575 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The overall base composition is 40.1% T, 13.8% C, 37.9% A and 8.1% G. Four protein-coding genes are initiated by ATT codon, three genes – by ATA codon and ATG start codon is found for six genes. Only tRNA-Lys, tRNA-Ile, tRNA-Arg are folded into the cloverleaf secondary structure, other tRNA have atypical structure with reduced T- or D-arms.

Complete mitochondrial genome of the Yellownose skate: Zearaja chilensis (Rajiformes, Rajidae)

The complete sequence of mitochondrial DNA of a Yellownose skate, Zearaja chilensis was determined for the first time. It is 16,909 bp in length covering 2 rRNA, 22 tRNA and 13 protein coding genes with the identical gene order and structure as those of other Rajidae species. The nucleotide of L-strand is composed of low G (14.3%), and slightly high A + T (58.9%) nucleotides. The strong codon usage bias against the use of G (6.0%) is found at the third codon positions. Twelve of the 13 protein coding genes use ATG as the start codon while COX1 starts with GTG. As for the stop codon, only ND4 shows an incomplete stop codon TA. This is the first report of the mitogenome for a species in the genus Zearaja, providing a valuable source of genetic information on the evolution of the family Rajidae and the genus Zearaja as well as for establishment of a sustainble fishery management plan of the species.

The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae)

The complete mitochondrial DNA (mtDNA) sequence of Rhodeus fangi is 16,733 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes and 2 non-coding regions. Base composition of the genome is A (28.54%), G (17.67%), C (27.03%) and T (26.76%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes. The complete mitogenome of the R. fangi can provide a basic data for phylogenetic relationship study and useful information for taxonomic identification of the R. smithii complex in genus Rhodeus.

The complete mitochondrial genome of the Zig-zag eel Mastacembelus armatus (Teleostei, Mastacembelidae)

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Mastacembelus armatus was determined. The mitochondrial genome is 16,486 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a noncoding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand are 25.28% of A, 29.13% of T, 14.65% of C and 30.93% of G, with a slight AT bias of 54.41%. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand.

Comparative analyses of the complete mitochondrial genomes of the two ruminant hookworms Bunostomum trigonocephalum and Bunostomum phlebotomum

Bunostomum trigonocephalum and Bunostomum phlebotomum are blood-feeding hookworms of sheep and cattle, causing considerable economic losses to the live stock industries. Studying genetic variability within and among hookworm populations is critical to addressing epidemiological and ecological questions. Mitochondrial (mt) DNA is known to provide useful markers for investigations of population genetics of hookworms, but mt genome sequence data are scant. In the present study, the complete mitochondrial DNA (mtDNA) sequences of the sheep and goat hookworm B. trigonocephalum were determined for the first time, and the mt genome of B. phlebotomum from yak in China was also sequenced for comparative analyses of their gene contents and genome organizations. The lengths of mt DNA sequences of B. trigonocephalum sheep isolate, B. trigonocephalum goat isolate and B. phlebotomum China yak isolate were 13,764bp, 13,771bp and 13,803bp in size, respectively. The identity of the mt genomes was 99.7% between B. trigonocephalum sheep isolate and B. trigonocephalum goat isolate. The identity of B. phlebotomum China yak isolate mt genomes was 85.3% with B. trigonocephalum sheep isolate, and 85.2% with B. trigonocephalum goat isolate. All the mt genes of the two hookworms were transcribed in the same direction and gene arrangements were consistent with those of the GA3 type, including 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes, but lacking ATP synthetase subunit 8 gene. The mt genomes of B. trigonocephalum and B. phlebotomum were similar to prefer bases A and T, the contents of A+T are 76.5% (sheep isolate), 76.4% (goat isolate) and 76.9% (China yak isolate), respectively. Phylogenetic relationships reconstructed using concatenated amino acid sequences of 12 protein-coding genes with three methods (maximum likelihood, Bayesian inference and neighbor joining) revealed that the B. trigonocephalum and B. phlebotomum represent distinct but closely-related species. These data provide novel and useful genetic markers for studying the systematics, and population genetics of the two ruminant hookworms.

The complete mitochondrial genome sequence of Coreoperca whiteheadi (Perciformes: Serranidae)

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Coreoperca whiteheadi was determined. The complete mtDNA genome sequence of C. whiteheadi is 16,483 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome is estimated to be 28.30% for A, 29.33% for C, 16.06% for G and 26.32% for T, respectively, with a high A + T content (54.62%). The complete mitogenome of the C. whiteheadi could contribute to basic researches on population history, molecular systematics and phylogeography. It is also helpful to the reasonable utilization and development of rational management strategies for C. whiteheadi resource.

The complete mitochondrial genome of Aspiorhynchus laticeps and its phylogenetic analysis

The complete nucleotide sequence of the mitochondrial genome (mitogenome) of Aspiorhynchus laticeps was determined. The length of the complete mitochondrial DNA sequence of A. laticeps is 16,591bp, which consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding region ‘D-loop’. Except for the D-loop, another non-coding region named replication origin of L-strand (OL) region was also found. According to the phylogenetic analysis, A. laticeps has a closer relationship with Schizothorax.

The complete mitochondrial genome of the Gray's grenadier anchovy Coilia grayii (Teleostei, Engraulidae)

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Coilia grayii was determined. The mitochondrial genome was 16,851 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a non-coding control region as those found in other vertebrates, with the gene identical to that of typical vertebrates. The overall base composition of the heavy strand were 26.09% of A, 31.14% of T, 15.58% of C and 27.19% of G, with a slight AT bias of 57.23%. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand.