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Article

Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae

by
Tianyan Yang
*,
Yuping Liu
and
Zijun Ning
Fishery College, Zhejiang Ocean University, Zhoushan 316022, China
*
Author to whom correspondence should be addressed.
Animals 2023, 13(3), 362; https://doi.org/10.3390/ani13030362
Submission received: 3 December 2022 / Revised: 15 January 2023 / Accepted: 18 January 2023 / Published: 20 January 2023
(This article belongs to the Section Aquatic Animals)
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Abstract

:

Simple Summary

It is generally known that the order of mitochondrial genes is highly conserved, but to date, along with the gradual increase of teleostean mtDNA sequences in the GenBank database, the gene rearrangement events have been identified in all the published complete mitogenomes of Ophichthidae species. This amusing finding makes it necessary to carry out studies on mitogenome characteristics and phylogenetic evolution of this fish group. Here, we chose Ophichthus evermanni and O. erabo as representatives, and obtained the whole mtDNA sequences using the Illumina high-throughput sequencing technology. The novel gene rearrangement and phylogenetic relationships indicated that Ophichthidae might be a monophyletic group and formed a sister group with Muraenesocidae.

Abstract

The family Ophichthidae has the largest number and the most various species (about 359 valid species) in the order Anguilliformes worldwide. Both morphological and molecular characteristics have been used to assess their taxonomic status. However, due to the ambiguous morphological features, molecular data such as mitochondrial DNA sequences have been implemented for the correct identification and classification of these fishes. In this study, the gene arrangement and structure characteristics of two Ophichthidae mitochondrial genomes were investigated for the first time. The total mitogenome lengths of O. evermanni and O. erabo were 17,759 bp and 17,856 bp, respectively. Comparing with the ancestral mitochondrial gene order, the irregular gene rearrangement happened between ND6 and tRNA-Pro (P) genes with another similar control region emerging between tRNA-Thr (T) and ND6 genes, which could be explained by the tandem duplication and random loss (TDRL) model appropriately. ML phylogenetic tree demonstrated that the family Ophichthidae was monophyletic origin, but genus Ophichthus might be polyphyletic because of the confused cluster relationships among different species.

1. Introduction

The family Ophichthidae comprises 62 genera and 356 species across the globe belonging to two subfamilies, the Myrophinae (70 species) and the Ophichthinae (289 species), respectively. It has the most abundant species of Anguiliformes and represents various morphological characteristics [1]. Ophichthidae fish are widely distributed in the continental shelf of all tropical and subtropical oceans, with the water depths ranging from the intertidal to 1300 m [2]. Their snake-sharped bodies can easily burrow in muddy substrates or coral reefs by hard pointed rayless tail-tips or acute snouts [3]. As the most in quantity and species among eels, the classification and identification of Ophichthidae species is still in confusion because of ambiguous morphological features and variable body shapes at different growth stages [3,4]. Since the concept of molecular systematics was first proposed in 1965, it has been considered a powerful tool to solve the traditional taxonomic problems and provide new insights in phylogenetic relationships of living organisms [5]. Mitochondrial DNA (mtDNA) is one of the most valuable and popular molecular markers in the fields of molecular systematics, population genetics and evolutionary biology at multiple taxonomic levels [6,7].
The typical mitochondrial genome is a covalently double-stranded cyclic DNA and normally consists of two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and non-genic regions (control region and the origin of light strand replication). The sequential order of genes in mitochondrial DNA initially tends to be conserved in metazoan [8]. However, in recent years, cases of mitochondrial rearrangement have subsequently been reported in some amphibians [9,10], reptiles [11,12,13], aves [14,15,16], and arthropods [17,18], with the rapid development of sequencing technology. Intraspecific rearrangements of mitogenomes are rarely found in bony fishes, but certain flatfishes [19,20,21,22,23], Antarctic notothenioids [24,25], and deep-sea fishes [26,27] had the rearranged gene order. According to the teleostean complete mtDNA sequences published in NCBI database, the probabilities of gene rearrangements are much higher in Anguiliformes. The previous research has been performed in the systematic evolution of Elopomorpha fishes based on mtDNA genes [28,29,30,31,32]. Nevertheless, individual gene markers of partial fragments may not supply adequate evidence to explain the kinships among Anguiliformes, especially phylogenetic relationships of the teleost fishes grouped into the family Ophichthidae have been poorly understood.
Variability of mitochondrial gene order among animal phyla contains quantitatively meaningful information for phylogenetic reconstruction. Therefore, gene arrangement is considered a useful phylogenetic character [33,34]. In this study, we obtained the complete mitochondrial DNA sequences of two representative snake eels Ophichthus evermanni (Jordan & Richardson, 1909) and O. erabo (Jordan & Snyder, 1901) using next-generation sequencing (NGS) technology for the first time, and a novel mitochondrial reorganization was discovered in comparison with normal gene order in other vertebrate lineages. Simultaneously, 23 rearranged complete mtDNA sequences of Anguilliformes available from GenBank were downloaded to construct the phylogenetic tree. The comparative mitogenomics results would provide references for further molecular identification and phylogenetics research on Ophichthidae.

2. Materials and Methods

2.1. Sampling, DNA Extraction, and High-Throughput Sequencing

Specimens of O. evermanni (female, body length 77.1 cm and body weight 571.63 g) and O. erabo (male, body length 73.44 cm and body weight 389.32 g) were captured from the coastal waters of Xiamen (118°34′ E, 24°15′ N) China in December 2020 and January 2021, respectively. The snake eels were characterized and identified using both morphometric and molecular methods after euthanizing them with 200 mg/L tricaine methanesulfonate (MS-222) solution for about 20 min [35]. Fresh muscle tissues were clipped from the body and immediately preserved in absolute ethanol for long-term storage.
The genomic DNA was extracted according to standard phenol-chloroform method [36], and then assessed by 1% agarose gel electrophoresis and Qubit 2.0 (Invitrogen, CA, USA), respectively. The quantified DNA samples were randomly broken into small fragments (about 300 bp) using Covaris M220 Focused-ultrasonicator (Covaris, MA, USA). The paired-end libraries were constructed and subsequently sequenced via 300 bp paired-end Illumina HiSeq 2500 platform following manufacturer’s recommendations.

2.2. Mitogenome Assembly and Annotation

The raw data were filtered by clipping adapters, duplicated reads and short reads (<50 bp), the reads with proportion of uncertain bases “N” exceeding 10% and low quality reads (<Q20) using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic (accessed on 15 March 2022)) [37]. Multiple iterations and splicing were performed to assemble the mitochondrial genome by Getorganells (https://github.com/Kinggerm/GetOrganelle (accessed on 3 April 2022)) [38]. Bases correcting, mis-assemblies fixing, and gaps filling were conducted by Pilon 1.23 [39]. The complete mitochondrial genome sequences were annotated with the online tool Mitofish (http://mitofish.aori.u-tokyo.ac.jp/ (accessed on April 18 2022)) and the annotation results were checked manually for the further analysis. The entire mitogenome sequences were deposited to GenBank database using Sequin, under the accession numbers OM421636 for O. evermanni and OP154196 for O. erabo.

2.3. Sequence Analysis

Protein-coding genes (PCGs) were examined by translating into their corresponding amino acid sequences to correct premature or truncated stop codons using MEGA 11 [40]. The tRNA genes were predicted and identified using the default search mode of the online tool tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/ (accessed on 4 May 2022)) [41] and their cloverleaf structures were visualized by diagram online tool tRNAdb (http://rna.tbi.univie.ac.at/forna/ (accessed on 8 May 2022)) [42]. The location of origin of light-strand replication (OL) was identified via sequence homology alignment, and the putative secondary structure was inferred using Mfold web server (http://www.unafold.org/ (accessed on 10 May 2022)) [43]. The pattern graphs for gene order rearrangement were designed and drew by IBS 1.0 [44].
The nucleotide and amino acid composition calculations and the relative synonymous codon usage (RSCU) analysis were performed in MEGA 11 [40], and nucleotide composition skewness was calculated by the following formulas: AT-skew = (A − T)/(A + T) and GC-skew = (G − C)/(G + C) [45]. The values of nonsynonymous substitution (Ka)/synonymous substitution (Ks) were determined by KaKs_Calculator 2.0 software (https://ngdc.cncb.ac.cn/biocode/tools/BT000001 (accessed on 2 June 2022)) [46].

2.4. Phylogenetic Analysis

Twenty-three Anguilliformes mitogenomes existing gene rearrangements were downloaded from the GenBank database for phylogenetic analysis, with Neocyema erythrosoma (AP018345) belonging to Saccopharyngiformes, Cyematidae be selected as an outgroup. Twelve PCGs without stop codons were concatenated for the phylogenetic analysis. The ND6 gene was excluded because of its poor phylogenetic performance [47,48]. Multiple sequences were aligned by MegAlign program in DNAstar Lasergene software package [49]. The use of the maximum likelihood (ML) method in developing phylogenetic requires a model of evolution [50]. Therefore, a general-time reversible + gamma + invariants (GTR + G + I) nucleotide substitution model was selected from the Model Test conducted using MEGA before phylogenetic inference. DAMBE 5.0 was taken to measure the nucleotide substitution saturation [51], and then PhyML 3.0 was used to construct the phylogenetic tree with node support being calculated by 1000 bootstrap replicates to estimate confidence of tree topology [52]. The graphic representation was performed and manually edited with iTOL (https://itol.embl.de/ (accessed on 18 June 2022)).

3. Results

3.1. Mitogenome Characteristics and Organization

The total lengths of the mitochondrial genomes were 17,759 bp (O. evermanni) and 17,856 bp (O. erabo), respectively (Figure 1 and Table 1). Only ND6 and eight tRNA genes were encoded on the L-strand. A total of 78 bp and 98 bp intergenic gaps were observed, ranging from 1 to 18 bp. The largest overlap detected between ATP8 and ATP6 genes was 10 bp in length, followed with 7 bp overlap between ND4L and ND4 genes. The similarity of entire PCGs between two species varied from 76.5% (Cyt b) to 87.0% (COII).
The proportions of four nucleotides were listed as follows: A = 31.27%, G = 16.19%, C = 26.22%, T = 26.32% in O. evermanni, and A = 32.07%, G = 16.25%, C = 26.24%, T = 25.44% in O. erabo, respectively, showing approximate equilibria between C and T as well as an obvious bias of A. The contents of A and C exhibited high values at the third codon position, indicating that the codon usage preferred A and C at this position. All the AT-skews were positive except six genes (CRs, COI, ATP6, COIII, ND3, and ND6) in O. evermanni, and five genes (ND1, COI, ND3, ND4L, and Cyt b) in O. erabo, whereas negative GC-skews were lowest in ATP8 and highest in tRNAs both in two snake eels (Table 2).
The nucleotide composition and skewness of 25 Anguilliformes mitogenome were analyzed in Supplementary Table S1. The results showed those overall base compositions of two fishes possessed a higher A + T bias of 57.59% (O. evermanni) and 57.50% (O. erabo), indicating positive AT-skew and negative GC-skew. The average AT-skews of twenty-five eels was 0.108, ranging from 0.069 in Muraenesox bagio to 0.170 in Paraconger notialis, while the average GC-skew was −0.230, ranging from −0.261 in Thalassenchelys sp. to −0.164 in Conger japonicas.

3.2. Novel Gene Arrangement and the Possible Pathway

The arrangement of mtDNA genes of two fishes deviated from the classic vertebrate type. ND6 and tRNA-Glu genes were located between tRNA-Thr and tRNA-Pro genes, and another highly homologous control region appeared in the upstream of the ND6 gene. Excluding ND6, the tRNA-Glu translocation and CR repeat sequence of the remaining genes was consistent with normal mitochondrial genomic order in the vertebrate (Figure S1). The hypothesized intermediate steps of gene rearrangement were as follows. First, the gene cluster “ND6–tRNA-Glu (E)–Cyt b–tRNA-Thr (T)–tRNA-Pro (P)–CR” was tandemly duplicated, and then random deletions of redundant genes containing original ND6, tRNA-Glu (E), tRNA-Pro (P) as well as the copied Cyt b and tRNA-Thr (T) occurred, which most likely resulted in the observed gene order and associated intergenic spacers in O. evermanni and O. erabo.

3.3. Protein Coding Genes (PCGs) and Codon Usages

The total lengths of the PCGs in O. evermanni and O. erabo were 11,519 bp and 11,518 bp, respectively, accounting for 64.86% and 64.50% of the whole sequences. The A + T contents in the regions were 57.40% and 56.90%, which were slightly lower compared with that of the entire mitogenomes. Lower guanine content and higher adenine content were exhibited in the 1st codon position, while the 2nd position did not display deflection of A, T and C proportions. An anti g bias was noted in the 3rd codon position, which was as same as the typical vertebrates [53].
Just like other bony fishes, the 12 PCGs in the mtDNA of two snake eels were located on the majority strand excluding the ND6 gene. The start codons were completely consistent with each other, and all of them started with the typical ATG, except for the codon for the COI gene, which used the GTG and ND6 gene with CTA as the initiation codon. In both species ND2, ND3, ND4, and COII ended with the incomplete stop codon T--, yet in O. evermanni, ATP6 and Cyt b used TA- and AA- as termination codons, respectively, which would be completed by adding a poly A tail during RNA processing and act as the complete functional termination codons in the processes of polyadenylation and polycistronic transcription cleavage [54].
A total of 3658 (O. evermanni) and 3657 (O. erabo) amino acids were present in the 13 PCGs without the stop codons, respectively. Two fish species owned the similar codon usage with the most commonly used amino acids being Leu (13.48% in O. evermanni and 13.50% in O. erabo), while the Cys (1.46% in O. evermanni and 1.73% in O. erabo) was the most rarely used (Figure S2). The content of AT-rich codon families (Phe, Ile, Met, Tyr, Asn, and Lys) was higher than that of GC-rich codon families (Pro, Ala, Arg, and Gly). The relative synonymous codon usage (RSCU) values of PCGs were summarized in Figure 2. All stop codons were excluded from the analysis to avoid biases due to incomplete stop codons. The frequency of use of codons has no difference from other degenerate codons if the RSCU value equals 1 [55], and it was found that most of the over-represented codons were A and U ending types (RSCU > 1) of PCGs in the mitogenomes of O. evermanni and O. erabo.

3.4. Ribosomal and Transfer RNA Genes

Next, 12S rRNA and 16S rRNA genes were situated between tRNA-Phe (F) and tRNA-LeuUUA (L1) with tRNA-Val (V) sandwiched in between them, which was similar to other vertebrate mitogenomes to date [47,53]. The lengths of rRNAs occupied a sum of 14.99% (2662 bp) and 14.96% (2672 bp) of the whole mitochondrial genomes, with positive AT-skew values as 0.279 and 0.303, respectively. The A + T content of 16S rRNA gene (57.25% in O. evermanni and 58.42% in O. erabo) was slightly greater than that of 12S rRNA gene (53.39% in O. evermanni and 53.26% in O. erabo), both contributing to the overall total rRNAs A + T content of 55.86% and 56.55%.
The size range of 22 tRNAs was from 65 bp for tRNA-Cys (C) to 76 bp for tRNA-LeuUUA (L). Majority tRNAs placed in H-strand while minority of them were in L-strand. Two kinds of tRNA-Leu (L) and tRNA-Ser (S) were discovered in the mtDNA of both species with the anticodons listed: tRNA-LeuUUA (L1) = TAA, tRNA-LeuCUA (L2) = TAG, tRNA-SerUCA (S1) = TGA, and tRNA-SerAGC (S2) = GCT. The comprehensive secondary structures of tRNA genes for both O. evermanni and O. erabo were shown in Supplementary Figure S3. The traditional clover-leaf structures of tRNA genes were identified, including amino acid receptor arm, anticodon arm, pseudouracil (TΨC) arm and dihydrouracil (DHU) arm, and their connected loops. Only tRNA-SerAGC (S2) was an exception because it was lacking the DHU arm. In addition to standard Watson–Crick base pairs (A-U and G-C), there were 36 bp mismatches present in the tRNA secondary structures, all of which formed a noncanonical bond (G-U pairs). Moreover, DHU and TΨC arms were seemed to be more conserved than the other two in consideration of the lower variation of base pairs.

3.5. Noncoding Regions

In this study, the noncoding regions included the light strand origin (OL) as well as two highly homologous control regions (CRs), and this phenomenon was noticed in the published mitochondrial genome of O. brevicaudatus [56]. The ancestral CR was still located between tRNA-Pro (P) and tRNA-Phe (F), as well as the duplicated one was between tRNA-Thr (T) and ND6 gene. The OL is situated within a tRNA gene cluster, which is often referred to as the WANCY region [57]. It was 21–34 bp to long in nine Ophichthidae species, and the single stranded DNA folding pattern showed that this region possibly formed a stable hairpin structure with a GC rich stem and a 5–12 bp small loop in length (Table S2). The use of stem codons showed more pyrimidines at the 5′ end of the OL sequence. No typical conserved sequence motif 5′-GCCGG-3′ was detected in the upstream of the stem, which was necessary for vitro replication of the L-strand in mammals [58,59].

3.6. Selective Pressure Analysis of PCGs

The nonsynonymous substitution (Ka) and synonymous substitution (Ks) of protein-coding sequences are two important parameters to quantify the selective pressure and evolutionary dynamics across closely related species [60]. The ratios of Ka/Ks of two snake eels were calculated to determine selective pressure levels imposed on 13 PCGs. We found the ratios of the 12 PCGs were all below 1, ranging from 0.0113 (COI) to 0.3302 (Cyt b), indicating a strong repair mechanism against deleterious mutations on these protein genes. Only ND6 gene presented the value larger than 1 (Figure S4), which demonstrated that it was subject to positive selection.

3.7. Phylogenetic Analysis

ML phylogenetic tree were constructed on the basis of linked sequences of 12 PCGs (without stop codons). DAMBE was conducted to test the nucleotide substitution saturation prior to phylogenetic analysis. The observed Iss value was 0.4760, and it was smaller than Iss.c values both in assuming a symmetrical tree (0.8495) and assuming an extreme asymmetrical tree (0.6262) when all three codon positions were considered as a whole.
The reconstructed ML tree revealed that all Ophichthidae species gathered together, but the clustering relations among genera within this family were confused (Figure 3). According to the taxonomic classification, species belonging to the genus of Ophichthus were supposed to cluster in the same topological clade, whereas O. erabo was even outermost-situated at the clade of Ophichthidae. The family Ophichthidae was monophyletic and formed a sister group with Muraenesocidae under a higher bootstrap support rate (97%).

4. Discussion

Three indexes of A + T content, AT-skew, and GC-skew were usually used to describe the patterns of nucleotide composition and strand asymmetry in DNA sequences, especially when the latter two could clearly reflect the strand bias in nucleotide composition of metazoan mitogenomes [61]. In the present study, the GC-skew values of the 13 PCGs among the two species were negative, demonstrating base C were more plentiful than G. Moreover, the absolute values of GC-skew were larger than those of AT-skew, conforming to conventional preferences that GC-skew was more obvious [62]. A strong AT-bias in the 3rd codon position and the preferred codons were influenced by compositional constraints. The results confirmed that codon usage bias and the AT bias of the 3rd codon position were positively correlated in the mitogenomes [63,64].
Shuffling, translocation, and inversion are the main types of gene reorganization of fish mitogenomes [65]. Six models have hitherto been proposed to explain the rearrangement mechanism: tandem duplication and random loss (TDRL), tandem duplication and nonrandom loss (TDNL), dimer-mitogenome and nonrandom loss (DMNL), double replication and random loss (DRRL), intra-mitochondrial recombination and tRNA mis-priming [20,21]. Among the available models for gene rearrangement events, the TDRL model that was assumed to be triggered by gene duplication was the most appropriate one to explicate the gene rearrangement of Anguilliformes mitogenomes [56,66,67,68]. According to this mode, it was speculated that the tandem duplication and subsequent deletion events occurred between the ND6 gene and CR both in O. evermanni and O. erabo.
Noncoding regions are scattered through the whole genome in spite of compact mitogenome of typical teleosts [69]. Variations (duplication or degeneration) in CR, the large non-coding region (LNR) in mtDNA have very important evolutionary values in metazoan mitochondria, because it contains regulatory elements involving in mtDNA replication and transcription [70]. Two separate CRs with identical or highly similar nucleotide sequences are rare in vertebrates. Duplicate CRs have been happened in the mitogenomes of some birds [71,72,73], turtles [74], snakes [11,75], and frogs [76] to date. In ray-finned fishes, Lee et al. [77] described two CRs in mtDNA of Rivulus marmoratus for the first time, and subsequently a deep-sea gulper eel Saccopharynx lavenbergi [27], three flatfishes (Crossorhombus azureus, Samariscus latus and Laeops lanceolata) [19,78], and a newly named pomfret Pampus minor [79] displayed the similar mitogenomic structure. In our study, two CRs with higher similarity (94.5% in O. evermanni and 88.6% in O. erabo) were found in two Ophichthus species. At present, hypotheses such as tandem duplication, dimerization, and illegitimate recombination are proposed to explain how duplicated CRs are generated [80]. Additionally, it is reported that duplicate CRs have evolved in either concerted evolution [11,70,75,78], independent evolution [72], or both [70,71] in fishes and other animals. The possible evolutionary pattern and originated mechanism of the duplicate CRs still need more specimens for deeper analysis.
For most proteins, Ka = Ks means neutral mutation, Ka < Ks indicates negative (purifying) selection and Ka > Ks suggests a positive (diversifying) selection, respectively [81,82]. It was revealed that only ND6 gene experienced positive selection in our study. The proton-translocating NADH-quinone oxidoreductase (Complex I), a multisubunit integral membrane enzyme, catalyzes electron transfer from NADH through the respiratory chain of both bacteria and eukaryotic organelles. In addition, it provides about 40% of the proton-motive force required to synthesize ATP in vertebrates [83,84]. Mitochondrial DNA-encoded ND6 subunit is an indispensable part of Complex I. As the benthic and cave-dwelling fishes with a preference for slithering in muddy substrates, mutations leading to amino acid changes of ND6 imply that they are undergoing evolutionary selection associated with hypoxia tolerance in snake eels [48,85]. Besides, larger fluctuation in AT/GC-skew value in ND6 also suggested that the mutational pressure on it might be significantly different from other genes from another perspective.
In this study, the test of substitution saturation indicated the set of aligned nucleotide sequences experienced little substitution saturation and consequently phylogenetic analysis was feasible [86]. These findings of molecular phylogenetic analysis coincided with previous taxonomic studies on snake eels [87,88], which showed that Ophichthidae fishes occurring mitochondrial gene rearrangements should be diagnosed as a monophyletic group because of the highly unlikely homoplasy [33], and evidence supplied by other researchers also validated this conclusion [56,66,68].

5. Conclusions

The current study provided the mitogenomic characteristics of two snake eels (O. evermanni and O. erabo) from Xiamen offshore sea by high-throughput sequencing technology, with the total lengths of 17,759 bp and 17,856 bp, respectively. Different from the typical bony fishes, the complete mtDNAs of both species contained 37 genes (2 rRNAs, 22 tRNAs and 13 PCGs), two CRs, and the OL. Moreover, a novel gene arrangement obviously occurred in the region from ND6 to CR, and the presumptive arrangement mechanism could be explained by TDRL model. The present gene order and associated intergenic spacers could have resulted from an occurrence of duplication in this gene cluster followed by random deletion of five redundant genes ND6, Cyt b, tRNA-Glu (E), tRNA-Thr (T) and tRNA-Pro (P). The ratio of Ka and Ks indicated that only ND6 gene underwent a diversifying selection, which might be related to adaptive evolution of hypoxia tolerance in this fish group. Phylogenetic analysis through 25 Anguilliformes mitochondrial genomes with gene rearrangements showed that Ophichthidae was monophyletic origin and had close relationships with Muraenesocidae. In summary, our research results provided useful information for in-depth understanding of phylogenetics and evolutionary mechanism in family Ophichthidae.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ani13030362/s1, Figure S1: Inferred process of mitochondrial gene rearmament in both Ophichthus species; Figure S2: Amino acid compositions in the mitogenomes of two snake eels; Figure S3: Inferred secondary structures of the 22 tRNA genes of two Ophichthus species; Figure S4: The rates of non-synonymous substitutions (Ka) and synonymous substitutions (Ks) for each PCG in pairwise mitochondrial genome of O. evermanni and O. erabo; Table S1: Composition and skewness of mitogenomes in 25 Anguilliformes species with novel gene order; Table S2: The OL structure in the mitogenomes of nine Ophichthidae fishes;

Author Contributions

Conceptualization, T.Y.; methodology, Y.L. and Z.N.; writing—original draft preparation, T.Y.; writing—review and editing, Y.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Science and Technology Planning Project of Zhoushan, grant number 2022C41022.

Institutional Review Board Statement

The animal study protocol was approved by the Ethics Committee of Zhejiang Ocean University (protocol code: ZJOU-ECAE20211876, date of approval: 16 December 2021).

Informed Consent Statement

Not applicable.

Data Availability Statement

The datasets presented in this study were submitted to The National Center for Biotechnology Information (NCBI) database with the accession numbers OM421636 and OP154196.

Acknowledgments

We would like to express our sincere thanks to Runhong Wu for his help in sample collecting.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Fricke, R.; Eschmeyer, W.N.; Van der Laan, R. (Eds.) Eschmeyer’s Catalog of Fishes: Genera, Species, References. 2022. Available online: http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp (accessed on 13 December 2022).
  2. McCosker, J.E. FAO Ophichthidae: Shrimp eels, worm eels and sand eels. In FAO Guide to the Living Resources of the Eastern Central Atlantic; Carpenter, K., Ed.; FAO: Rome, Italy, 2015; pp. 160–170. [Google Scholar]
  3. McCosker, J.E. The osteology, classification and relationships of the eel family Ophichthidae. Proc. Calif. Acad. Sci. 1977, 41, 1–123. [Google Scholar]
  4. Tang, W.Q.; Zhang, C.G. A taxonomic study on snake eel family Ophichthidae in China with the review of Ophichthidae (Pisces, Anguilliformes). J. Shanghai Fish. Univ. 2004, 13, 16–22. (In Chinese) [Google Scholar]
  5. Zukerkandl, E.; Pauling, L. Evolutionary divergence and convergence in proteins. In Evolving Genes and Proteins; Bryson, V., Vogel, H.J., Eds.; Academic Press: New York, NY, USA, 1965; pp. 97–166. [Google Scholar]
  6. Avise, J.C.; Arnold, J.; Ball, R.M.; Bermingham, E.; Lamb, T.; Neigel, J.E.; Reeb, C.A.; Saunders, N.C. Intraespecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst. 1987, 18, 489–522. [Google Scholar] [CrossRef]
  7. Scheffler, I.E. Mitochondrial, 2nd ed.; Wiley-Liss Publication: New York, NY, USA, 2007. [Google Scholar]
  8. Boore, J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27, 1767–1780. [Google Scholar] [CrossRef] [Green Version]
  9. Su, X.; Wu, X.B.; Yan, P.; Cao, S.Y.; Hu, Y.L. Rearrangement of a mitochondrial tRNA gene of the concave-eared torrent frog, Amolops tormotus. Gene 2007, 394, 25–34. [Google Scholar] [CrossRef]
  10. Yuan, S.Q.; Yun, X.; Zheng, Y.C.; Zeng, X.M. Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri. Peerj 2016, 4, e2786. [Google Scholar] [CrossRef] [Green Version]
  11. Kumazawa, Y.; Ota, H.; Nishida, M.; Ozawa, T. Gene rearrangements in snake mitochondrial genomes: Highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Mol. Biol. Evol. 1996, 13, 1242–1254. [Google Scholar] [CrossRef]
  12. Yan, J.; Li, H.; Zhou, K. Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships. BMC Genom. 2008, 9, 569. [Google Scholar] [CrossRef] [Green Version]
  13. Kumazawa, Y.; Miura, S.; Yamada, C.; Hashiguchi, Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genom. 2014, 15, 930. [Google Scholar] [CrossRef] [Green Version]
  14. Singh, T.R.; Shneor, O.; Huchon, D. Bird mitochondrial gene order: Insight from 3 warbler mitochondrial genomes. Mol. Biol. Evol. 2008, 25, 475. [Google Scholar] [CrossRef] [Green Version]
  15. Zhou, X.P.; Lin, Q.X.; Fang, W.Z.; Chen, X.L. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genom. 2014, 15, 573. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  16. Eberhard, J.R.; Wright, T.F. Rearrangement and evolution of mitochondrial genomes in parrots. Mol. Phylogenet. Evol. 2016, 94, 34–46. [Google Scholar] [CrossRef] [PubMed]
  17. Campbell, N.J.; Barker, S.C. An unprecedented major rearrangement in an arthropod mitochondrial genome. Mol. Biol. Evol. 1998, 12, 1786–1787. [Google Scholar] [CrossRef] [Green Version]
  18. Tyagi, K.; Kumar, V.; Poddar, N.; Prasad, P.; Tyagi, I.; Kundu, S.; Chandra, K. The gene arrangement and phylogeny using mitochondrial genomes in spiders (Arachnida: Araneae). Int. J. Biol. Macromol. 2020, 146, 488–496. [Google Scholar] [CrossRef]
  19. Shi, W.; Dong, X.L.; Wang, Z.M.; Miao, X.G.; Wang, S.Y.; Kong, X.Y. Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes. BMC Evol. Biol. 2013, 13, 173. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  20. Shi, W.; Miao, X.G.; Kong, X.Y. A novel model of double replications and random loss accounts for rearrangements in the mitogenome of Sssamariscus latus (Teleostei: Pleuronectiformes). BMC Genom. 2014, 15, 352. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  21. Gong, L.; Shi, W.; Yang, M.; Li, D.H.; Kong, X.Y. Novel gene arrangement in the mitochondrial genome of Bothus myriaster (Pleuronectiformes: Bothidae): Evidence for the dimer-mitogenome and non-random loss model. Mitochondrial DNA 2016, 27, 3089–3092. [Google Scholar] [CrossRef] [PubMed]
  22. Luo, H.R.; Kong, X.Y.; Chen, S.X.; Shi, W. Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the three spot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae). BMC Genom. 2019, 20, 792. [Google Scholar] [CrossRef]
  23. Gong, L.; Lu, X.T.; Luo, H.R.; Zhang, Y.; Shi, W.; Liu, L.Q.; Lü, Z.M.; Liu, B.J.; Jiang, L.H. Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int. J. Biol. Macromol. 2020, 149, 1232–1240. [Google Scholar] [CrossRef]
  24. Zhuang, X.; Cheng, C.H.C. ND6 gene “lost” and found: Evolution of mitochondrial gene rearrangement in Antarctic notothenioids. Mol. Biol. Evol. 2010, 27, 1391–1403. [Google Scholar] [CrossRef] [Green Version]
  25. Lin, C.Y.; Lin, W.W.; Kao, H.W. The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids. Zool. J. Linn. Soc. Lond. 2012, 165, 521–533. [Google Scholar] [CrossRef] [Green Version]
  26. Miya, M.; Nishida, M. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene rearrangements in bony Fishes. Mar. Biotechnol. 1999, 1, 416–426. [Google Scholar] [CrossRef]
  27. Inoue, J.G.; Miya, M.; Tsukamoto, K.; Nishida, M. Evolution of the deep-sea gulper eel mitochondrial genomes: Large-scale gene rearrangements originated within the eels. Mol. Biol. Evol. 2003, 20, 1917–1924. [Google Scholar] [CrossRef] [Green Version]
  28. Obermiller, L.E.; Pfeiler, E. Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences. Mol. Phylogenet. Evol. 2003, 26, 202–214. [Google Scholar] [CrossRef]
  29. Wang, C.H.; Kuo, C.H.; Mok, H.K.; Lee, S.C. Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. Zool. Scr. 2003, 32, 231–241. [Google Scholar] [CrossRef]
  30. Inoue, J.G.; Miya, M.; Tsukamoto, K.; Nishida, M. Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Mol. Phylogenet. Evol. 2004, 32, 274–286. [Google Scholar] [CrossRef] [PubMed]
  31. Chen, J.N.; López, J.A.; Lavoué, S.; Miya, M.; Chen, W.J. Phylogeny of the Elopomorpha (Teleostei): Evidence from six nuclear and mitochondrial markers. Mol. Phylogenet. Evol. 2014, 70, 152–161. [Google Scholar] [CrossRef] [PubMed]
  32. Dornburg, A.; Friedman, M.; Near, T.J. Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei). Mol. Phylogenet. Evol. 2015, 89, 205–218. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Sankoff, D.; Leduc, G.; Antoine, N.; Paquin, B.; Cedergren, L.R. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. USA 1992, 89, 6575–6579. [Google Scholar] [CrossRef] [Green Version]
  34. Rawlings, T.A.; Collins, T.M.; Bieler, R. A major mitochondrial gene rearrangement among closely related species. Mol. Biol. Evol. 2001, 18, 1604–1609. [Google Scholar] [CrossRef] [Green Version]
  35. Mortazavi, F.; Stankiewicz, A.J.; Zhdanova, I.V. Looking through brains with fast passive CLARITY: Zebrafish, rodents, non-human primates and humans. Bio-Protocol 2019, 9, 1–23. [Google Scholar] [CrossRef] [PubMed]
  36. Maniatis, T.; Fritsch, E.F.; Sambrook, J. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: New York, NY, USA, 1982. [Google Scholar]
  37. Bolger, A.M.; Marc, L.; Bjoern, U. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014, 15, 2114–2120. [Google Scholar] [CrossRef] [PubMed]
  38. Jin, J.J.; Yu, W.B.; Yang, J.B.; Song, Y.; Li, D.Z. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020, 21, 241. [Google Scholar] [CrossRef] [PubMed]
  39. Walker, B.J.; Abeel, T.; Shea, T.; Priest, M.; Earl, A.M. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 2014, 9, e112963. [Google Scholar] [CrossRef] [PubMed]
  40. Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar] [CrossRef] [PubMed]
  41. Lowe, T.M.; Chan, P.P. tRNAscan-SE on-line: Search and contextual analysis of transfer RNA genes. Nucleic Acids Res. 2016, 44, 54–57. [Google Scholar] [CrossRef]
  42. Kerpedjiev, P.; Hammer, S.; Hofacker, I.L. Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams. Bioinformatics 2015, 31, 3377–3379. [Google Scholar] [CrossRef] [Green Version]
  43. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406–3415. [Google Scholar] [CrossRef]
  44. Liu, W.Z.; Xie, Y.B.; Ma, J.Y.; Luo, X.T.; Nie, P.; Zuo, Z.X.; Lahrmann, U.; Zhao, Q.; Zheng, Y.Y.; Zhao, Y.; et al. IBS: An illustrator for the presentation and visualization of biological sequences. Bioinformatics 2015, 31, 3359–3361. [Google Scholar] [CrossRef] [Green Version]
  45. Perna, N.T.; Kocher, T.D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 1995, 41, 353–358. [Google Scholar] [CrossRef]
  46. Zhang, Z.; Li, J.; Zhao, X.Q.; Wang, J.; Wong, G.K.; Yu, J. KaKs_Calculator: Calculating Ka and Ks through model selection and model averaging. Genom.Proteom. Bioinf. 2006, 4, 259–263. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Miya, M.; Takeshima, H.; Endo, H.; Ishiguro, N.B.; Inoue, J.G.; Mukai, T.; Satoh, T.P.; Yamaguchi, M.; Kawaguchi, A.; Mabuchi, K. Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 2003, 26, 121–138. [Google Scholar] [CrossRef] [PubMed]
  48. Luo, A.; Zhang, A.B.; Ho, S.Y.; Xu, W.J.; Zhu, C.D. Potential efficacy of mitochondrial genes for animal DNA barcoding: A case study using eutherian mammals. BMC Genom. 2011, 12, 84. [Google Scholar] [CrossRef] [Green Version]
  49. Burland, T.G. DNASTAR’s Lasergene Sequence Analysis Software; Humana Press: Totowa, NJ, USA, 2000; pp. 71–91. [Google Scholar]
  50. Piontkivska, H. Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used. Mol. Phylogenet. Evol. 2004, 31, 865–873. [Google Scholar] [CrossRef] [PubMed]
  51. Xia, X.H. DAMBE 5: A Comprehensive software package for data analysis in molecular biology and evolution. Mol. Biol. Evol. 2013, 30, 1720–1728. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  52. Guindon, S.; Dufayard, J.F.; Lefort, V.; Anisimova, M.; Hordijk, W.; Gascuel, O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59, 307–321. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  53. Satoh, T.P.; Miya, M.; Mabuchi, K.; Nishida, M. Structure and variation of the mitochondrial genome of fishes. BMC Genom. 2016, 17, 719. [Google Scholar] [CrossRef] [Green Version]
  54. Ojala, D.; Montoya, J.; Attardi, G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290, 470–474. [Google Scholar] [CrossRef]
  55. Sharp, P.M.; Tuohy, T.M.; Mosurski, K.R. Codon usage in yeast: Cluster analysis clearly dierentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14, 5125–5143. [Google Scholar] [CrossRef] [Green Version]
  56. Lü, Z.M.; Zhu, K.H.; Jiang, H.; Lu, X.T.; Liu, B.J.; Ye, Y.Y.; Jiang, L.H.; Liu, L.Q.; Gong, L. Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes. Int. J. Biol. Macromol. 2019, 135, 609–618. [Google Scholar] [CrossRef]
  57. Seutin, G.; Lang, B.F.; Mindell, D.P.; Morais, R. Evolution of the WANCY region in amniote mitochondrial DNA. Mol. Biol. Evol. 1994, 11, 329–340. [Google Scholar] [PubMed] [Green Version]
  58. Wong, T.N.; Clayton, D.A. In vitro replication of human mitochondria DNA: Accurate initiation at the origin of light-strand synthesis. Cell 1985, 42, 951–958. [Google Scholar] [CrossRef] [PubMed]
  59. Hixson, J.E.; Wong, T.W.; Clayton, D.A. Both the conserved stem-loop and divergent 5’-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J. Biol Chem. 1986, 261, 2384–2390. [Google Scholar] [CrossRef] [PubMed]
  60. Kryazhimskiy, S.; Plotkin, J.B. The population genetics of dN/dS. PLoS Genet. 2008, 4, e1000304. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  61. Hassanin, A.; Leger, N.; Deutsch, J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. Syst. Biol. 2005, 54, 277–298. [Google Scholar] [CrossRef] [PubMed]
  62. Yu, P.; Zhou, L.; Zhou, X.Y.; Yang, W.T.; Zhang, J.; Zhang, X.J.; Wang, Y.; Gui, J.F. Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes. Int. J. Biol. Macromol. 2019, 129, 339–350. [Google Scholar] [CrossRef]
  63. Chai, H.N.; Du, Y.Z.; Zhai, B.P. Characterization of the complete mitochondrial genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae). Int. J. Biol. Sci. 2012, 8, 561–579. [Google Scholar] [CrossRef] [Green Version]
  64. Sun, S.E.; Cheng, J.; Sun, S.; Sha, Z.L. Complete mitochondrial genomes of two deep-sea pandalid shrimps, Heterocarpus ensifer and Bitias brevis: Insights into the phylogenetic position of Pandalidae (Decapoda:Caridea). J. Oceanol. Limnol. 2020, 38, 816–825. [Google Scholar] [CrossRef]
  65. Gong, L.; Shi, W.; Si, L.Z.; Kong, X.Y. Rearrangement of mitochondrial genome in fishes. Zool. Res. 2013, 34, 666–673. (In Chinese) [Google Scholar]
  66. Inoue, J.G.; Miya, M.; Tsukamoto, K.; Nishida, M. Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): Novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for Anguilliform families. J. Mol. Evol. 2001, 52, 311–320. [Google Scholar] [CrossRef]
  67. San Mauro, D.; Gower, D.J.; Zardoya, R.; Wilkinson, M. A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome. Mol. Biol. Evol. 2006, 23, 227–234. [Google Scholar] [CrossRef] [PubMed]
  68. Zhang, K.; Zhu, K.H.; Liu, Y.F.; Zhang, H.; Gong, L.; Jiang, L.H.; Liu, L.Q.; Lü, Z.M.; Liu, B.J. Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes. Sci. Rep. 2021, 11, 2411. [Google Scholar] [CrossRef] [PubMed]
  69. Lee, W.J.; Conroy, J.; Howell, W.H.; Kocher, T.D. Structure and evolution of teleost mitochondrial control regions. J. Mol. Evol. 1995, 41, 54–66. [Google Scholar] [CrossRef] [PubMed]
  70. Shao, R.; Barker, S.C.; Mitani, H.; Yayoi, A.; Masahito, F. Evolution of duplicate control regions in the mitochondrial genomes of metazoa: A case study with Australasian Ixodes ticks. Mol. Biol. Evol. 2005, 22, 620–629. [Google Scholar] [CrossRef]
  71. Eberhard, J.R.; Wright, T.F.; Bermingham, E. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Mol. Biol. Evol. 2001, 18, 1330–1342. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  72. Abbott, C.L.; Double, M.C.; Trueman, J.W.H.; Robinson, A.; Cockburn, A. An unusual source of apparent mitochondrial heteroplasmy: Duplicate mitochondrial control regions in Thalassarche albatrosses. Mol. Ecol. 2005, 14, 3605–3613. [Google Scholar] [CrossRef]
  73. Morris-Pocock, J.A.; Taylor, S.A.; Birt, T.P.; Friesen, V.L. Concerted evolution of duplicated mitochondrial control regions in three related seabird species. BMC Evol. Biol. 2010, 10, 14. [Google Scholar] [CrossRef] [Green Version]
  74. Zheng, C.F.; Nie, L.W.; Wang, J.; Zhou, H.X.; Hou, H.Z.; Wang, H.; Liu, J.J. Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big headed turtle, Platysternon megacephalum. PLoS ONE 2013, 8, e82854. [Google Scholar] [CrossRef] [Green Version]
  75. Kumazawa, Y.; Ota, H.; Nishida, M.T. Ozawa, The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 1998, 150, 313–329. [Google Scholar] [CrossRef]
  76. Gomes, C.; Rodrigues-Filho, L.F.D.S.; Sodré, D.; Neckel-Oliveira, S.; Gordo, M.; Gallati, U.; Sequeira, F.; Vallinoto, M. Concerted evolution in the mitochondrial control region of the Amazon small-bodied frog Pseudopaludicola canga (Anura, Leiuperidae). Mitochondrial DNA A 2016, 27, 4270–4273. [Google Scholar] [CrossRef]
  77. Lee, J.S.; Miya, M.; Lee, Y.S.; Kim, C.G.; Park, E.H.; Aoki, Y.; Nishida, M. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish. Gene 2001, 280, 1–7. [Google Scholar] [CrossRef] [PubMed]
  78. Li, D.H.; Wei, S.; Munroe, T.A.; Gong, L.; Kong, X.Y. Concerted evolution of duplicate control regions in the mitochondria of species of the flatfish family Bothidae (Teleostei: Pleuronectiformes). PLoS ONE 2015, 10, e0134580. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  79. Yan, Y.B.; Cheng, Q.Q. Study on molecular taxonomy of genus Pampus base on complete mitochondrial genome structure. Mar. Fish. 2022, 44, 31–44. (In Chinese) [Google Scholar]
  80. Boore, J.L. The Duplication/Random Loss Model for Gene Rearrangement Exemplified by Mitochondrial Genomes of Deuterostome Animals, Comparative Genomics; Springer: Dordrecht, The Netherlands, 2000; pp. 133–147. [Google Scholar]
  81. Muse, S.V. Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 1996, 13, 105–114. [Google Scholar] [CrossRef] [PubMed]
  82. Yang, Z.; Bielawski, J.P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 2000, 15, 496–503. [Google Scholar] [CrossRef]
  83. Lazarou, M.; Thorburn, D.R.; Ryan, M.T.; McKenzie, M. Assembly of mitochondrial complex I and defects in disease. BBA Mol. Cell Res. 2009, 1793, 78–88. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  84. Efremov, R.G.; Baradaran, R.; Sazanov, L.A. The architecture of respiratory complex I. Nature 2010, 465, 441–445. [Google Scholar] [CrossRef]
  85. Mark, F.C.; Lucassen, M.; Strobel, A.; Barrera-Oro, E.; Papetti, C. Mitochondrial function in Antarctic nototheniids with ND6 translocation. PLoS ONE 2012, 7, e31860. [Google Scholar] [CrossRef] [Green Version]
  86. Xia, X.H.; Xie, Z.; Salemi, M.; Chen, L.; Wang, Y. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 2003, 26, 1–7. [Google Scholar] [CrossRef]
  87. Liu, D. Study on Comparative Morphology of the Olfactory Organ and Phylogeny of the Snake-Eel Fishes from China. Master’s Thesis, Shanghai Ocean University, Shanghai, China, 2005. (In Chinese). [Google Scholar]
  88. Zhang, Z.L.; Lin, R.R.; Xing, B.P. Suitability analysis of mitochondrial COI gene used as DNA barcode for Ophichthyidae. J. Appl. Oceanogr. 2017, 36, 411–416. (In Chinese) [Google Scholar]
Animals 13 00362 g001 550
Figure 1. Circular mitochondrial genome maps of two Ophichthus fishes. (a) O. evermanni and (b) O. erabo.
Figure 1. Circular mitochondrial genome maps of two Ophichthus fishes. (a) O. evermanni and (b) O. erabo.
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Animals 13 00362 g002 550
Figure 2. Relative synonymous codon usages (RSCUs) in the mitogenomes of (a) O. evermanni and (b) O. erabo. Bars of different colors correspond to the codons with the same color.
Figure 2. Relative synonymous codon usages (RSCUs) in the mitogenomes of (a) O. evermanni and (b) O. erabo. Bars of different colors correspond to the codons with the same color.
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Animals 13 00362 g003 550
Figure 3. Phylogenetic tree of 25 Anguilliformes species constructed by Maximum Likelihood (ML) method based on concatenated sequences of 12 PCGs.
Figure 3. Phylogenetic tree of 25 Anguilliformes species constructed by Maximum Likelihood (ML) method based on concatenated sequences of 12 PCGs.
Animals 13 00362 g003
Table
Table 1. Features of the mitochondrial genomes of two Ophichthus species.
Table 1. Features of the mitochondrial genomes of two Ophichthus species.
GeneDirectionStrandStart to EndSize/bpIntergenic Length/bpStart CodonStop CodonAnticodonSimilarity/%
O. evermanni/O. eraboO. evermanni/O. eraboO. evermanni/O. eraboO. evermanni/O. eraboO. evermanni/O. eraboO. evermanni/O. erabo
tRNA-Phe (F)+H1–68/1–6968/69 GAA/GAA85.5
12S rRNA+H69–1027/70–1036959/967 86.5
tRNA-Val (V)+H1028–1098/1037–110771/71 TAC/TAC94.4
16S rRNA+H1099–2801/1108–28121703/1705 84.6
tRNA-LeuUUA (L1)+H2802–2877/2813–288876/76 TAA/TAA90.8
ND1+H2878–3846/2889–3857969/969 ATG/ATGTAA/TAG 79.3
tRNA-Ile (I)+H3850–3922/3861–393373/733/3 GAT/GAT89.0
tRNA-Gln (Q)-L3922–3992/3933–400371/71−1/−1 TTG/TTG90.1
tRNA-Met (M)+H3992–4060/4003–407169/69−1/−1 CAT/CAT85.5
ND2+H4061–5117/4072–51281057/1057 ATG/ATGT--/T-- 76.7
tRNA-Trp (W)+H5118–5186/5129–520069/72 TCA/TCA86.1
tRNA-Ala (A)-L5188–5256/5202–527069/691/1 TGC/TGC85.5
tRNA-Asn (N)-L5258–5330/5272–534473/731/1 GTT/GTT94.5
OL+H5335–5368/5351–537634/264/6 61.8
tRNA-Cys (C)-L5375–5439/5394–545965/666/17 GCA/GCA86.4
tRNA-Tyr (Y)-L5440–5510/5460–553071/71 GTA/GTA85.9
CO I+H5512–7152/5532–71721641/16411/1GTG/GTGTAG/TAA 84.5
tRNA-SerUCA (S1)-L7169–7239/7191–726171/7116/18 TGA/TGA95.8
tRNA-Asp (D)+H7245–7312/7267–733468/685/5 GTC/GTC88.2
CO II+H7319–8009/7341–8031691/6916/6ATG/ATGT--/T-- 87.0
tRNA-Lys (K)+H8010–8084/8032–810675/75 TTT/TTT90.7
ATP8+H8086–8253/8108–8275168/1681/1ATG/ATGTAA/TAA 80.5
ATP6+H8244–8926/8266–8949683/684−10/−10ATG/ATGTA-/TAA 78.9
CO III+H8927–9712/8949–9734786/7860/−1ATG/ATGTAA/TAA 85.2
tRNA-Gly (G)+H9712–9783/9734–980572/72−1/−1 TCC/TCC86.1
ND3+H9784–10132/9806–10154349/349 ATG/GTGT--/T-- 81.1
tRNA-Arg (R)+H10133–10202/10155–1022470/70 TCG/TCG97.1
ND4L+H10203–10499/10225–10521297/297 ATG/ATGTAA/TAA 85.5
ND4+H10493–11873/10515–118951381/1381−7/−7ATG/ATGT--/T-- 80.7
tRNA-His (H)+H11874–11942/11896–1196469/69 GTG/GTG95.7
tRNA-SerAGC (S2)+H11943–12012/11965–1203470/70 GCT/GCT67.5
tRNA-LeuCUA (L2)+H12013–12085/12035–1210773/73 TAG/TAG95.9
ND5+H12086–13921/12108–139431836/1836 ATG/ATGTAA/TAA 79.3
Cyt b+H13936–15077/13959–150981142/114014/15ATG/ATGAA-/TAA 76.5
tRNA-Thr (T)+H15095–15166/15116–1518772/7217/17 TGT/TGT91.7
CR1+H15167–16132/15188–16224966/1037 67.1
ND6-L16133–16651/16225–16743519/519 CTA/CTACAT/CAT 77.3
tRNA-Glu (E)-L16652–16720/16744–1681269/69 TTC/TTC85.5
tRNA-Pro (P)-L16724–16794/16820–1689071/713/7 TGG/TGG85.9
CR2+H16795–17759/16891–17856965/966 72.4
Table
Table 2. Composition and skewness of mitogenomes in two Ophichthus species.
Table 2. Composition and skewness of mitogenomes in two Ophichthus species.
O. evermanni/O. erabo
A%T%G%C%A + T%AT-SkewGC-Skew
tRNAs30.93/31.6024.63/24.8120.13/19.6824.31/23.9155.56/56.410.113/0.120−0.094/−0.097
rRNAs35.73/36.8320.14/19.7219.68/19.5724.46/23.8855.86/56.550.279/0.303−0.108/−0.099
CRs31.75/36.4531.85/27.3615.69/15.0820.71/21.1263.59/63.80−0.002/0.142−0.138/−0.167
ND127.04/26.2126.42/26.7315.79/17.5430.75/29.5153.46/52.940.012/−0.010−0.321/−0.254
ND234.56/34.3424.27/24.6012.65/13.2528.52/27.8158.83/58.940.175/0.165−0.385/−0.355
COI27.54/27.4828.34/28.4018.22/18.4625.90/25.6655.88/55.88−0.014/−0.016−0.174/−0.163
COII29.23/31.1128.80/27.0616.79/15.4825.18/26.3458.03/58.180.007/0.070−0.200/−0.260
ATP835.12/36.3125.60/27.3811.31/8.3327.98/27.9860.71/63.690.157/0.140−0.424/−0.541
ATP629.28/28.9530.60/27.6312.15/12.5727.96/30.8559.88/56.58−0.022/0.023−0.394/−0.421
COIII27.35/27.3527.48/26.5917.56/18.4527.61/27.6154.83/53.94−0.002/0.014−0.222/−0.199
ND328.37/24.3630.37/32.9513.47/16.0527.79/26.6558.74/57.31−0.034/−0.150−0.347/−0.248
ND4L28.62/27.6127.27/27.9513.80/13.8030.30/30.6455.89/55.560.024/−0.006−0.374/−0.379
ND430.27/30.9927.52/26.7214.12/13.6128.10/28.6757.78/57.710.048/0.074−0.331/−0.356
ND531.81/33.3326.96/26.2513.56/13.3427.67/27.0758.77/59.590.083/0.119−0.342/−0.340
Cyt b39.50/28.0714.26/28.6814.07/16.4032.18/26.8453.76/56.750.469/−0.011−0.392/−0.241
ND629.42/40.6630.56/12.9114.80/13.4925.22/32.9559.98/53.56−0.019/0.518−0.260/−0.419
PCGs30.23/30.3427.17/26.5614.89/15.2127.71/27.8957.40/56.900.053/0.066−0.301/−0.294
1st codon site29.61/30.3428.43/24.7114.89/18.0727.08/26.8858.04/55.050.020/0.102−0.290/−0.196
2nd codon site30.44/26.8428.46/31.7213.07/14.5128.02/26.9458.90/58.560.034/−0.083−0.364/−0.299
3rd codon site30.64/33.9024.62/23.2116.70/13.0128.04/29.8755.26/57.110.109/0.187−0.253/−0.393
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MDPI and ACS Style

Yang, T.; Liu, Y.; Ning, Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals 2023, 13, 362. https://doi.org/10.3390/ani13030362

AMA Style

Yang T, Liu Y, Ning Z. Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals. 2023; 13(3):362. https://doi.org/10.3390/ani13030362

Chicago/Turabian Style

Yang, Tianyan, Yuping Liu, and Zijun Ning. 2023. "Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae" Animals 13, no. 3: 362. https://doi.org/10.3390/ani13030362

APA Style

Yang, T., Liu, Y., & Ning, Z. (2023). Comparative Mitogenomic Analysis of Two Snake Eels Reveals Irregular Gene Rearrangement and Phylogenetic Implications of Ophichthidae. Animals, 13(3), 362. https://doi.org/10.3390/ani13030362

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