The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates

Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (O_L) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.

Characterization of the complete mitogenome of the endangered freshwater fish Gobiobotia naktongensis from the Geum River in South Korea: evidence of stream connection with the Paleo-Huanghe

BACKGROUND

The freshwater fish Gobiobotia naktongensis (Teleostei, Cypriniformes, and Gobionidae) is an endangered class I species whose population size has been greatly reduced.

OBJECTIVE

To successfully protect and restore the highly endangered freshwater fish G. naktongensis from the Geum River in South Korea.

METHODS

The mitogenome was characterized using the primer walking method with phylogenetic relationships.

RESULTS

The complete mitogenome of G. naktongensis Geum River was 16,607 bp, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA (tRNA) genes. Seventeen substitutions were found by comparing the tRNA regions between G. naktongensis Geum and Nakdong Rivers and G. pappenheimi; most were specific to G. naktongensis Nakdong River, with changes in their secondary structures. The comparison between G. naktongensis Geum River and G. pappenheimi revealed differences in the lengths of the D-loop and two tRNAs (tRNAArg and tRNATrp) and the secondary structures in the TΨC-arm of tRNAHis. In the phylogenetic tree, G. naktongensis Geum River did not cluster with its conspecific specimen from the Nakdong River in South Korea, but showed the closest relationship to G. pappenheimi in mainland China.

CONCLUSIONS

Our results support the existence of the Paleo-Huanghe River connecting the Korean peninsula and mainland China, suggesting that G. naktongensis in the Geum River should be treated as a different evolutionarily significant unit separated from that in the Nakdong River. The complete mitogenome of G. naktongensis Geum River provides essential baseline data to establish strategies for its conservation and restoration.

New complete mitogenome datasets and their characterization of the European catfish (Silurus glanis)

We present new complete mitogenome sequences of Silurus glanis (S. glanis) from 4 samples such as male and female individuals from two countries (Hungary, Czech Republic). The complete mitochondria were determined from genome sequencing by using Illumina MiSeq platform resulting in long, 300 bp. paired-end reads. De novo assembly was performed resulting in one nod (scaffold) covering the total mitochondria in each sample. The mitochondrial genomes were circular, double-stranded molecules of 16,524 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. These sequences were deposited in the NCBI GeneBank under the accession numbers (MW796040, MW796041, MW796042, MW796043) and compared with the only available S. glanis mitochondrial genome (NC_014261.1) sequenced by unidentified technology and showed 99% similarity. We found in seq1 82, in seq2 82, seq3 83, seq4 82 nucleotide alterations involving 10 protein-coding genes and meaning 29 amino acid substitutions as well.

The complete mitochondrial genome of Trifida elongate and comparative analysis of 43 leafhoppers

In this study, the mitochondrial genome of Trifida elongate was sequenced, and comparative analysis of T. elongate and other 43 leafhoppers was performed based on the mitochondrial genome. The mitochondrial genome sequence length of T. elongate was 14,924 bp. It comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transport RNA (tRNA) genes, and 1 non-coding control region. The control region is located between the rrnS and trnI genes, is characterized by two tandem repeats and three simple sequence repeats. Phylogenetic analysis showed that T. elongate is closely related with Bolanusoides shaanxiensis and Limassolla lingchuanensis (bootstrap value = 92% and posterior probabilities = 1). Analysis of synonymous and non-synonymous nucleotide substitutions showed that Ka/Ks value of the 13 protein-coding genes of 8 subfamily leafhoppers were less than 1 ranging from 0.0315 to 0.9928. atp8 had the highest Ka/Ks value whereas cox1 had the lowest Ka/Ks value. This study provides information on the structure and sequence characteristics of the mitochondrial genome of T. elongata. Typhlocybinae is clustered with (Cicadellinae+(Idiocerinae+(Mileewinae+(Nirvaninae+(Evacanthinae+Ledrinae))))).

Novel Gene Rearrangement and the Complete Mitochondrial Genome of Cynoglossus monopus: Insights into the Envolution of the Family Cynoglossidae (Pleuronectiformes)

Cynoglossus monopus, a small benthic fish, belongs to the Cynoglossidae, Pleuronectiformes. It was rarely studied due to its low abundance and cryptical lifestyle. In order to understand the mitochondrial genome and the phylogeny in Cynoglossidae, the complete mitogenome of C. monopus has been sequenced and analyzed for the first time. The total length is 16,425 bp, typically containing 37 genes with novel gene rearrangements. The tRNA-Gln gene is inverted from the light to the heavy strand and translocated from the downstream of tRNA-Ile gene to its upstream. The control region (CR) translocated downstream to the 3'-end of ND1 gene adjoining to inverted to tRNA-Gln and left a 24 bp trace fragment in the original position. The phylogenetic trees were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 32 tonguefish species and two outgroups. The results support the idea that Cynoglossidae is a monophyletic group and indicate that C. monopus has the closest phylogenetic relationship with C. puncticeps. By combining fossil records and mitogenome data, the time-calibrated evolutionary tree of families Cynoglossidae and Soleidae was firstly presented, and it was indicated that Cynoglossidae and Soleidae were differentiated from each other during Paleogene, and the evolutionary process of family Cynoglossidae covered the Quaternary, Neogene and Paleogene periods.

Molecular identification and phylogenetic analysis of the mitogenome of Solenaia oleivora MG

Solenaia oleivora, belongs to Bivalvia, Unionidae, and Gonideinae, is a burrowing bivalve uniquely distributed in China. In this study, the complete mitochondrial genome of S. oleivora MG was sequenced and determined. The complete mitogenome of S. oleivora MG is 16,392 bp in total length, consist of 22 tRNA genes, 13 protein-coding genes (PCGs), and 2 rRNA genes. The overall base composition of the S. oleivora MG mitogenome is 36.90% A, 23.85% T, 27.09% C, and 12.16% G, respectively, exhibits a similar AT bias (60.75%) feature to other invertebrate bivalve mitogenomes. The phylogenetic analysis that S. oleivora MG clustered in genus Solenaia. This result provides useful data to the conservation and sustainable utilization of S. oleivora MG and other invertebrate mussels.

Identification and phylogenetic analysis of the mitochondrial genome of Hemibarbus labeo BML (Cypriniformes: Cyprinidae)

The complete mitochondrial genome of Hemibarbus labeo BML (Cypriniformes: Cyprinidae) is 16,612 bases in length. It consists of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 1 non-coding region. Its overall nucleotide composition is A: 29.85%, G: 17.07%, T: 25.86%, and C: 27.23%, respectively, with an A + T rich feature (55.71%). The gene arrangement and organization of the mitogenome from H. labeo BML were very similar to other Cyprinidae fishes. The phylogenetic analysis showed that H. labeo BML clustered in genus Hemibarbus. These results will contribute to the taxonomy and conservation biology studies of H. labeo.

Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

The complete mitochondrial genome of Liparis ochotensis and a preliminary phylogenetic analysis

Liparis ochotensis is a snailfish commonly confused with similar fish species because of unclear morphological characteristics. Moreover, molecular genetic studies have not been conducted for snailfish in Korea. Here, we report the complete mitogenome sequence of L. ochotensis, obtained via long PCR using universal primers for the fish mitogenome. The L. ochotensis mitogenome is 17,522 bp long, comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. A neighbour-joining phylogenetic tree based on CO1 sequences depicted a close relationship with Liparis gibbus. The complete mitogenome is a valuable resource to classify and conserve L. ochotensis.

Molecular identification and phylogenetic analysis of mitogenome of the Xenocypris davidi from Cao’e River

In this study, the complete mitochondrial genome sequence of a Xenocypris davidi from Cao’e River was sequenced. The complete mitogenome of X. davidi was 16,630 bp in length, it contains the structure of 22 transfer RNA genes, 13 protein coding genes, 2 ribosomal RNA genes, and 1 non-coding region. The gene arrangement and organization in the mitogenome of X. davidi were in accordance with other Cyprinidae fishes. The results of phylogenetic analysis revealed that the mitochondrial genome sequence could provide useful information for the conservation genetics and evolution study of X. davidi.

Structure and variation of the mitochondrial genome of fishes

Background

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets.

Results

An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species.

Conclusions

Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.

Mitochondrial genomes of Heterakis gallinae and Heterakis beramporia support that they belong to the infraorder Ascaridomorpha

Heterakis gallinae and Heterakis beramporia are the most prevalent nematode infecting native chicken breed, causing major economic losses. In the present study, the complete mitochondrial genomes (mt) of H. gallinae and H. beramporia were amplified by long-PCR and then sequenced. The complete mt genomes of H. gallinae and H. beramporia were 13,973bp and 14,012bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. All genes are transcribed in the same direction and the gene arrangement is identical to Ascaridia spp. Phylogenetic analysis based on the 12 protein-coding genes revealed that the family Heterakidae (represented by H. gallinae and H. beramporia) was more closely related to the infraorder Ascaridomorpha than it was to the infraorder Oxyuridomorpha. The present study determined the complete mt genome sequences for two Heterakis species, providing useful markers for studying the systematics, population genetics, and molecular epidemiology of these Heterakis parasites.

Mitochondrial DNA study in domestic chicken

Mitochondrial DNA has the characteristic of quick evolution, matrilineal inheritance, and simple molecular structure, and it serves as the most used marker for molecular study. As an important role of genomics, studying it can help understand the origins, history, and adaptation of domestication. Because of its wide spread popularity, chicken is one of the important domestic animals, which provides humans with a stable source of protein, including both meat and eggs. This article reviews recent studies of chicken mitochondrial DNA. Mitochondrial D-loop and mitochondrial genomics pinpoint the geographic origins of the domestic chicken which was multiple origins; moreover, the mitochondria gene mutation has an association with high-altitude adaptation and the mitochondria-associated diseases' study in poultry is not performed.

The complete mitochondrial genome of Brachymystax lenok tsinlingensis (Salmoninae, Salmonidae) and its intraspecific variation

The Manchurian trout, Brachymystax lenok tsinlingensis, is endangered in Korea, where the southern range limit for this cold-freshwater fish occurs. In this study, the complete mitochondrial genome of Korean B. lenok tsinlingensis was sequenced and its genetic characteristics were identified. The mitogenome of B. lenok tsinlingensis comprises 16,748 base pairs containing 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) and one major non-coding region (control region), making it similar to the majority of vertebrate mitogenomes. Interestingly, at the base of the stem region of OL in B. lenok tsinlingensis, the conserved motif is replaced by a 5'-ACCGG-3' motif instead of the 5'-GCCGG-3'. We also identified an 81-base-pair tandem-repeat motif in the control region, the length of which is reduced by one nucleotide compared to those in B. lenok and Hucho species. The number of repeat motifs differed between Korean and Chinese B. lenok tsinlingensis, with two and three reiterations, respectively. The control region of B. lenok and its relatives will be used as a genetic marker in evolution/genetic studies and as a PCR-based marker for rapid identification of their lineages.

The complete mitochondrial genome organization of Schizothorax Plagiostomus (Teleostei: Cyprinidae) from Northern Pakistan

Schizothorax plagiostomus, a fresh water fish, is an economically important fish of Pakistan. In this study, the complete mitochondrial DNA (mtDNA) sequence of S. plagiostomus was explored. The mitogenome length was found to be 16 563bp with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). All genes were encoded on the heavy strand except ND6 and few tRNA genes. The overall base composition of S. plagiostomus of the heavy strand was T 25.5%, C 27.0%, A 29.8% and G 17.8%, A + T content 55.3% and G + C content 44.7%. The phylogenetic tree suggests that S. esocinus, S. progastus, S. richardsonii and S. plagiostomus may have closer affinities than other fish of the genus Schizothorax. This mitogenome sequence would be useful for phylogenetic analysis and conservation of this species in Pakistan.

Identification and phylogenetic analysis of the mitogenome of Sarcocheilichthys parvus Nichols (Cypriniformes: Cyprinidae)

In the present study, the complete mitogenome sequence of a Sarcocheilichthys parvus Nichols was sequenced and identified. It contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 non-coding regions. The phylogenetic analysis showed that the mitogenome sequence could be useful data in the field of systematics and conservation biology for S. parvus Nichols and other aquatic species.

The complete mitochondrial genome sequence of Schizopygopsis pylzovi (Cypriniformes: Cyprinidae)

Schizopygopsis pylzovi Kessler (Cypriniformes: Cyprinidae), an endemic species to China, is a major commercial fish in the upper reaches of the Yellow River. The complete mitochondrial DNA genome of S. pylzovi was sequenced. The mitogenome is 16,704 bp in length and includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The basic composition of S. pylzov is 28.5% for A, 27.0% for T, 26.1% for C, and 18.4% for G, with a slight AT bias of 55.5%. Gene order is similar to that of the typical vertebrate, as is nucleotide composition and codon usage. The complete mitogenome sequence of S. pylzovi would be useful to further phylogenetic analysis and genetic conservation for this endemic species.

The complete mitochondrial genome sequence of Herzensteinia microcephalus (Cypriniformes: Cyprinidae)

Herzensteinia microcephalus (Herzenstein, 1891) is the highest naturally occurring cyprinid in the world, and inhabits rivers in the Tibetan Plateau at elevations of 4500-5200 m. Few studies on this species have been contributed. In this study, we got the mitochondrial genome sequences of H. microcephalus. The mitogenome of H. microcephalus is16,726 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). The overall nucleotide base composition is 28.41% for A, 27.16% for T, 26.04% for C and 18.38% for G. This study can provide important molecular theory basis for carrying out the study on the genetics, phylogeny and adaptive evolution of Herzensteinia.

Identification and analysis of the mitogenome of Sarcocheilichthys parvus (Cypriniformes: Cyprinidae)

The complete mitogenome sequence of Sarcocheilichthys parvus was identified using polymerase chain reaction and sequenced with primer walking method. The complete mitogenome was 16,674 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The gene arrangement and composition of S. parvus was similar to most other fishes.

Mitochondrial DNA sequence of the hybrid of Takifugu flavidus (♀) × Takifugu rubripes (♂)

The complete mitochondrial genome of the hybrid of Takifugu flavidus (♀) × Takifugu rubripes (♂) was sequenced and characterized. The total length of the mitogenome is 16,443 bp. It contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall nucleotide composition of the heavy strand is 30.05% A, 25.79% T, 15.07% G and 29.09% C, with an A + T content of 55.84%. Except for ND6 gene and eight tRNA genes, other genes are encoded on the heavy strand. The complete mitogenome of the hybrid of T. flavidus (♀) × T. rubripes (♂) should contribute to further studies on mitochondrial inheritance mechanism.

Characterization of the complete mitochondrial genome of Hemibarbus sp.090914 (Cypriniformes: Cyprinidae)

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.

Complete mitochondrial genome sequence of Tridentiger bifasciatus and Tridentiger barbatus (Perciformes, Gobiidae): a mitogenomic perspective on the phylogenetic relationships of Gobiidae

The fishes of suborder Gobioidei is the largest group of those in present living Perciformes, which contains about 2,200 species belonging to 270 genera of 9 families in the world. The monophyly and phylogenetic relationships of gobies have been controversial and disputable for a long time. In the present study, the complete mitochondrial genome of the shimofuri goby Tridentiger bifasciatus (T. bifasciatus) and shokihaze goby Tridentiger barbatus (T. barbatus) were firstly determined. The two mitochondrial genomes were both consisted of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one major control region (CR). They shared similar features with those of other gobies in terms of gene arrangement, base composition, and tRNA structures. The CR was absence of typical conserved blocks (CSB-E, and CSB-F) respectively for the T. bifasciatus and T. barbatus. Phylogenomic analyses, which based on 12 concatenated protein-coding genes and complete mitochondrial genome sequences, revealed that there were two groups within the Gobiidae. A large group consisted of the Amblyopinae, Gobionellinae, Oxudercinae and Sicydiinae, and Amblyopinae was nested in Oxudercinae and they were both paraphyletic to Sicydiinae. The other group was the Gobiinae. As a whole, our phylogenetic data was different from the traditionally classification of Gobiidae, but supported the new phylogenetic taxonomy view of Thacker (Copeia 2009:93-104, 2009).

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 sequence of Chuanchia labiosa (Cypriniformes: Cyprinidae)

Chuanchia labiosa Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is the sole species of genus Chuanchia and is endemic to China. This species plays an important role in the upper reaches of the Yellow River and has been listed in both the China Red Data Book of Endangered Animal and the China Species Red List. In this study, the complete mitochondrial DNA genome sequence of C. labiosa was determined. The mitogenome is 16,705 bp in length, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Overall basic composition of mitochondrial genome of C. labiosa is 28.39% for A, 27.16% for T, 26.09% for C, and 18.36% for G with a slightly high A + T content (55.55%). The complete mitogenome sequence of C. labiosa would be useful for stock evaluation and further conservation genetic studies for this endangered species.

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

Platypharodon extemus is a monotypic species of Schizothoracine fishes and it was listed as Endangered species in the "China Red Data Book (Pisces)", Vulnerable (V) by the National Environmental Protection Agency and Endangered Species Scientific Commission. So far, little mitochondrial genome information of this genus has been described. In this study, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 16,668 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 noncoding regions. The base composition of this mitochondrial genome was 28.6% A, 27.3% T, 18.2% G, 25.9% C, with a high A + T content (55.9%). The complete mitochondrial genome of P. extremus would be of great utility in the phylogenetic analysis of the schizothoracine fishes and also provide meritorious insights into the deeper problems of the phylogenic analysis.

Complete sequence of the mitochondrial genome of Odontamblyopus rubicundus (Perciformes: Gobiidae): genome characterization and phylogenetic analysis

Odontamblyopus rubicundus is a species of gobiid fishes, inhabits muddy-bottomed coastal waters. In this paper, the first complete mitochondrial genome sequence of O. rubicundus is reported. The complete mitochondrial genome sequence is 17119 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region and an L-strand origin as in other teleosts. Most mitochondrial genes are encoded on H-strand except for ND6 and seven tRNA genes. Some overlaps occur in protein-coding genes and tRNAs ranging from 1 to 7 bp. The possibly nonfunctional L-strand origin folded into a typical stem-loop secondary structure and a conserved motif (5'-GCCGG-3') was found at the base of the stem within the tRNACys gene. The TAS, CSB-2 and CSB-3 could be detected in the control region. However, in contrast to most of other fishes, the central conserved sequence block domain and the CSB-1 could not be recognized in O. rubicundus, which is consistent with Acanthogobius hasta (Gobiidae). In addition, phylogenetic analyses based on different sequences of species of Gobiidae and different methods showed that the classification of O. rubicundus into Odontamblyopus due to morphology is debatable.

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.

Complete mitochondrial genome sequence of golden pompano Trachinotus ovatus

The complete mitochondrial genome of Trachinotus ovatus was determined by the polymerase chain reaction (PCR). The mitogenome is 16,564 bp long and has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The overall base composition of mitogenome is estimated to be 29.0% for A, 28.9% for C, 26.2% for T, 15.9% for G, respectively, with a high A + T content (55.2%). With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The control region contains a dinucleotide repeat motif, (AT)5. This mitogenome sequence would play an important role in population genetics and the molecular taxonomy of T. ovatus.

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.

The complete mitochondrial genome sequence of Takifugu flavidus (Tetraodontiformes: Tetrodontidae)

The complete mitochondrial genome of Takifugu flavidus (Tetraodontiformes: Tetrodontidae) was obtained in this study. The mitogenome is 16,449 bp in size and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall nucleotide composition of the heavy strand was 29.88% A, 25.81% T, 15.28% G and 29.03% C, with a slight AT bias of 55.69%. Except for ND6 gene and eight tRNA genes, other genes are encoded on the heavy strand. The mitochondrial genome data of T. flavidus should contribute to phylogenetic analysis and studies on genetic structure, as well as molecular phylogeny and species identification of Tetrodontidae.

The complete mitochondrial genome sequence of Pampus chinensis (Perciformes: Stromateidae)

In this study, the complete mitochondrial genome of Pampus chinensis (Perciformes: Stromateidae) was determined. The mitogenome is 16,535 bp in length, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The overall mtDNA nucleotide base composition of P. chinensis is A 29.72%, C 28.10%, G 15.34%, and T 26.84%, with an A + T content of 56.56%. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. The mitochondrial genome of P. chinensis may be helpful to the studies on stock evaluation and conservation genetics of P. chinensis resource, as well as molecular phylogeny of Stromateidae.

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.

Mitochondrial genomes of Japanese Babina frogs (Ranidae, Anura): unique gene arrangements and the phylogenetic position of genus Babina

Genus Babina is a member of Ranidae, a large family of frogs, currently comprising 10 species. Three of them are listed as endangered species. To identify mitochondrial (mt) genes suitable for future population genetic analyses for endangered species, we determined the complete nucleotide sequences of the mt genomes of 3 endangered Japanese Babina frogs, B. holsti, B. okinavana, and B. subaspera and 1 ranid frog Lithobates catesbeianus. The genes of NADH dehydrogenase subunit 5 (nad5) and the control region (CR) were found to have high sequence divergences and to be usable for population genetics studies. At present, no consensus on the phylogenetic position of genus Babina has been reached. To resolve this problem, we performed molecular phylogenetic analyses with the largest dataset used to date (11,345 bp from 2 ribosomal RNA- and 13 protein-encoding genes) in studies dealing with Babina phylogeny. These analyses revealed monophyly of Babina and Odorrana. It is well known that mt gene rearrangements of animals can provide usable phylogenetic information. Thus, we also compared the mt gene arrangements among Babina species and other related genera. Of the surveyed species, only L. catesbeianus manifested typical neobatrachian-type mt gene organization. In the B. okinavana, an additional pseudogene of tRNA-His (trnH) was observed in the CR downstream region. Furthermore, in the B. holsti and B. subaspera, the trnH/nad5 block was translocated from its typical position to the CR downstream region, and the translocated trnH became a pseudogene. The position of the trnH pseudogene is consistent with the translocated trnH position reported in Odorrana. Consequently, the trnH rearrangement seems to be a common ancestry characteristic (synapomorphy) of Babina and Odorrana. Based on the "duplication and deletion" gene rearrangement model, a single genomic duplication event can explain the order of derived mt genes found in Babina and Odorrana.

The complete mitochondrial genome sequence of Siniperca undulate (Perciformes: Percichthyidae)

In this paper, the complete mitochondrial DNA (mtDNA) sequence of Siniperca undulate was determined. The complete mtDNA genome sequence of S. undulate was 16,504 bp in length. It consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and 2 non-coding regions. Overall base composition of mitogenome was estimated to be 28.38% for A, 29.43% for C, 16.46% for G and 25.73% for T, respectively, with a high A + T content (54.11%). The complete mitogenome of the S. undulate can provide a basic data for the studies on population history, molecular systematics, phylogeography, stock evaluation and conservation genetics. It is also helpful to the reasonable utilization and development of rational management strategies for S. undulate resource.

A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations

Groupers of the family Epinephelidae are a diverse and economically valuable group of reef fishes. To investigate the evolution of their mitochondrial genomes we characterized and compared these genomes among 22 species, 17 newly sequenced. Among these fishes we identified three distinct genome organizations, two of them never previously reported in vertebrates. In 19 of these species, mitochondrial genomes followed the typical vertebrate canonical organization with 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region. Differing from this, members of genus Variola have an extra tRNA-Ile between tRNA-Val and 16S rRNA. Evidence suggests that this evolved from tRNA-Val via a duplication event due to slipped strand mispairing during replication. Additionally, Cephalopholisargus has an extra tRNA-Asp in the midst of the control region, likely resulting from long-range duplication of the canonical tRNA-Asp through illicit priming of mitochondrial replication by tRNAs. Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. Divergence rates vary among the protein-coding genes, and the three cytochrome oxidase subunits (COI, II, III) are the most conserved, while NADH dehydrogenase subunit 6 (ND6) and the ATP synthase subunit 8 (ATP8) are the most divergent. We then tested the phylogenetic utility of this new mt genome data using 12 protein-coding genes of 48 species from the suborder Percoidei. From this, we provide further support for the elevation of the subfamily Epinephelinae to family Epinephelidae, the resurrection of the genus Hyporthodus, and the combination of the monotypic genera Anyperodon and Cromileptes to genus Epinephelus, and Aethaloperca to genus Cephalopholis.

The complete mitochondrial genome of mud carp Cirrhinus molitorella (Cypriniformes, Cyprinidae)

The complete mitochondrial genome of Cirrhinus molitorella was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,602 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 32.32% for A, 15.26% for G, 25.00% for T, 27.41% for C, respectively, with a high A + T content (57.32%). The control region contains a dinucleotide repeat motif, (TA)12, a termination-associated sequence and three conserved sequence blocks. The complete mitochondrial genome sequence of C. molitorella 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 C. molitorella resource.

Complete mitochondrial genome of Osteochilus salsburyi (Cypriniformes, Cyprinidae)

Osteochilus salsburyi (Cypriniformes, Cyprinidae) is a small-sized fish of significant economic value. In this paper, the complete mitogenome sequence of O. salsburyi was first determined. It is 16,599 bp in length and consists of a typical vertebrate genome structure including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and a control region. 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 in descending order is A (33.0%), T (26.5%), C (25.4%), and G (15.0%), with a slight AT bias of 59.5%. This information of O. salsburyi mitogenome could contribute not only to the development of efficient conservation strategy on vulnerable genetic diversity but also to the identification of useful genetic markers for distinction across species boundary.

Complete mitochondrial genome of Microphysogobio alticorpus (Cypriniformes, Cyprinidae)

In this study, we determined the complete mitochondrial (mt) genome of Microphysogobio alticorpus (Cypriniformes, Cyprinidae). This mt genome, consisting of 16,568 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a noncoding control region (CR) as those found in other vertebrates, with the gene order identical to that of typical vertebrates. The overall base composition of the heavy strand shows T: 26.03%, C: 26.73%, A: 30.20% and G: 17.04%, apparently with a slight AT bias. The two rRNA genes of 12S rRNA (958 bp) and 16S rRNA (1693 bp) are located between tRNA(Phe) and tRNA(Leu()(UUR)) and separated by the tRNA(Val) gene. CR, of 890 bp in length, is located between tRNA(Pro) and tRNA(Phe).

Origin of Chinese goldfish and sequential loss of genetic diversity accompanies new breeds

BACKGROUND

Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy-body shape, dorsal fin, eye shape, and tailfin-were selected for hypothesis-testing to identify those that better correspond to evolutionary history.

PRINCIPAL FINDING

Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F(ST) and N(m) revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima's D and Fu and Li's D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher's exact test identified matrilineal constraints on domestication.

CONCLUSIONS

Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy--Grass-goldfish, Egg-goldfish, and Wen-goldfish--better reflected the history of domestication.

Complete mitochondrial genome sequence of Gymnocypris dobula (Cypriniformes: Cyprinidae)

Gymnocypris dobula is listed as Vulnerable (VU) status in the IUCN's Red List of Threatened Species. In this paper, complete mitochondrial DNA sequence of G. dobula was determined. The complete mitogenome is 16,720 bp in length, and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information of G. dobula is conducive to futher studies on molecular systematics, stock evaluation and conservation genetics.

The complete mitochondrial genome structure of Schizothorax oconnori (Cypriniformes: Cyprinidae)

Schizothorax oconnori is mainly distributed in the Yarlung Zangbo River drainage in Tibet, China. S. oconnori is assessed as least concern species in International Union for Conservation of Nature Red List. In this paper, we determined the complete mitochondrial DNA (mtDNA) sequence of S. oconnori. The mitogenome is 16,590 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). The complete mitogenome sequence information of S. oconnori can be used in the studies on molecular systematics, stock evaluation and conservation genetics and will be helpful in the development of rational management strategies and sustainable utilization for S. oconnori resource.

The complete mitochondrial genome sequence of Ancherythroculter nigrocauda (Cypriniformes:Cyprinidae)

Ancherythroculter nigrocauda is a fish endemic to the upper reaches of the Yangtze River in China. In this study, we determined and analyzed the complete mitochondrial DNA (mtDNA) sequence of this species. The mitogenome is 16,623 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (O(L)) and control region (D-loop). This mitogenome sequence data can contribute to elucidate the evolutionary mechanisms, molecular systematics, and biogeography of Ancherythroculter and is useful to conservation genetics and stock evaluation for A. nigrocauda.

The complete mitochondrial genome sequence of Schizothorax wangchiachii (Cypriniformes: Cyprinidae)

In this study, the complete mitochondrial DNA (mtDNA) sequence of Schizothorax wangchiachii has been determined. The mitogenome is 16,593 bp in length. It consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 non-coding regions: origin of light-strand replication (OL) and control region (D-loop). The complete mtDNA sequence of S. wangchiachii can contribute to elucidate the evolutionary mechanisms and biogeography of Schizothorax and is useful to stock evaluation and conservation genetics for S. wangchiachii.