Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution

BACKGROUND

Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.

RESULTS

Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.

CONCLUSIONS

This study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.

Transcriptome Analysis of Peritoneal Cells Reveals the Early Immune Response of Flounder (Paralichthys olivaceus) to Inactivated Vibrio anguillarum Immunization

Vibrio anguillarum (V. anguillarum) is a bacterium that seriously harms flounder and other aquaculture species. Vaccination is an effective means of preventing vibriosis and is mainly administered by intraperitoneal injection. Effective antigen processing at the initial stage of immunization is essential to elicit adaptive immune responses and improve vaccine efficacy. To understand the early immune response of flounder caused by inactivated V. anguillarum, we detected the transcriptome profiles of the cells in the peritoneal cavity (PoPerCs) after inactivated V. anguillarum immunization. More than 10 billion high-quality reads were obtained, of which about 89.33% were successfully mapped to the reference genome of flounder. A total of 1985, 3072, 4001, and 5476 differentially expressed genes were captured at 6, 12, 24, and 48 h post immunization, respectively. The hub module correlated with the immunization time was identified by WGCNA. GO and KEGG analysis showed that hub module genes were abundantly expressed in various immune-related aspects, including the response to stimuli, the immune system process, signal transducer activity, autophagy, the NOD-like receptor signaling pathway, the toll-like receptor signaling pathway, the T cell receptor signaling pathway, and Th17 cell differentiation. Additionally, genes related to Th cell differentiation are presented as heatmaps. These genes constitute a complex immune regulatory network, mainly involved in pathogen recognition, antigen processing and presentation, and Th cell differentiation. The results of this study provide the first transcriptome profile of PoPerCs associated with inactivated V. anguillarum immunity and lay a solid foundation for further studies on effective V. anguillarum vaccines.

Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean

The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.

Characterization of the mitochondrial Huso huso genome and new aspects of its organization in the presence of tandem repeats in 12S rRNA

BACKGROUND

The sturgeon group has been economically significant worldwide due to caviar production. Sturgeons consist of 27 species in the world. Mitogenome data could be used to infer genetic diversity and investigate the evolutionary history of sturgeons. A limited number of complete mitogenomes in this family were sequenced. Here, we annotated the mitochondrial Huso huso genome, which revealed new aspects of this species.

RESULTS

In this species, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H. huso had a pseudo-tRNA-Glu between ND6 and Cytb and a 52-nucleotide tandem repeat with two replications in 12S rRNA. This duplication event is probably related to the slipped strand during replication, which could remain in the strand due to mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements were also seen in the control region of the mitochondrial genome, which included termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in rRNA and tRNA, while protein-encoded genes and nonencoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 12 protein-encoding genes.

CONCLUSIONS

In H. huso sequencing, we identified a distinct genome organization relative to other species that have never been reported. In recent years, along with the advancement in sequencing identified more genome rearrangements. However, it is an essential aspect of researching the evolution of the mitochondrial genome that needs to be recognized.

Genome assembly and annotation at the chromosomal level of first Pleuronectidae: Verasper variegatus provides a basis for phylogenetic study of Pleuronectiformes

High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.

Sequencing and Characterization of Mitochondrial Protein-Coding Genes for Schizothorax niger (Cypriniformes: Cyprinidae) with Phylogenetic Consideration

The present study was conducted to get more information about the genome and locate the taxonomic position of Schizothorax niger in Schizothoracinae through mitochondrial 13 protein-coding genes (PCGs). These PCGs for S. niger were found to be 11409 bps in length ranging from 165 (ATPase 8) to 1824 bps (NADH dehydrogenase subunit 5) and encode 3801 amino acids. In these PCGs, 4 genes overlap on the similar strands, while one shown on the opposite one: ATPase 6+8 and NADH dehydrogenase subunit 4+4L overlap by 7 nucleotides. Similarly, ND5-ND6 overlap by 4 nucleotides, while ATP6 and COIII overlap by 1 nucleotide. Similarly, four commonly used amino acids in S. niger were Leu (15.6 %), Ile (10.12 %), Thr (8.12 %), and Ala (8.7 %). The results presented that COII, COIII, NDI, ND4L, and Cytb had substantial amino acid conservation as compared to the COI gene. Through phylogenetic analysis, it was observed that S. niger is closely linked with S. progastus, S. labiatus, S. plagiostomus, and S. nepalensis with high bootstrap values. The present study provided more genomic data to know the diversity of the mitochondrial genome and its molecular evolution in Schizothoracinae.

Transcriptome analysis reveals temperature-dependent early immune response in flounder (Paralichthys olivaceus) after Hirame novirhabdovirus (HIRRV) infection

Hirame novirhabdovirus (HIRRV), as a highly pathogenic fish virus, is frequently prevalent in a variety of aquaculture fish in recent years, which seriously threatens the healthy development of aquaculture industry. Epidemiological studies show that the outbreak of HIRRV is obviously temperature dependent. Virus proliferation experiments in vitro and in vivo at different temperatures indicate the antiviral response of flounder is a main reason affect the replication of HIRRV. The RNA-Seq was used to analyze the different antiviral response in flounder which infected with HIRRV at different temperatures, the experiment set two temperatures of 10 °C and 20 °C. The flounder infected with HIRRV by artificial injection, and the spleens were collected at 24 h after infection. Meanwhile, the fish injected with EPC supernatant at different temperatures were set as control groups. It can obtain four pairwise comparison groups if determine a single variable, and the differentially expressed genes were further selected. The results showed that after infection with HIRRV at 10 °C and 20 °C, the differentially expressed genes in spleen were significantly enriched in inflammatory and immune-related pathways like Arachidonic acid metabolism, Cytokine-cytokine receptor interaction, Toll-like receptor (TLR) signaling pathway, RIG-I-like receptor (RLRs) signaling pathway, NOD-like receptor (NLR) signaling pathway and Cytosolic DNA-sensing pathway etc. In addition, the expression of phagocytes, lysosomes, endocytosis related genes were significantly upregulated at high temperature whether HIRRV positive or not. But compared to the infected flounder at 10 °C, some genes of RLRs signaling pathway were significantly upregulated at 20 °C, it can be speculated that RLRs pathway may be related to the anti-HIRRV response of flounder. Therefore, key genes of RLRs signaling pathway including mda5, lgp2, mita, mavs, irf3, irf7, ifn I-3 and ifn-γ were selected, and the temporal expression patterns of these genes in infected flounder at different temperatures were further detected by qRT-PCR. The results showed that HIRRV infection can significantly stimulate and activate the RLRs pathway of flounder, and the response level of this pathway was significantly higher at 20 °C than 10 °C. In general, this study provides important data for the further study about the pathogenesis of HIRRV infection in flounder.

The complete mitochondrial genome of Amur ide (Leuciscus waleckii waleckii)

In this study, the complete mitochondrial genome of Leuciscus waleckii waleckii was sequenced and got a whole length of 16605 bp. This genome was contain 2 rRNA, 22 tRNA, 13 protein-coding genes, 1 control region (D-loop) and 1 replication origin. And the nucleotide composition of this mitochondrial genome is 27.72% for A, 26.28% for T, 27.23% for C and 18.77% for G. To clarify the phylogenetic relationship of the Leuciscus waleckii waleckii, we concluded the phylogenetic tree using 12 PCGs (except ND6) of mitochondrial genome in Leuciscus waleckii waleckii and 16 other cyprinid fish by Bayesian inference (BI) methods and maximum-likelihood (ML). And the result show that Leuciscus waleckii waleckii was close to other Leuciscus species, especially Leuciscus baicalensis.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

Complete mitochondrial genomes of eight seahorses and pipefishes (Syngnathiformes: Syngnathidae): insight into the adaptive radiation of syngnathid fishes

Background

The evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns.

Results

We sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts.

Conclusions

Our study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1430-3) contains supplementary material, which is available to authorized users.

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production

Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.

The complete mitochondrial genome of Pseudorhombus dupliocellatus (Pleuronectiformes: Paralichthyidae)

The Pseudorhombus dupliocellatus belongs to family Paralichthyidae of Pleuronectiformes. In this study, the complete mitochondrial genome of P. dupliocellatus is determined and described. The mitogenome is 16 621 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, a control region, and a L-strand replication origin. The arrangement of the mitogenome is identical to that of the typical teleost. The overall base composition is 26.9%, 25.3%, 31.0%, and 16.8% for A, T, C, and G, respectively, with a slight bias on A+T content (52.2%). The phylogenetic tree of 13 species all in Pleuronectiformes demonstrated that P. dupliocellatus, as well as the other Paralichthyidae fishes containing Paralichthys olivaceus and Pseudorhombus cinnamoneus, clustered in a clade and had a closer relationship with Pleuronectidae species than Bothidae ones. This study is expected to contributing to the systematic evolution of Paralichthyidae and further Pleuronectiformes.

Complete mitochondrial genome sequences of three rhombosoleid fishes and comparative analyses with other flatfishes (Pleuronectiformes)

Background

Peltorhamphus novaezeelandiae, Colistium nudipinnis, and Pelotretis flavilatus belong to the family Rhombosoleidae of Pleuronectiformes. Their high phenotypic similarity has provoked great differences in the number and nomenclature of the taxa that depend primarily on morphological features. These facts have made it necessary to develop molecular markers for taxonomy and phylogenetic studies. In this study, the complete mitogenomes (mtDNA) of the three rhombosoleid fishes were determined for the comparative studies and potential development of molecular markers in the future.

Results

The lengths of the complete mitogenome of the three flatfishes are 16,889, 16,588, and 16,937 bp in the order mentioned above. The difference of lengths mainly results from the presence of tandem repeats at the 3′-end with variations of motif length and copy number in the control regions (CR). The gene content and arrangement is identical to that of the typical teleostean mtDNA. Two large intergenic spacers of 28 and 18 bp were found in P. flavilatus mtDNA. The genes are highly conserved except for the sizes of ND1 (which is 28 bp shorter than the two others), ND5 (13 bp longer), and tRNA Glu (5 bp longer) in P. flavilatus mtDNA. The symbolic structures of the CRs are observed as in other fishes, including ETAS, CSB-F, E, D, C, B, A, G-BOX, pyrimidine tract, and CSB2, 3.

Conclusions

Comparative genomic analysis within rhombosoleids revealed that the mitogenomic feature of P. flavilatus was significantly different from that of the two others. Base composition, gene arrangement, and CR structure were carried on in the 17 mitogenomes. Apart from gene rearrangement in two tongue soles (Cynoglossus semilaevis and Cynoglossus abbreviatus), the gene order in 15 others is identical to that of the typical fish mitogenomes. Of the 16 studied mitogenomes, 15 species (except for Zebrias zebrinus) have tandem repeats at the 3′-, 5′-, or both 3′- and 5′-ends of the CRs. Moreover, the motif length and copy number intraspecies or interspecies are also variable. These phenomena fully indicate the diversity of repeats in flatfish mtDNA and would provide useful data for studies on the structure of mitogenomes in fishes.

Gene rearrangements in the mitochondrial genome of Cynoglossus bilineatus (Pleuronectiformes: Cynoglossidae)

Cynoglossus bilineatus (Cynoglossidae, Soleoidei) is characterized by both eyes on the left side of the body and with a rounded snout and a short rostral hook. Here we first report the mitogenome of this tongue sole, which is 16,454 bp in length, and gene rearrangements have been observed. Particularly, the tRNA-Gln gene encoded by the light strand (L-strand) has translocated to the heavy strand (H-strand), along with the tRNA-Ile gene shuffling. In addition, the putative control region has translocated downstream to a position between the ND1 and tRNA-Gln genes, leaving a 26-bp intergenic spacer in its original position. However, the arrangement of the rest genes is identical to that of the typical teleost. This result could contribute to a better understanding the molecular mechanisms of gene rearrangement in fish mitogenome as well as phylogenetic study of Cynoglossidae and Pleuronectiformes.

The complete mitochondrial genome of Cricetulus kamensis (Rodentia: Cricetidae)

The Cricetulus kamensis is endemic to China and is popular as pet. In the present study, the complete mitogenome of C. kamensis was first determined. It was 16,270 bp in length and the composition and arrangement of its genes are analogous to most other mammals. The overall base composition of heavy strand is 33.2% A, 26.8% T, 27.2% C and 12.7% G. The sequence is highly G-C poor (∼40%) and A is the most numerous nucleotide followed by T >C >G, which is similar to other mammalian mitochondrial genomes. It is notable that three extra bases "CAT" were inserted in cytb at the 3' end position and no stop codon was found for this coding region. The mitogenome sequence of C. kamensis could contribute to a better solution of its phylogenetic position and phylogenetic relationship within Cricetinae in the future.

The complete mitochondrial genome sequence of Brachirus orientalis (Pleuronectiformes: Soleidae)

The oriental sole Brachirus orientalis (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and orbicular-ovate body. In this paper, the complete mitochondrial genome sequence of this sole was first determined. The total length is 16,602 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations, and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 30.4%, 28.6%, 15.3%, and 25.7% for A, C, G, and T, with a high A + T content (56.1%). The determination of B. orientalis complete mitogenome sequence could contribute to phylogenetic study on Soleidae and Pleuronectiformes.

Phylogenetic relationships of Russian far eastern flatfish (Pleuronectiformes, Pleuronectidae) based on two mitochondrial gene sequences, Co-1 and Cyt-b, with inferences in order phylogeny using complete mitogenome data

The systematics and phylogeny of flatfish is investigated on the complete sequence of nucleotides at subunit 1 cytochrome c oxidase (Co-1) and cytochrome b (Cyt-b) genes. In total 17 species from our collection and some species from GenBank were analyzed. Four types of trees were built: Bayesian (BA), maximum likelihood (ML), maximum parsimony (MP), and neighbor joining (NJ). These trees showed similar topology. Two separate clusters on the trees support subfamily Hippoglossoidinae and Hippoglossinae subdivision and monophyletic status of these taxa. The subfamily Pleuronectinae also can be considered monophyletic, if the tribe Microstomini is excluded from it and genus Lepidopsetta is moved into the tribe Pleuronectini. Mitogenomes represented by 25 complete sequences from NCBI GenBank were analyzed. After alignment two sets of nucleotide sequences were formed and investigated independently. One set included 13 structural genes (14,886 bp), the second set comprised by the mtDNA without ND6 gene (10,457 bp). Both data sets give congruent phylogenetic signal that agreed with conventional views on the taxonomy of the order Pleuronectiformes; however, the first set gives better topology. In BA gene tree there are two well supported nodes which include the representatives of suborders Pleuronectoidei and Psettoidei. Within Pleuronectoidei two superfamilies, Pleuronectoidea and Soleidea are highly supported in BA but in all four kinds of gene trees (BA, ML, MP and NJ) the only superfamily Pleuronectoidea is well supported. At the top of hierarchy, all flatfishes belonging to the order Pleuronectiformes forming also a monophyletic clade in our data, with support level of 100% but in BA tree only. The monophyly of the family Pleuronectidae is well supported both by single gene data and by complete mtDNA sequences.

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei)

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade "Syngnathiformes" following the latest nuclear DNA studies with some revisions on the included families.

The complete mitochondrial genome of the tessellated leatherjacket Thamnaconus tessellatus (Tetraodontiformes: Monacanthidae)

The long PCR and primer walking methods were applied for obtaining the complete mitochondrial genome of the tessellated leatherjacket Thamnaconus tessellatus. The complete mitochondrial genome was 16,437 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication and a control region. The arrangements and characteristics of these segments shared common features with other teleosts. Extended termination associated sequence domain (TAS, cTAS), central conserved sequence block domain (CSB-F, CSB-E, CSB-D) and conserved sequence block domain (CSB-1, CSB-2, CSB-3) were identified in the control region.

The complete mitochondrial genome of Solea ovata (Pleuronectiformes: Soleidae)

Solea ovata (Pleuronectiformes: Soleidae) is characterized by eyes on right side and an ovata body with small ctenoid scales on both sides. In this article, the complete mitogenome of Solea ovata was first determined. The total length is 16,782 bp, containing 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a L-strand replication origin (OL). Except eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. Overall base composition is 29.2% A, 29.4% C, 15.9% G, and 25.5% T with a slight AT bias of 54.7%. The determination of S. ovata complete mitogenome could contribute to understanding the systematic evolution of the genus Solea and further phylogenetic study on Soleidae and Pleuronectiformes.

The complete mitochondrial genome sequence of Heteromycteris japonicus (Pleuronectiformes: Soleidae)

The bamboo sole Heteromycteris japonicus (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and a rostral hook. In this article, the complete mitochondrial genome sequence of this sole was first determined. The total length is 17,111 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12 S and 16 S), as well as a putative control region and a putative L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. Overall base composition of the mitogenome is 29.2%, 27.5%, 16.3% and 27.1% for A, C, G and T, with a high A + T content (56.3%). The determination of H. japonicus mitogenome sequence could contribute to understanding the systematic evolution of the genus Heteromycteris and further phylogenetic study on Soleidae and Pleuronectiformes.

The complete mitochondrial genome of a striped sole Zebrias zebrinus (Pleuronectiformes: Soleidae)

Zebrias zebrinus belongs in the family Soleidae of Pleuronectiformes. There are overlaps in the ranges of identification characters between Z. zebrinus and another striped sole Z. fasciatus. In this study, the complete mitochondrial genome of Z. zebrinus was first determined. The total length was 16,758 bp, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes (12S and 16S), as well as a putative control region and a putative L-strand replication origin (O(L)). Gene contents, locations, and arrangements were identical to those of typical bony fishes. The overall base composition of the mitogenome was 28.7%, 30.0%, 15.2%, and 26.1% for A, C, G, and T, respectively, with an A + T content of 54.8%. This result would expect the contribution to the molecular identification of this species and further phylogenetic study of Soleidae and Pleuronectiformes.

Phylogenetic studies of three sinipercid fishes (Perciformes: Sinipercidae) based on complete mitochondrial DNA sequences

The sinipercids are a group of 12 species of freshwater percoid fish endemic to East Asia and their phylogenetic placements have perplexed generations of taxonomists. We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three sinipercid fishes (Siniperca chuatsi, S. kneri, and S. scherzeri) to characterize and compare their mitochondrial genomes. The mitochondrial genomes of S. chuatsi, S. kneri, and S. scherzeri were 16,496, 17,002, and 16,585 bp in length, respectively. The organization of the three mitochondrial genomes is similar to those reported from other fish mitochondrial genomes, which contains 37 genes (13 protein-coding genes, 2 ribosomal RNAs, and 22 transfer RNAs) and a major non-coding control region. Among the 13 protein-coding genes of all the three sinipercid fishes, three reading-frame overlaps were found on the same strand. There is an 81-bp tandem repeat cluster at the end of CSB-3 in the S. scherzeri control region. The complete mitochondrial genomes of the three sinipercids should be useful for the evolutionary studies of sinipercids and other vertebrate species.

Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): genome characterization and phylogeny applications

Cichlid fishes have played an important role in evolutionary biology and aquaculture industry. Nile tilapia (Oreochromis niloticus), blue tilapia (Oreochromis aureus) and Mozambique tilapia (Oreochromis mossambicus), the useful models in studying evolutionary biology within Cichlid fishes, are also mainly cultured species in aquaculture with great economic importance. In this paper, the complete nucleotide sequence of the mitochondrial genome for O. niloticus and O. aureus were determined and phylogenetic analyses from mitochondrial protein-coding genes were conducted to explore their phylogenetic relationship within Cichlids. The mitogenome is 16,625 bp for O. niloticus and 16,628 bp for O. aureus, containing the same gene order and an identical number of genes or regions with the other Cichlid fishes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one putative control region. Phylogenetic analyses using three different computational algorithms (maximum parsimony, maximum likelihood and Bayesian method) show O. niloticus and O. mossambicus are closely related, and O. aureus has remotely phylogenetic relationship from above two fishes.

A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion

The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae, Cynoglossidae, Pleuronectiformes). The genome is 16 371 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 2 main noncoding regions, the putative control region and the light-strand replication origin. A striking finding of this study is that the tRNAGln gene is translocated from the light to the heavy strand (Q inversion). This is accompanied by shuffling of the tRNAIle gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNAGln gene. The remaining gene order is identical to that of typical fish mitogenomes. Additionally, unique characters of this mitogenome, including a high A+T content and length variations of 8 protein-coding genes, were found through comparison of the mitogenome sequence with those from other flatfishes. All the features detected and their relationships with the rearrangements, as well as a possible rearrangement pathway, are discussed. These data provide interesting information for better understanding the molecular mechanisms of gene reorganization in fish mitogenomes.

Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri)

In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.

Cytochrome oxidase 1 gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae) of Far East Russia with inferences in phylogeny and taxonomy

Mitochondrial DNA at the cytochrome oxidase 1 (Co-1) gene region was sequenced for six flatfish species (in total, 11 sequences of at least 539 base pairs) from the Far East of Russia and compared with other sequences of Pleuronectiformes, comprising altogether 26 flatfish sequences and two outgroup sequences (Perciformes). An analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in (T + C):(A + G) content, supporting earlier findings. Average scores of the p-distances for different scales of the evolutionary history at the Co-1 gene revealed a clear pattern of increased nucleotide diversity at four different levels: (1) intraspecies, (2) intragenus, (3) intrafamily, and (4) intra-order. Scores of average p-distances of the four categories of comparison in flatfishes were (1) 0.17 +/- 0.09%, (2) 10.60 +/- 1.57%, (3) 12.40 +/- 0.27%, and (4) 19.93 +/- 0.05%, respectively (mean +/- standard error). These data jointly with current knowledge support the concept that speciation in the order Pleuronectiformes mostly follows a geographic mode through accumulation of numerous small genetic changes over a long period of time. A phylogenetic tree for 26 sequences of flatfishes and two other fishes belonging to ray-finned fishes (Actinopterigii) was developed using the Co-1 gene and four different analytical approaches: neighbour-joining, Bayesian (BA), maximum parsimony (MP), and maximum likelihood. The analysis revealed a monophyletic origin for the representatives of Pleuronectidae, which is the principal flatfish family investigated (73-100% support level in our MP and BA analyses). According to the current and literary data, the monophyletic origin for the six compared flatfish families was well supported. Species identification on a per-individual basis (barcoding tagging) was high.

Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha)

Percomorpha has been described as the "(unresolved) bush at the top" of the teleostean phylogenies and its intrarelationships are intrinsically difficult to solve because of its huge diversity (>15,000 spp.) and ill-defined higher taxa. Patterns of facial nerves, such as those of the ramus lateralis accessorius (RLA), have been considered as one of the candidate characters to delimit a monophyletic group within the percomorphs. Six families of the suborder Percoidei (Arripidae, Dichistiidae, Kyphosidae, Terapontidae, Kuhliidae, and Oplegnathidae) and suborder Stromateoidei (including six families) share the unique pattern 10 of RLA and it has been suggested that those fishes form a monophyletic group across the two perciform suborders. To evaluate the usefulness of the RLA pattern 10 as a phylogenetic marker within the percomorphs, we newly determined whole mitochondrial genome (mitogenome) sequences for the 13 species having RLA pattern 10 and their putatively, closely-related species (5 spp.). Unambiguously aligned sequences (14,263 bp) from those 18 species plus 50 percomrphs and two outgroups (total 70 species) were subjected to partitioned maximum likelihood and Bayesian analyses. The resulting trees clearly indicated that there were at least two independent origins of the unique facial nerve pattern: one in a common ancestor of Kyphosidae, Terapontidae, Kuhliidae, and Oplegnathidae and another one in that of the percoid Arripidae and Stromateoidei. Thus further detailed anatomical studies are needed to clarify the homology of this character between the two lineages. It should be noted that the latter two taxa (Arripidae and Stromateoidei) formed an unexpected, highly-supported monophyletic group together with Scombridae and possibly Chiasmodontidae and Bramidae, all lacking RLA pattern 10 (the former two are members of other perciform suborders Scombroidei and Trachinoidei, respectively). This novel, trans-subordinal clade has never been suggested by any morphological studies, although they share a common ecological characteristic, dwelling in the pelagic realm and often associated with long-distance migrations.

Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences

Series Atherinomorpha, with its plentiful number of species and highly diversified ecological and morphological characters, is the most successful fish group at the surface layer of the ocean and many freshwater habitats, comprising 1552 species classified into three orders, six suborders, 21 families, and 193 genera. The group includes one of the most important research model organisms, the medaka (Oryzias latipes), together with diverse fishes with morphological, physiological, and ecological specializations, such as highly developed pectoral fins to glide, self-fertilization, and live-bearing. In this study, we examined the whole mitochondrial genomes (mitogenomes) from 17 species representing all of the three orders and six suborders within Atherinomorpha, with data from 70 additional percomorph species as ingroups, and two non-percomorph outgroup species. We subjected the unambiguously aligned mitogenome sequences to partitioned maximum likelihood and Bayesian phylogenetic analyses. The resulting phylogenies recovered a monophyletic Atherinomorpha within the Percomorpha, and demonstrated its phylogenetic affinity to the percomorph fishes (including cichlids) spawning demersal eggs with filaments. This study, further, provided the first molecular evidence for the monophyly of the respective atherinomorph orders (Atheriniformes, Beloniformes, and Cyprinodontiformes) with high posterior probabilities and mostly high bootstrap values, providing an important basis for the future studies on the phylogeny and evolution of this diverse group.

The complete mitochondrial genome of rock carp Procypris rabaudi (Cypriniformes: Cyprinidae) and phylogenetic implications

Rock carp, Procypris rabaudi (Tchang), is an endemic fish species in China. We sequenced the complete mitochondrial genome of it by high-fidelity polymerase chain reaction with conserved primers and primer walking sequencing method. The complete mitochondrial genome of rock carp is 16595 bp in length and contains 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of most other vertebrates. The origin of L-strand replication (OL) in rock carp mitochondrion is located in a cluster of five tRNA genes (WANCY region) with 35 nucleotides in length. The control region is located between the tRNA-Pro and tRNA-Phe genes and is 943 bp in length. Three conserved sequence blocks (CSB), an extended termination associated sequence (ETAS), an AT-repeat microsatellite sequence and a putative promoter sequence for H-strand transcription (HSP) were identified within this region. The microsatellite sequence has a very low variation, with only one repeat alteration in 50 checked individuals (from 12 to 13 repeats). The phylogenetic analysis for rock carp was performed with Bayesian and Maximum likelihood (ML) methods based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result suggested that traditional taxonomic barbines possibly originated more early than cyprininaes; rock carp was placed at the position between barbines and cyprininaes, while has a closer relationship with cyprininaes than barbines.

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

We determined the whole mitochondrial genome sequence for spotted green pufferfish, Tetraodon nigroviridis (Teleostei: Tetraodontiformes). The genome (16,488 bp) contained 37 genes (two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes) plus control region as found in other vertebrates, with the gene order identical to that of typical vertebrates. The sequence was used to estimate phylogenetic relationships and divergence times among major lineages of fishes, including representative model organisms in fishes. We employed partitioned Bayesian approaches for these two analyses using two datasets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding the ND6 gene) and concatenated nucleotide sequences from the 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The resultant trees from the two datasets were well resolved and largely congruent with those from previous studies, with spotted green pufferfish being placed in a reasonable phylogenetic position. The approximate divergence times between spotted green pufferfish and model organisms in fishes were 85 million years ago (MYA) vs. torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records.

The complete mitochondrial genome of the Senegal sole, Solea senegalensis Kaup. Comparative analysis of tandem repeats in the control region among soles

The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. The mitochondrial DNA was 16,659 base pairs (bp) in length. Sequence features of the 13 protein-coding genes, two ribosomal RNAs and 22 transfer RNAs are described. The non-coding control region (1017 bp) was compared with those of the closely related soles Solea solea and Solea lascaris. The typical conservative blocks were identified. A cluster of 42 and 22 tandemly arrayed repeats was detected near the 3' end of control region in S. solea and S. lascaris, respectively. On the contrary, only two (93.8% of haplotypes) or three copies (6.2%) of an 8-bp repeated sequence motif was found in S. senegalensis. Phylogenetic analysis showed that 7 out of 9 of haplotypes bearing three copies grouped in a separate cluster. Possible mechanisms influencing the evolution of control region among soles are discussed.

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts

The fishes currently recognized as members of the order Gasterosteiformes (sticklebacks, pipefishes, and their relatives) number 278 species, classified into two suborders (Gasterosteoidei and Syngnathoidei), 11 families and 71 genera. Members of this group exhibit unique appearances, many of which are derived from armored bodies with bony plates in various forms. Although recent molecular phylogenetic studies have repeatedly questioned the monophyly of this order, none of the studies examined all of the representative families and the phylogenetic reality of the group has remained unclear. In this study, we examined whole mitochondrial genome (mitogenome) sequences from 13 gasterosteiform species representing all 11 families in the order, and subjected them to partitioned maximum likelihood and Bayesian analyses, with additional data from other percomorphs and outgroups (75 mitogenome sequences considered overall, including 10 newly determined). The resultant phylogenies indicated explicitly that previously recognized members of Gasterosteiformes had diverged basally within the Percomorpha into three different clades with the following subgroups: Syngnathoidei, Gasterosteoidei (minus Indostomidae), and Indostomidae. Monophyly of the order Gasterosteiformes and any combinations of the three subgroups were confidently rejected by statistical tests. Syngnathoidei (together with Dactylopteroidei) formed a monophyletic group, a sister-group relationship between Gasterosteoidei (minus Indostomidae) and Zoarcoidei was reconfirmed and Indostomidae was nested within the Synbranchiformes, rendering the latter group paraphyletic. Our study demonstrates a new perspective of gasterosteiform phylogeny, which will provide fundamental information for future studies of phylogeny, systematics, and evolution.