Mitochondrial DNA

Published by Informa Healthcare
Online ISSN: 1940-1744
Publications
Article
Abstract Hemibarbus is a genus of cyprinid fishes distributed in eastern Asia. In the present study, we report here the complete mitochondrial genome of the Hemibarbus sp.090914 (Cypriniformes: Cyprinidae). Our results show that the complete mitochondrial DNA of Hemibarbus sp.090914 is 16,610 bp in length, and predicted to encode all the 37 genes that are typical for the vertebrates.
 
Article
Abstract Recently, a growing number of reports had shown the association between mitochondrial DNA (mtDNA) sequence variants and aplastic anemia (AA). Owing to its high mutation rate, mtDNA variant had become biomarker for clinical and molecular diagnosis for AA. However, the relationship between mtDNA variant and AA was largely unknown. In this study, we reanalyzed the possible association between a "pathogenic" mutation A10055G in mt-tRNA(Gly) gene and AA, through the application of bioinformatics tool, we found that this mutation did not alter the secondary structure of tRNA(Gly), the pathogenicity scoring system indicated that the score of this mutation was only two points and belonged to a "neutral polymorphism", suggested that the role of A10055G mutation in clinical expression in AA needed to be further experimentally addressed.
 
Article
Abstract This study evaluates the mitochondrial noncoding regions by using the Sanger sequencing method for application in Forensic Science. FTA® Technology (FTA™ paper DNA extraction) was utilized to extract DNA. Portion of coding region encompassing positions from (10,716 to 11,184) amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column were then sequenced and detected using the ABI 3730 × L DNA Analyzer. A new polymorphic positions 10,750 and 10,790 that are described may be suitable sources in future for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence, most promising for identification variants.
 
Number of studies citing the DNA taxonomy (Tautz et al. 2003) in the past 7 years (2003–2009) based on the scopus database: (a) total number of studies, (b) number of experimental studies per application, and (c) number of experimental studies per taxonomic group.  
Number of studies citing DNA barcoding (Hebert et al. 2003a,b) in the past 7 years (2003–2009) based on the scopus database: (a) total number of studies, (b) number of experimental studies per application, and (c) number of experimental studies per taxonomic group.  
Article
In 2003, two different approaches-DNA taxonomy and DNA barcoding-were simultaneously proposed to overcome some of the perceived intrinsic weaknesses of the traditional morphology-based taxonomical system, and to help non-taxonomists to resolve their crucial need for accurate and rapid species identification tools. After 7 years, it seems unlikely that a completely new taxonomical system based on molecular characters only (DNA taxonomy) will develop in the future. It is more likely that both morphological and molecular data will be simultaneously analyzed, developing what has been coined as "integrative taxonomy". Concerning DNA barcoding, it is now clear that it does not focus on building a tree-of-life nor to perform DNA taxonomy, but rather to produce a universal molecular identification key based on strong taxonomic knowledge that is collated in the barcode reference library. The indisputable success of the DNA barcoding project is chiefly due to the fact that DNA barcoding standards considerably enhance current practices in the molecular identification field, and standardization offers virtually endless applications for various users.
 
Article
Abstract Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes/Leigh (MELAS/LS) overlap syndrome is a mitochondrial disorder subtype with clinical and magnetic resonance imaging (MRI) features that are characteristic of both MELAS and Leigh syndrome (LS). Here, we report an MELAS/LS case presenting with cortical deafness and seizures. Cranial MRI revealed multiple lesions involving bilateral temporal lobes, the basal ganglia and the brainstem, which conformed to neuroimaging features of both MELAS and LS. Whole mitochondrial DNA (mtDNA) sequencing and PCR-RFLP revealed a de novo heteroplasmic m.10197 G > A mutation in the NADH dehydrogenase subunit 3 gene (ND3), which was predicted to cause an alanine to threonine substitution at amino acid 47. Although the mtDNA m.10197 G > A mutation has been reported in association with LS, Leber hereditary optic neuropathy and dystonia, it has never been linked with MELAS/LS overlap syndrome. Our patient therefore expands the phenotypic spectrum of the mtDNA m.10197 G > A mutation.
 
Electrophoretic analysis of chicken-specific amplification products (95 bp) obtained from (1) raw chicken meat, (2) cattle raw meat, (3) raw sheep meat, (4) binary mixture (chicken raw meat 50% and cattle raw meat 50 %), (5) chicken balls, (6) chicken sausage-1, (7) chicken luncheon, (8) chicken sausage-2, (9) chicken burger, (10) chicken sausage-2, (11) chicken sausage-3, (12) chicken burger-2, (13) chicken mined meat, (14) chicken minced meat-2, (15) chicken minced meat-3. A 100 bp DNA ladder was loaded at the right side of the figure.  
Sequences of the 12S primers used in this study.
Electrophoretic analysis of turkey-specific amplification products (122 bp) obtained from (1) raw chicken meat, (2) cattle raw meat, (3) binary mixture (chicken raw meat 50% and cattle raw meat 50%), (4) raw sheep meat, (5) chicken balls, (6) chicken sausage-1, (7) chicken luncheon, (8) chicken sausage-2, (9) chicken burger, (10) chicken sausage-2, (11) chicken sausage-3, (12) chicken burger-2, (13) chicken mined meat, (14) chicken minced meat-2, (15) chicken minced meat-3. A 100 bp DNA ladder was loaded at the right side of the figure.
Species-specific amplification results.
Article
Abstract The aim of this study is to detect the fraudulent in chicken products constitutes in order to protect consumers in Saudi Arabia from illegal substitutions. Two different approaches were used in this study, direct sequencing of specific fragments of amplified mitochondrial 12S rRNA gene in addition to species-specific PCR primers for confirmation of the obtained Blast search results. The results showed that all processed chicken products were identified as chicken (Gallus gallus) by 90-98% homology depending on obtained sequence quality. Samples labeled with chicken luncheon (samples tested in this study) were identified as turkey meat (Meleagris gallopavo) by 98% homology, suggesting adulteration with inedible parts of turkey in chicken luncheon ingredients. The results showed also that not only chicken luncheon was mixed with inedible parts of turkey but also all chicken products tested in this study (chicken balls, chicken burger, chicken sausage and chicken mined meat) contained this turkey meat. Applying methods used in this study could be useful for accurate and rapid identification of commercial processed meat.
 
Article
Abstract To study the genetic relationships of Pomacea canaliculata collected from rice fields in China, the mitochondrial (mt) 12S and 16S of 9 P. canaliculata isolates from 5 southern provinces in China were sequenced and analyzed. The intra-specific sequence variations of P. canaliculata were 0-1.1% for 12S and 0--0.6% for 16S, while the inter-specific variations among common Pomacea species in mt 12S and 16S were 3.0-11.7% and 2.3-10.1%, respectively. Phylogenetic analysis based on combined sequences of mt 12S and 16S revealed complex genetic structure of P. canaliculata in China. Two phylogenetic groups of P. canaliculata were indicated in China with one group sistered to P. canaliculata isolates from USA, and two groups were even found in the same province. The phylogenetic relationships of Pomacea spp. also could be effectively inferred by combined sequences of mt 12S and 16S. These findings provided basic information for further study of population genetics and diffusion pattern of P. canaliculata in China as well as in the world.
 
Article
Characterization of species-specific molecular markers and development of a method for identification of Indian deer species is necessary to monitor illegal trade of parts and products for better conservation and management of the endangered species. In this investigation, we characterized the 12S rRNA gene sequence for differentiation of Indian deer species and developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based method for their identification. Universal primers were used for the amplification of the mitochondrial 12S rRNA gene from genomic DNA of chital or spotted deer, hog deer, barking deer, sika deer, musk deer and sambar. PCR products of chital, hog deer and Himalayan musk deer were cloned and sequenced for the first time. Among the Indian deer species, more than 90% similarity was observed in the mitochondrial 12S rRNA gene. The sequences of the above deer species were restriction mapped with the help of Lasergene (DNAstar Inc., Madison, WI, USA). PCR amplicon of these deer species were subjected to restriction digestion with Rsa1, Dde1, Bsr1 and BstSF1 endonucleases that showed a species-specific RFLP pattern. This technique provides a reliable and efficient tool for identification of deer species using a variety of biomaterials.
 
Article
Abstract An effective DNA-based molecular method had been used to identify avian species from meats. The method combined the use of a pair of universal primers, which amplified about 440-bp fragment of the mitochondrial 12S rRNA gene. A total of 99 meat samples were tested and 17 haplotypes were identified by DNA sequencing, which representing 14 avian species. One avian species was listed as the national first-grade protected animal in China and the IUCN endangered species. Two avian species were under the national second-grade state protection. The proposed method represents a straightforward and robust method for the accurate identification of avian species that could be used by law enforcement agencies as a tool for the control of illegal trade of meat from protected species.
 
Article
The efficacy of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial 12S rRNA gene in identification of goat cashmere and sheep wool samples was evaluated. The specific fragments of the mitochondrial 12S rRNA gene, which were about 440 bp, were obtained using the PCR. Restriction enzyme digestion of the PCR products with endonucleases BspT I and Hinf I revealed species-specific RFLP patterns. Application of this technique on mixed samples could identify goat cashmere and sheep wool from each other within the proportion of 8:1. The technique, however, could detect only one species when the proportion of mixture was more than 9:1. The PCR-RFLP technique was demonstrated to possess potential value in precise identification of goat cashmere and sheep wool.
 
Collection sites (marked f) for wild samples from Mahanadi (Cuttack (20.27 N85.52 E)), Godavari (Rajahmundry (16.59 N81.47 E)), and Krishna (Vijayawada (16.31 N80.37 E).  
Neighbor joining tree of six species (LR, Labeo rohita; CC, Catla catla; CM, Cirrhinus mrigala; LF, Labeo fimbriatus; LB, Labeo bata; CR, Cirrhinus reba) based on COI using Kimura-2-Parameter with Salmo salar as out-group.  
Neighbor joining tree of six species (LR, Labeo rohita; CC, Catla catla; CM, Cirrhinus mrigala; LF, Labeo fimbriatus; LB, Labeo bata; CR, Cirrhinus reba) based on 16 S rRNA using Kimura-2-Parameter with Salmo salar as out-group.  
Article
Abstract The 5' region of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) is the standard marker for DNA barcoding. However, 16 S rRNA has also been advocated for DNA barcoding in many animal species. Herein, we directly compare the usefulness of COI and 16 S rRNA in discriminating six cultivable carp species: Labeo rohita, Catla catla, Cirrhinus mrigala, Labeo fimbriatus, Labeo bata and Cirrhinus reba from India. Analysis of partial sequences of these two gene fragments from 171 individuals indicated close genetic relationship between Catla catla and Labeo rohita. The results of the present study indicated COI to be more useful than 16 S rRNA for DNA barcoding of Indian carps.
 
Article
Abstract The aim of this study is to set up a protocol for identification of the adulteration in mutton based on mitochondrial 16S rRNA gene. The multiplex polymerase chain reaction (multi-PCR) assay was carried out to trace the impure DNA in mutton. A universal primer pair yielded an approximate 610 bp fragment in mutton, pork, duck, chicken, horse and cat meats. The amplicons of multi-PCR assay represented the species-specific products, which could be discriminated by the size ranging from 106 bp to 532 bp. Subsequently, the authentication of each fragment was also confirmed by sequencing. Random analyses of adulterants with various meats yielded the identical results to their components, showing the suitability of the multi-PCR assay for tracing of adulterant meats with high-accuracy and precision. This assay was sensitive to detect the species-specific DNA in different proportional mixtures of mutton and duck/pork (9.1%-90.9%). In conclusion, this multi-PCR assay successfully discriminated the double-, triple-, quadruple-, and quintuple-mixtures containing variant counterparts. This method will be particularly useful in the detection of mutton adulteration in processed foods further.
 
Sample collection sites.  
Sample collection sites of different Barilius species.
Images of Barilius bakeri (A), B. gatensis (B), B. vagra (C), B. bendelisis (D) and B. tileo (E).
Polymorphic sites showing base substitutions (transitionþtransversion) in 16 S rDNA sequences of Barilius species with five other Indian cyprinid fishes (dots showing similarity of bases).  
Article
Abstract Barilius is an important genus of fish family Cyprinidae, which comprises 22 species from Indian region. This study aimed to characterize five commonly occurring Bariline species, for example, Barilius bakeri. Barilius gatensis. Barilius vagra. Barilius bendelisis and Barilius tileo, across the country using partial mitochondrial 16 S rRNA gene, to estimate the order of inter- and intra-species divergence among these species and to establish phylogenetic and evolutionary relationships. The average inter-specific divergence was estimated as 7.10%. Intra-specific divergence of 0.20% and 0.10% was observed in B. gatensis and B. bendelisis that exhibited three and two haplotypes with 0.70 and 0.60 haplotype diversities, respectively. The NJ and MP phylogenetic trees were constructed using 16 S rRNA sequences along with sequences of the other five Indian cyprinid species retrieved from NCBI. Phylogenetic trees revealed five discrete branches each as a distinct species of the genus and exhibited identical phylogenetic relationship with other cyprinids. The study provided adequate information to distinguish the five Barilius species and indicated the suitability of 16S rRNA gene sequences in genetic divergence and phylogenetic studies.
 
Location and host species for the samples collected in the Tibet Plateau. Thirty-one and fourteen hydatid cysts were obtained from sheep in Qinghai and Tibet, respectively. Seventeen cysts were obtained from humans in Sichuan.  
Information regarding the 16 S gene sequences of the different Echinococcus cestodes used in this study.
A network of mtDNA haplotypes was illustrated by TCS 1.2 using statistical parsimony. Haplotype H1 lies at the center of the network. The length of the lines approximately indicates the number of mutational steps. The size of the circles approximately indicates the number of individuals.  
The phylogenetic tree obtained via the neighbor-joining (NJ) based on the 16 S gene. It showed that the haplotype H7 clustered with G6 genotype in a separate clade, while the rest haplotypes all grouped with G1 and G3 to form a single large clade.
Article
Abstract Echinococcus granulosus is the etiological agent of cystic echinococcosis, a major zoonotic disease of both humans and animals. In this study, we assessed genetic variability and genetic structure of E. granulosus in the Tibet plateau, using the complete mitochondrial 16 S ribosomal RNA gene for the first time. We collected and sequenced 62 isolates of E. granulosus from 3 populations in the Tibet plateau. A BLAST analysis indicated that 61 isolates belonged to E. granulosus sensu stricto (genotypes G1-G3), while one isolate belonged to E. canadensis (genotype G6). We detected 16 haplotypes with a haplotype network revealing a star-like expansion, with the most common haplotype occupying the center of the network. Haplotype diversity and nucleotide diversity were low, while negative values were observed for Tajima's D and Fu's Fs. AMOVA results and Fst values revealed that the three geographic populations were not genetically differentiated. Our results suggest that a population bottleneck or population expansion has occurred in the past, and that this explains the low genetic variability of E. granulosus in the Tibet Plateau.
 
Sampling locations from the north of Turkey’s 40 8 north latitude. M1: I  ̇  ̆neada, Rumelifeneri, Silivri; M2: U  ̧makdere S  ̧ arko  ̈y; M3: Kaplıkaya Bursa, Go  ̈ kdere Bursa, Adapazarı; K1: Ak  ̧akoca Du  ̈ zce, Mengen Bolu; K2: Mengen Bolu, Yı  ̆ılca Du  ̈ zce, Kızılcahamam; K3: Pınarba  ̧ı Kastamonu, S  ̧ enpazar Kastamonu; K4: Sinop; K5: Ordu, Giresun, Trabzon, Gu  ̈ mu  ̈  ̧hane; K6: Trabzon, Gu  ̈ mu  ̈  ̧hane; K7: Artvin, Rize; D1: Posof, Ardahan; D2: S  ̧ enkaya, Erzurum. 
Median joining network of 13 haplotypes detected in the 16S rRNA dataset. Median vectors are shown with black squares and population nodes are drawn as gray, proportional to frequencies. Specimens sharing same haplotypes are given in Table III. 
Median joining network of 20 haplotypes detected in the cytochrome b dataset. Median vectors are shown with black squares and population nodes are drawn as gray, proportional to frequencies. Specimens sharing same haplotypes are given in Table IV. 
Neighbor joining tree generated using the 16S rRNA dataset. Neighbor joining tree is drawn to scale, with branch lengths in the same units as those of the genetic distances. Optimal tree with the sum of branch length 0.4982634 is shown. Evolutionary distance among specimens was computed using Kimura 2-parameter model. Bootstrap tests of 1000 replicates are given next to branches. 
Article
The taxonomic situation of Anguis fragilis species is still unclear in Turkey. In order to clarify this situation, we used the DNA sequences of 16S rRNA and cytochrome b genes to analyze the phylogenetic relationship among A. fragilis populations. A total of 13 haplotypes in 16S rRNA dataset and 20 haplotypes in cytochrome b dataset were detected. Kimura 2-parameter genetic distance was found to be 0.012 for 16S rRNA and 0.026 for the cytochrome b dataset. Neighbor joining (NJ) trees were constructed to analyze phylogenetic relationship among specimens and were supported with median joining networks. Results indicate a clear genetic structuring in A. fragilis populations sampled from north of 40° north latitude of Turkey. Both mitochondrial gene sequences successfully detected the intraspecific variation among specimens of different populations. Genetic structuring, correlated with geographic distance, was found to be significant at the specimens sampled from edge populations of peripherally isolated climatic conditions.
 
Article
Abstract The complete mitochondrial genome of Echeneis naucrates is 16,611 bp in length. It comprises a control region, 13 protein-coding genes, 2 ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs), with an arrangement typical of vertebrate mitochondrial genomes. Base composition on the heavy strand is 30.24% A, 25.45% C, 15.02% G and 29.29% T. The control region is 940 bp in length, containing putative termination associated sequences (TASs) and conserved sequence blocks (CSBs). Two copies of a tandem repeat (AATATTAT) were found in all six individuals investigated. The hypothesis of selection for an optimal number of repeats as well as the evolutionary dynamics of tandem repeats in E. naucrates control regions await further investigations.
 
Article
In Xia's taxonomic revision, Gomphocerus rufus (Linnaeus, 1758), Chorthippus chinensis and Phlaeoba albonema belong to the families Gomphoceridae, Arcypteridae and Acrididae, respectively; whereas in Otte's taxonomic analysis of Orthoptera, all three species belong to the subfamily Gomphocerinae, family Acrididae. We determined the mitochondrial genomes (mitogenomes) of G. rufus, compared these with 10 other caeliferan mitogenomes, and performed phylogenetic analyses in order to clarify the relationships of the three families in Xia's taxonomic revision and which study is more accurate in defining the relationships of the three families. Furthermore, the mitogenome of Primnoa arctica (Zhang and Jin, 1985) was determined. This is the first mitogenome of the subfamily Catantopinae, superfamily Acridoidea. Through the comparison of mitogenomes from six subfamilies of the superfamily Acridoidea and one species of Pyrgomorphoidea, we hope to summarize a general law on the composition of the caeliferan mitogenome. The two molecules contain the same set of mitochondrial genes for 22 tRNAs, 2 rRNAs, 13 proteins, and a non-coding, AT-rich region. The base composition, gene order, and codon usage of the two genomes conform to those reported for other caeliferan species. Both genomes possess the rearrangement of tRNA(Lys) and tRNA(Asp). Compared with their ancestral mitogenome, this is a significant difference between the mitogenome of the suborders Caelifera and Ensifera or other Metazoa. A stem-loop structure that is similar to a previously presumed one (that probably involved in replication initiation) was found at the A+T-rich region of each mitogenome. In the phylogenetic analyses, the species from suborders Caelifera and Ensifera cluster, respectively, as monophyletic groups, and the two suborders cluster as sister groups. Within Caelifera, the subfamily Gomphocerinae appears to be a paraphyletic group in the analyses of the protein-coding gene (PCG) dataset and a monophyletic group in the analyses of rRNA dataset. The subfamily Oedipodinae is a monophyletic group; superfamily Acridoidea is a monophyletic group, and Pyrgomorphoidea is a sister to Acridoidea. Regarding Xia's revision, the families Gomphoceridae and Arcypteridae are closely related, and the family Acrididae is a paraphyletic group. Overall, the phylogenetic analyses in our study are in accordance with Otte's taxonomic analysis.
 
Article
Abstract The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
 
Continued. 
Article
Abstract The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
 
Article
Abstract Thunnus alalunga is an excellent food fish and is of great importance in recreational fisheries. In the study, the complete mitochondrial genome (mitogenome) of T. alalunga is sequenced and annotated, which is a circular DNA molecule with 16,527 bp in length. The overall nucleotide base composition of T. alalunga mitogenome is as follows: A, 28.37%; G, 16.69%; T, 25.46%; and C, 29.49%, with the A+T content of 53.83%, showing an obvious anti-G bias. The entire mitogenome encodes 37 genes in all, comprising 13 protein-coding genes (ATP6 and ATP8, COI-III, Cytb, ND1-6 and 4L), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (12S and 16S rRNAs). The complete mitochondrial genome sequence of T. alalunga can provide useful information for the studies on molecular systematics, stock evaluation, and conservation genetics of teleost fishes.
 
Article
Abstract We evaluated genetic differentiation among ten presumed Japanese threadfin bream, Nemipterus japonicus populations along the coast of Peninsular Malaysia based on the partial sequence of the mitochondrial cytochrome b gene (982 bp). Genetic divergences (Kimura-2 parameter) ranged from 0.5% to 0.8% among nine of the ten populations while these nine populations were 4.4% to 4.6% diverged from the Kuala Besar population located at the Northeast coast. The constructed Neighbour Joining (NJ) phylogenetic trees based on haplotypes showed the Kuala Besar population forming an isolated cluster. The Analysis of Molecular Variance (AMOVA) of the ten populations a priori assigned into four regions, revealed that most of the variation occurred within population with a fairly low but significant level of regional differentiation (FST = 0.07, p < 0.05, FSC = 0.00, p > 0.05 and FCT = 0.07, p < 0.05) attributed to the Kuala Besar population. p Value after Bonferroni correction revealed that only pairwise FST values involving the Kuala Besar population with the other nine populations were significant. Thus, this study revealed that the N. japonicus populations off Peninsular Malaysia were panmictic. However, the Kuala Besar population, although morphologically identical was composed of a genetically discrete taxon from the rest. These findings are important contributions in formulating sustainable fishery management policies for this important fishery in Peninsular Malaysia.
 
Annotation of the complete mitochondrial genome of M. longicarpus. 
Article
Abstract The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
 
Article
Abstract The complete mitochondrial genome sequence of the lined seahorse Hippocampus erectus was first determined in this article. The total length of H. erectus mitogenome is 16,529 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of the H. erectus mitochondrial genome were similar to the typical vertebrates. The overall base composition of H. erectus is 31.8% A, 28.6% T, 24.3% C and 15.3% G, with a slight A + T rich feature (60.4%).
 
Distribution of pollock and origins of samples. Note : The Pacific distribution of Walleye Pollock is shown in dark grey. Samples sites are North Cape, Norway; Sado Island, Sea of Japan; Bogoslof Island, Aleutians, Bering Sea; Nanaimo, British Columbia, eastern Pacific. This figure is reproduced in colour in Mitochondrial DNA online. 
Phylogenetic relationships among 13 pollock mtDNA genomes with respect to an Atlantic Cod outgroup. Note : Numbers above the branches are the percentage support in 10,000 branch-and-bound maximum parsimony bootstrap replicates. Placement of the root with respect to B1 and Epac is unresolved. This figure is reproduced in colour in Mitochondrial DNA online. 
Article
Ursvik et al. compared the complete mitochondrial DNA (mtDNA) genome sequences of Walleye Pollock (Gadus ( = Theragra) chalcogrammus) from the Pacific Ocean with a pair of fish from an isolated population of Norwegian pollock in the Barents Sea. They concluded that the Norwegian population was recently introduced from the Pacific. We test this hypothesis within a temporal framework provided by a phylogeographic analysis of complete genomes from the pollocks' sister species, Atlantic Cod (Gadus morhua), and their divergence 3.5 mya. Pollock have a coalescent ancestor 189 +/- 25 kya. The two Norwegian fish have a common ancestor 87 +/- 7 kya, which suggests an ancient origin rather than a recent human-mediated introduction. Mitochondrial genomic biodiversity in pollock antedates the most recent glacial cycle. The clade structure of the whole-genome tree indicates that previously described single-locus mtDNA haplotypes and haplogroups are typically paraphyletic.
 
Article
The use of DNA barcodes has been proposed as a promising tool for identifying species. The efficacy of this tool for invasive species requires further exploration. The species status of the small Indian mongoose, an exotic invasive in several parts of the world, has been contentious due to morphological similarity with its congeners in its natural habitat. Although the small Indian mongoose is recognized as Herpestes javanicus, this nomenclature has been used interchangeably with Herpestes auropunctatus. Here, we demonstrate the utility of using DNA barcoding approaches with mtDNA cytochrome b to discriminate between the two species and other sympatric members of the genus Herpestes (Herpestes naso, Herpestes urva, and Herpestes edwardsii). Using the diagnostic DNA positions we obtain, we can identity specimens of nonnative populations of the small Indian mongoose from the Caribbean and Hawaiian Islands to their species of origin. A singe diagnostic site accomplishes the identification of H. javanicus versus H. auropunctatus. Our results indicate that the nonnative mongoose populations from the Caribbean and Hawaiian Islands are H. auropunctatus, and not H. javanicus.
 
Article
The complete mitochondrial genome of Cirrhinus mrigala was determined using the polymerase chain reaction. The mitogenome (16,594 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The overall base composition on the heavy strand was as follows: A: 32.0%, G: 15.5%, C: 28.0%, T: 24.55% and the A+T content: 56.5%. The control region contains a dinucleotide repeat motif, (TA)(14), a termination-associated sequence and three conserved sequence blocks. These mitogenome sequence data would play an important role in population genetics and the molecular taxonomy of cultivable cyprinids in India.
 
Article
Abstract The complete nucleotide sequence of mitogenome of the great snakehead, Channa marulius (Channidae), was determined and found to be 16,569 base pairs in length. The content and arrangement of different genes on the mitogenome was found similar to other typical teleosts. The overall base composition of the L-strand was found to be T (19.1%), C (31.5%), A (34.8%) and G (14.6%). The control region was 915 nt long and without any repetitive region. The mitogenome sequence data would be useful for studying phylogenetic relationship of C. marulius with other perciform species.
 
Article
Abstract We characterized mitochondrial ATP synthase (ATPase) 6 and 8 genes in Labeo calbasu (Hamilton, 1822) and determined genetic variation in wild populations across the natural distribution in Indian rivers. A total of 206 individuals were sampled from 11 riverine sites belonging to distinct geographical locations covering five major river basins. Sequencing of 842 base pairs of ATPase 6/8 revealed 21 haplotypes with haplotype diversity ranging from 0.1250 (River Satluj) to 0.8846 (River Bhagirathi). Analysis of molecular variance (AMOVA) of mitochondrial DNA (mtDNA) data revealed significant genetic differentiation among sites (FST = 0.192, p < 0.0001) which was indicative of moderate level of genetic structuring in the wild L. calbasu populations. The patterns of genetic divergence and haplotype network of mtDNA revealed distinct clades present in Indian rivers. The analysis of data demonstrated the potential of ATPase 6/8 genes in determining the genetic diversity and indicated considerable sub-structuring in wild calbasu populations present in different rivers.
 
Locations of sampling station.
Details of sampling sites and other relative information of C. garua during 2009-2010.
Different haplotypes and their consensus sequences detected in six populations of C. garua (dots refer to identical positions to reference consensus sequence).
UPGMA clustering between six different populations of C. garua . 
AMOVA analyses of cytochrome b sequences for six populations of C. garua.
Article
Abstract Clupisoma garua (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. This study investigates the genetic diversity and population structure of six Indian populations of C. garua using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). We sequenced cyt b gene of 64 individuals collected from five distant rivers: Ganga, Gomti, Betwa, Gandak and Brahmaputra. Sequencing of 1054 bp cyt b mtDNA fragment revealed the presence of 19 haplotypes with a haplotype diversity value of 1.000 and a nucleotide diversity value of 0.0258 ± 0.00164. The Gandak river fish population showed highest nucleotide diversity. The fixation index analysis indicated significant genetic divergence among populations from different geographical areas. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylo-geographic structure. The hierarchical analysis of molecular variance revealed that intra-group variation among populations was highly significant. The results of this study suggest that C. garua populations, especially geographically isolated groups, have developed significant genetic structures within the population. In addition, tests of neutrality suggest that C. garua may have experienced a population expansion. The study results establish cyt b as polymorphic and a potential marker to determine the population structure of C. garua. Information of genetic variation and population structure generated from this study would be useful for planning effective strategies for the conservation and rehabilitation of Schilibid cat fishes.
 
Article
Abstract Complete mitochondrial genome of catfish, Eutropiichthys vacha, was isolated by LA PCR (TakaRa LAtaq, Dalian, China); and sequenced by Sanger's method to obtain the complete mitochondrial genome, which is listed Critically Endangered and Red-listed species. The complete mitogenome was 16,478 bp in length and contains 13 typical vertebrate protein-coding genes, 2 rRNA and 22 tRNA genes. The whole genome base composition was estimated to be 31.06% A, 27.59% C, 15.65% G, and 25.68% T. The complete mitochondrial genome of catfish, E. vacha provides the fundamental tool for genetic breeding and conservation studies.
 
Result of the analysis of molecular variance (AMOVA) testing genetic structure of C. mrigala based on Cytochrome b sequences.
Median-joining network of haplotypes of C mrigala. Each circle represents a haplotype and circle size is proportional to the haplotype frequency. Numeral indicates the number of mutations and GenBank accession of haplotypes are shown in brackets.  
Article
A 307 bp segment of Cytochrome b gene of mtDNA was sequenced and analyzed for 90 individuals of Cirrhinus mrigala collected across the three rivers, namely Ganges, Narmada and Brahmaputra. Analyses revealed the presence of 14 haplotypes with haplotype diversity (h) ranging from 0.304 to 0.692, and nucleotide diversity (π) 0.002-0.043. The majority of variation was found within the population (96.21%), and the FST value (0.035) as well as the value of exact test of population differentiation (0.893) were found to be insignificant (p < 0.05). Analysis of molecular variance (AMOVA) also indicated insignificant differentiation among sub-populations. Generally, low genetic differences were observed even though those populations were from different geographic locations. The present study suggests a single panmictic population of C. mrigala across the three rivers of India.
 
Article
Abstract Pangasius pangasius, an endangered freshwater fish species, is an important component of capture fishery from Indian rivers. Samples collected through commercial catches from three riverine populations were analyzed with cytb (307 bp) and ATPase6&8 (842 bp) regions for population variation and differentiation. The sequences of the both the mitochondrial regions revealed high haplotype and low nucleotide diversity. Shallow genetic diversity based on ATPase6&8 was observed, however its haplotypes network clearly indicated two distinct mitochondrial lineages. Mismatch distribution suggested population bottlenecks followed by expansion in Mahanadi population. The present study indicated the ATPase6&8 to be a potential mitochondrial marker for studying the population sub-structuring in the wild population of P. pangasius.
 
Article
Abstract The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
 
Article
Abstract The complete mitochondrial genome of Schizothorax richardsonii, an endemic coldwater fish of Himalayas, was determined for the first time. The genome is 16,592 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2 rRNA genes and one putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was as follows: A: 29.9%, G: 17.7%, C: 26.9%, T: 25.5%, A + T content 55.4% and the G + C content 44.6%. The control region contains a microsatellite; (TA)13 exists between 16,469 and 16,494 bp. This study will provide the rationale for the management and conservation of the snow trout.
 
Article
Abstract Two complete mitochondrial genomes of the black marlin Istiompax indica were assembled from approximately 3.5 and 2.5 million reads produced by Ion Torrent next generation sequencing. The complete genomes were 16,531 bp and 16,532 bp in length consisting of 2 rRNA, 13 protein-coding genes, 22tRNA and 2 coding regions. They demonstrated a similar A + T base (52.6%) to other teleosts. Intraspecific sequence variation was 99.5% for three I. indica mitogenomes and 99.7% for X. gladius. A lower value (85%) was found for the I. platypterus mitogenomes from genbank and accredited to inadvertent inclusion of gene regions from a con-familial species in one record, highlighting the need for cautious downstream use of genbank data.
 
Article
Abstract The complete mitochondrial genome of Schizopyge niger, an endemic coldwater fish of Himalayas was determined for the first time. The genome is 16,585 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2rRNA genes and 1 putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was; A: 29.9%, G: 17.7%, C 27.1%, T 25.3%, A + T content 55.2% and the G + C content 44.8%. The control region was also consisted of a microsatellite locus (TA)13 between 16,471 to 16,496 bp. The present study will provide the rationale for the management and conservation of S. niger.
 
Article
Abstract The complete mitochondrial genome of Schizothorax esocinus, an endemic coldwater fish of Himalayas, was determined for the first time. The genome is 16,583 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2rRNA genes and 1 putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was; A 29.8%, G 17.8%, C 27%, T 25.4%, A + T content 55.2% and the G + C content 44.8%. The control region was also consisted of a microsatellite locus (TA) 13 between 16,463 to 16,488 bp. The present study will provide the rationale for the management and conservation of S. esocinus.
 
Article
Abstract The complete mitochondrial genome of the iconic Australian freshwater fish, the Murray Cod, Maccullochella peelii, was recovered from partial genome sequencing data using the HiSeq platform (Illumina, San Diego, CA). The mitogenome consists of 16,442 bp (58% A + T content) containing 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 768 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Maccullochella, and the fourth for the family Percichthyidae.
 
Continued. 
Article
Abstract This work presents the coral-inhabiting barnacle Nobia grandis Sowerby, 1839 complete mitochondrial genome, which is the first report from the family Pyrgomatidae (Cirripedia: Sessilia). The N. grandis mitochondrial genome is 15,032 bp in length, containing a total of 469 bp of non-coding nucleotides spreading in 11 intergenic regions (with the largest region of 376 bp). Compared with the pancrustacean ground pattern, there are not less than seven tRNAs rearranged in the N. grandis mitochondrial genome. Gene overlaps are founded in eight places. Nine PCGs (COX1-3, ATP6, ATP8, CYTB, ND2, ND3 and ND6) are encoded on the heavy strand while the remaining 4 PCGs and the two rRNAs are located on the light strand. As the first representative from the family Pyrgomatidae, the N. grandis mitochondrial genome will help us to explore the evolutionary history and molecular evolution of coral barnacles and Sessilia in future studies.
 
Article
Abstract Complete mitochondrial genome of catfish, Sperata seenghala, was isolated by LA PCR (TakaRa LAtaq, Dalian, China); and sequenced by Sanger's method to obtain the complete mitochondrial genome, which is listed Critically Endangered and red listed species. The complete mitogenome was 16,588 bp in length and contains 13 typical vertebrate protein-coding genes, 2 rRNA and 22 tRNA genes. The whole genome base composition was estimated to be 31.28% A, 27.80% C, 15.31% G, and 25.57% T. The complete mitochondrial genome of catfish, Sperata seenghala provides the fundamental tools for genetic breeding and conservation studies.
 
Article
Abstract The complete mitochondrial genome of Schizothorax progastus, an endemic coldwater fish of Himalayas, was determined for the first time. The genome was 16,575 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2rRNA genes and one putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was - A: 29.8%, G: 17.8%, C: 27%, T: 25.4%, A + T content: 55.2% and the G + C content: 44.8%. The control region also consisted of a microsatellite locus (TA)12 between 16,466 and 16,489 bp. The present study will provide the rationale for the management and conservation of S. progastus.
 
Article
Abstract In this study we sequenced and analyzed the complete mitochondrial genome (mitogenome) of the lined shore crab Pachygrapsus crassipes Randall, 1840 (Crustacea: Grapsidae). The full-length P. crassipes mitogenome is 15,652 bp in size, which encodes the same 37 genes as all metazoan mitogenomes. Both AT contents of the entire molecule as well as putative control region display lowest values among all mitogenomes of the brachyuran crabs determined to date. The mitochondrial gene order follows a classic crab-type arrangement that underwent a unique tRNA translocation from the pancrustacean ancestral pattern. Our results will provide important data for phylogenetic as well as biogeographic studies.
 
Gene map of the mitochondrial genome of Xya japonica . Transfer RNA ( tRNA ) genes are designated by the single letter abbreviation of corresponding amino acid. atp6 , ATPase subunit 6 gene; atp8 , ATPase subunit 8 gene; cox1 , cytochrome oxidase subunit I gene; cox2 , cytochrome oxidase subunit II gene; cox3 , cytochrome 
Gene map of the mitochondrial genome of Xya japonica. Transfer RNA (tRNA) genes are designated by the single letter abbreviation of corresponding amino acid. atp6, ATPase subunit 6 gene; atp8, ATPase subunit 8 gene; cox1, cytochrome oxidase subunit I gene; cox2, cytochrome oxidase subunit II gene; cox3, cytochrome oxidase subunit III gene; cob, cytochrome b gene; rrnL, large ribosomal RNA; rrnS, small ribosomal RNA. Genes coded in the opposite strand are shaded. 
Article
Abstract The complete mitochondrial genome of Xya japonica (Haan, 1842), which was collected from Hebei province of China, is reported here. It is 15,352 bp in length and contains 71.2% AT. All X. japonica protein-coding sequences start with a typical ATN codon except for the cytochrome oxidase subunit I (cox1), which start with CCG. The usual termination codon TAA and TAG were found from 13 protein-coding genes. All tRNA genes have the typical clover leaf structure, excluding trnS(AGN) that lacks the dihydrouracil arm. The sizes of the large and small ribosomal RNA genes are 1289 and 747 bp, respectively. The AT content of the A + T-rich region is 75.0%. The orientation and gene order of the X. japonica mitogenome is identical to Ellipes minuta and Gryllotalpa orientalis, there is no phenomenon of "DK rearrangement" which has been wide reported in Caelifera.
 
Article
Abstract The complete mitochondrial genome of Schizothorax labiatus, an endemic coldwater fish of Himalayas was determined for the first time. The genome is 16,582 bp in length and consists of 13 protein coding genes, 22 tRNAs, 2rRNA genes and one putative control region. The gene organization and its order were similar to other vertebrates. The overall base composition was; A: 29.8%, G: 17.7%, C 27%, T 25.5%, A + T content 55.3% and the G + C content 44.7%. The control region was also consisted of a microsatellite locus (TA)12 between 16,467 and 16,490 bp. The present study will provide the rationale for the management and conservation of S. labiatus.
 
Map showing the sampling sites of O. belangeri from Manipur, India.
Median-joining network of haplotypes of O. belangeri. Each circle represents a haplotype and circle size is proportional to haplotype frequency. Numeral indicates number of mutations and mutated positions are given in bracket.  
Mismatch distribution of all individuals of O. belangeri sampled (n ¼ 56). The black solid line represents the observed relative frequencies of nucleotide differences between pairs of individuals; the dashed line represents the distribution fitted to the data under a model of demographic expansion.
Article
Abstract Osteobrama belangeri is an important medium carp endemic to Manipur state in India Myanmar and Yunnan Province of China. Although the species is listed as Near Threatened species according to IUCN status with sizeable population available in Myanmar, it is Extinct in the Wild in Manipur. An 842 bp segment ATP synthase 6/8 region of mtDNA was sequenced and analysed for 56 O. belangeri individuals. Analysis of population differentiation showed no significant genetic differentiation between the four sampling localities (ΦST = -0.034, p = 0.819). Results were further corroborated by a non-significant nearest neighbour statistics (Snn = 0.223, p = 0.897) and exact test of population differentiation (p = 0.893). Phylogeographic analysis revealed two haplogroups, but there was no obvious phylogeographic pattern separating the sampling localities. The present study suggests a single panmictic population of O. belangeri in Indian region.
 
Article
Abstract The complete mitochondrial genome of the commercially important snout otter clam Lutraria rhynchaena was obtained from low-coverage shotgun sequencing data on the MiSeq platform. The L. rhynchaena mitogenome has 16,927 base pairs (69% A + T content) and made up of 12 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 953 bp non-coding AT-rich region. This is the first mitogenome to be sequenced from the genus Lutraria, and the seventh to be reported for the family Mactridae.
 
Article
Abstract The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.
 
Article
Abstract The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
 
Annotation of the complete mitochondrial genome of C. granulosus. 
Article
Abstract The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
 
Article
Abstract The complete mitochondrial genome sequence of the Desert Pupfish, Cyprinodon macularius (Gene accession number KM985373) has a length of 16,940 bp, and the arrangement consisted of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA, which are similar to other known mitogenomes for the family Cyprinodontidae.
 
Top-cited authors
Robert Hanner
  • University of Guelph
Sven Becker
  • Moonsinger Media Ltd., Vancouver, BC, Canada
Dirk Steinke
  • University of Guelph
Shu-Jun Wei
  • Beijing Academy of Agriculture and Forestry Sciences
Xiao Chen
  • Zhejiang University