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Article

The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis

by
Tangjun Xu
1,
Wenwen Zhang
2,
Yao Li
3,
Jiachen Wang
1,
Yawen Bai
1 and
Hongyi Liu
1,*
1
Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
2
Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
3
College of Ecology and Environment, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
*
Author to whom correspondence should be addressed.
Diversity 2024, 16(6), 346; https://doi.org/10.3390/d16060346
Submission received: 8 May 2024 / Revised: 3 June 2024 / Accepted: 6 June 2024 / Published: 14 June 2024
(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)
Browse Figures
Versions Notes

Abstract

:
Channidae (snakehead fish) is a family of medium-to-large freshwater carnivorous fish and contain the genus, Channa. Here, the complete mitogenomes of two Channa fish were determined and comparatively analyzed with the mitogenomes of 16 other Channidae fish species. The two newly sequenced complete mitogenomes were circular DNA molecules with sizes of 16,953 bp (Channa burmanica; OP954106) and 16,897 bp (Channa aurantimaculata; OQ134162). The mitogenomes were composed of 37 genes and one D-loop region. Positive AT skews and negative GC skews were found in the mitogenomes. Most protein-coding genes (PCGs) started with the conventional start codon, ATG; however, the sequence of the stop codon was variable. There was no obvious difference in relative synonymous codon usage among the two mitogenomes, and the two species shared a similar number of codon usage of mitogenomic PCGs, which was also similar to the mean values for the other 15 species of Channa. All Ka/Ks values were <1; cox1 had the lowest value, and atp8 had the highest. All of the tRNAs were typical clover structures, except trnS1. Phylogenetic analysis showed that C. burmanica and C. aurantimaculata shared a close relationship and that they were also closely related to C. gachua. These findings enrich the gene database of Channidae species, clarify the mitochondrial genome structure of the two species, and provide basic data for invasive biological surveillance in the future.

1. Introduction

Channidae, a family of Anabantiformes, is a family of medium-to-large carnivorous freshwater fish [1], which are also known as snakehead fish. They are characterized by peculiar morphological features, such as elongated cylindrical bodies, long and entirely soft-rayed dorsal and anal fins, a large mouth with well-developed teeth on both upper and lower jaws, and an accessory air-breathing apparatus known as the suprabranchial organ [2]. They have flattened heads and possess large scales on their heads, and their eyes are located in the dorsoventral position on the anterior part of the head. They are highly adaptable and can breathe with the help of the suprabranchial organ in the event of a lack of oxygen or being out of water [3]. At present, according to the information published in the Integrated Taxonomic Information System (https://itis.gov/), Channidae is divided into the genera Channa and Parachanna. Channa contains 53 species that are distributed across Asia [4,5,6,7,8,9,10], while Parachanna contains only 3 species that are distributed across Africa [11]. Previously, the classification of snakeheads was mainly based on morphological characteristics. However, because individuals vary significantly in color patterns during development, the different sizes and colors have resulted in juveniles and adults of the same species being described as distinct species [11]. The naming and classification of the Channidae are therefore confusing. There are over 100 nominal species of Channidae [12], but only 56 have been admitted. The vast majority of the remaining names are considered to be synonyms of the old names [13].
With the increasing globalization of trade, the threat of invasive alien species continues to increase, which can impact biodiversity and ecosystem functions. The wide-ranging diet, level of parental care, and fierce character give snakehead fish a high probability of becoming an invasive species [14]. Some snakehead fish are popular as food or ornamental fish in their native habitats. However, when snakehead fish were introduced to areas outside their natural range, they became highly invasive [11]. For example, Channa argus, an important commercial fish used as food in China [15], known for its fast growth, high meat content with few bone spurs, and tolerance to water pollution and diseases [15], has established several populations in the eastern United States, threatening local ecosystems [16]. In China, in addition to the native snakehead fish species, some exotic species have also been introduced as ornamental fish. A study in Shanghai has shown that non-native snakehead fish have invaded local waters [17]. Despite the attention snakeheads have received, there are substantial difficulties for accurate species identification. Moreover, they vary in their ecological requirements and potential invasive ability [18]. In order to prevent possible species invasion, and to better understand this kind of species, snakehead fish accurate identification and classification are very necessary.
It is difficult to identify snakehead fish by morphology because of the great difference in color patterns during ontogeny and the large number of species. Molecular identification can help solve this dilemma. The mitochondrion is an elementary eukaryotic organelle that exists in most eukaryotic cells. Mitochondria possess mitochondrial DNA (mtDNA), which has a closed circular double-stranded structure and self-replicates semi-conservatively [19,20]. In general, the mitogenome of Osteichthyes is a circular, double-stranded molecule, 16 to 23 kb in size, typically containing a standard set of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and one displacement loop (D-loop) region [21]. Owing to their maternal inheritance, high copy number, high mutation rate, relatively rapid evolutionary rate, and lack of genetic recombination, mitogenomes have been valuable and extremely popular markers in molecular ecology, evolutionary biology, population genetics, animal phylogenetic studies, and species identification [15]. Although some mitochondrial genes (such as cox1, cytb, and rrnL) have been widely used for phylogenetic analysis and species identification [13,16], partial mitochondrial sequences provide only limited information, missing information on gene rearrangement, genetic code changes, replication, and transcriptional regulation patterns. The complete mitochondrial genome sequence can provide higher resolution and sensitivity for the study of evolutionary relationships. In recent years, some molecular phylogenetic studies have solved the relationships between some of the species within the snakehead fish family. Ruber et al. divided the Asian genus Channa into eight distinct species groups (Argus, Asiatica, Gachua, Lucius, Marulius, Micropeltes, Punctata, and Striata groups) [12]. Wang et al. determined the phylogenetic relationships of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) and found three new pairs of sisters (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartia + C. gachua) [22]. However, this work still needs to be improved.
In this study, we determined the complete mitogenomes of two Channa species (C. burmanica and C. aurantimaculata), which are common and popular ornamental fish. We analyzed their mitochondrial genome, including the genome size, nucleotide composition, codon usage, and selective pressure on 13 protein-coding genes (PCGs) and compared them with the mitogenomes of 16 other Channidae species. The purpose of this study was to provide new data for the characterization of mitochondrial genomes in the Channidae family, to further refine the phylogenetic relationships between the snakehead fish groups, and to provide reliable molecular data for species invasion monitoring in the future.

2. Materials and Methods

2.1. Sample Collection and Identification

Specimens of C. burmanica and C. aurantimaculata were collected from the Qiqiaoweng pet market in Jiangsu Province, China. The specimens were identified based on the morphological characteristics described by FishBase (https://www.fishbase.de/). Only one individual per species was used for sequencing. Fresh tissues were dissected from fins and stored at −20 °C. Genomic DNA was extracted using a DNAiso reagent (Takara, Beijing, China). All remaining samples were stored in a cryogenic freezer at −80 °C at the Zoology Laboratory of Nanjing Forestry University.

2.2. Sequence Analysis and Assembly and Mitochondrial Genome Annotation

The library of mitogenome DNA was sequenced using the Illumina platform (Personal, Shanghai, China). The mitogenomes of C. stewartii (accession: OP402840) and C. bleheri (accession: OP186040) were used as templates for the two Channa species. Sequence contigs were assembled and trimmed using the medium sensitivity/fast option in the Geneious Prime 2021 software (https://www.geneious.com). Consensus sequences were constructed in Geneious Prime using a 99% base call threshold. The complete mitogenomes of C. burmanica and C. aurantimaculata were obtained.
MITOS WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) was used for sequence annotation [23], and all parts of the sequence were confirmed using BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 1 December 2022)). The two species were confirmed by BLASTn searches of the cox1 gene against GenBank, with top hits showing 100% identity in C. burmanica (GenBank Accession: MF496705) and C. aurantimaculata (GenBank Accession: EU342193), respectively. The tRNA and rRNA secondary structures were described by ViennaRNA Web Services (http://rna.tbi.univie.ac.at/ (accessed on 1 December 2022)) [24]. Circular gene maps were generated using the CGView Server (https://paulstothard.github.io/cgview/ (accessed on 1 December 2022)). MEGA11 was used to determine the base composition, the relative synonymous codon usage (RSCU) of each codon, and the nonsynonymous (Ka) and synonymous substitutions (Ks) [25]. Nucleotide compositional skewness was calculated according to the following formulas: AT skew = (A − T)/(A + T); GC skew = (G − C)/(G + C) [26].

2.3. Phylogenetic Analyses

The phylogenetic relationships were constructed using 17 Channa mitogenomes with a Parachanna mitogenome as an outgroup. Details of the species used in this study are listed in Table 1. Bayesian inference (BI) and maximum likelihood (ML) methods were used for phylogenetic analyses with the nucleotide sequences of the 13 PCGs. MAFFT v.7.313 was used to align all PCGs, and the best substitution model was identified by ModelFinder. Phylogenetic analysis was performed using PhyloSuite v.1.2.2 [27]. The BI method was used to construct a tree using the software MrBayes v.3.2.6 based on the model GTR + I + G4 (2 parallel runs, 1000 sample frequency, 10 million generations), and the initial 25% of the sampled data were discarded as burn-in [28]. The ML tree was constructed using IQ-TREE based on the model GTR + F + R4 for 100,000 ultrafast bootstraps [29]. The phylogenetic trees were visualized and edited using FigTree v.1.4.3 (http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 2 December 2022)).

3. Results and Discussion

3.1. Mitogenome Organization and Structure

The complete mitogenomes of C. burmanica and C. aurantimaculata were found to be 16,953 bp and 16,897 bp in size, respectively. Of these, the complete mitogenome of C. burmanica has the longest length, and C. aurantimaculata has the second longest. Both mitogenomes contained 37 typical mitochondrial genes (13 PCGs, 22 tRNAs, and two rRNAs) and one control region. Two rRNAs, 12 PCGs, and 14 tRNAs were found to be encoded on the major strand (J-chain), whereas the remaining genes (8 tRNAs and 1 PCG) were located on the minor strand (N-chain) (Figure 1). The gene arrangement and size of the two Channidae mitogenomes were typical of the Channidae and are highly conserved [22].
Both genomes had nine gene overlaps. The size of each overlap in both genomes was the same, except for the overlap between trnI and trnQ, which was three in C. burmanica and one in C. aurantimaculata. All overlap lengths ranged from 1 to 10 bp, and the longest overlap occurred between atp8 and atp6 (Table 2). Unusually, no overlap between tRNA and protein gene sequences was found in a previous study of five species of snakehead fish [22]. In this study, the complete mitogenomes of both C. burmanica and C. aurantimaculata have overlaps between tRNA and protein gene sequences. The overlaps were between ND2 and trnW and between cox3 and trnG. Both genomes had twelve intergenic spacers. The intergenic regions occur at 12 gene junctions, with the longest intergenic spacer between trnN and trnC (38 bp). This situation was similar to the genomes of other species of Channa [22].
However, C. burmanica and C. aurantimaculata had the longest mitogenomes in known Channa. Their lengths of PCGs, tRNAs and rRNAs were similar to other species of Channa. The difference in total length arises from the non-coding region. Bilaterian animals possess a large non-coding region referred to as the “control region”, or “D-loop” [30]. Most of the size variation among animal mitogenomes is due to differences in the length of non-coding regions [30]. The A + T content of C. burmanica and C. aurantimaculata was 53.67% and 55.68%, respectively. The A + T content in the Channidae mitogenomes ranged from 51.43% to 55.75%, as shown in the mitochondrial genomes of other fish [31]. The A + T content of PCGs, tRNAs, and rRNAs showed similar features to the complete mitogenome; however, the A + T content of the D-loop (60.00–70.03%) was higher than that of the other parts of the mitogenome. The AT skew was positive, while the GC skew was negative (Table 3). All Channidae mitogenomes have similar characteristics in these aspects.

3.2. PCGs and Codon Usage

The total lengths of the 13 PCGs of C. burmanica and C. aurantimaculata were 11,422 bp and 11,420 bp, respectively, which were similar to the other species in Channidae (Table 3). The lengths of individual PCGs ranged from 168 bp of atp8 to 1839 bp of nad5. All PCGs were located on the J-chain, except nad6, which was located on the N-chain. Most PCGs used the conventional start codon, ATG, except for cox1 and nad3, which started with GTG and ATA, respectively. Eight PCGs ended with the conventional stop codon, TAA, while nad6 ended with TAG and the other four PCGs (cox2, nad3, nad4, and cytb) had incomplete stop codons (T). According to previous studies, incomplete stop codons are commonly observed across fish mitogenomes and may be related to post-transcriptional modification [32,33].
There was no significant difference in the RSCU between the two species (Figure 2). The most frequently used codons are CGA and UGA. In contrast, the codons ACG and GCG are rarely used. The most commonly used codons are composed of A or T, and the rarely used ones are composed of C or G. This indicates that the RSCU value is positively correlated with the AT bias of the PCGs.
We found that the two species shared a similar number of codon usage of mitogenomic PCGs, which was also similar to the mean values for the other 15 species of Channa (Figure 3). Codons encoding Ile, Ala, and Leu1 were the most frequent, whereas those encoding Met, Cys, and Ser1 were the rarest. Among these, Leu1 showed the highest codon usage, which was presumed to play an important role in maintaining protein activity [34].
All Ka/Ks values were <1, indicating that all the PCGs evolved under purifying selection [35] (Figure 4). The value of atp8 was the highest of the 13 PCGs, which showed greater amino acid diversity since it was under the least selection pressure [36]. The cox1 gene had the lowest average Ka/Ks value, indicating that it was the most slowly evolving gene. Researchers believe that drastic selection pressure applied to cox1 has led to this result [36]. These results were consistent with recent findings and may be a general rule for the evolutionary rate of mitochondrial protein genes in Channa [22].
Although cox1 may be the most conserved mitochondrial protein gene of Channa, some studies have shown that sequence divergences at cox1 regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria [37]. In fact, cox1 is the most commonly used molecular marker for species identification and discovery [38]. Because atp8 has the fastest evolutionary rate, atp8 may be used as a suitable molecular marker for population genetic diversity [39].

3.3. Transfer RNAs, Ribosomal RNAs, and Displacement Loop Region

Similar to previous reports of other Channidae mitogenomes, the size and order of the arrangement of the transfer RNAs in C. burmanica and C. aurantimaculata mitogenomes were conserved [22]. The total length of the tRNAs in both mitogenomes was 1550 bp. The tRNA gene size ranged from 65 bp (trnC) to 75 bp (trnK) (Table 2). Some base pairs are not the classic bonds of A-U and C-G in the tRNA secondary structure. All tRNAs were of the standard cloverleaf structure, except trnS1. Only trnS1 could not fold into the typical cloverleaf structure; trnS1 showed a loss of the pseudo uracil (TΨC) arm, which was replaced with a simple loop (Figure 5).
The total length of the rRNAs in mitogenomes of C. burmanica was 2604 bp, and in mitogenomes of C. aurantimaculata, it was 2601 bp. The AT% was 52.69% and 53.94%. The rrnS was located between trnF and trnV, and the rrnL was located between trnV and trnL2. They do not overlap with the genes before and after. Previous research has suggested that, compared with rrnL, rrnS is more highly conserved in Channidae mitogenomes [22]. This situation was also observed in the current study. The length of rrnS in both mitogenomes was 948 bp, whereas rrnL was 1656 bp in length in C. burmanica and 1653 bp in C. aurantimaculata. In addition, the rrna secondary structures of the two species predicted by the software also showed that the secondary structures of rrnL of the two species were similar. However, the secondary structures of rrnS of the two species had great difference (Figure 6).
The D-loop region of all species of Channidae currently reported is located between trnP and trnF in the mitogenomes, and we found this to also be true for C. burmanica and C. aurantimaculata. The size of D-loop was 1314 bp in C. burmanica and 1258 bp in C. aurantimaculata. The A + T content of the D-loop was 65.14% in C. burmanica and 70.03% in C. aurantimaculata, much higher than that of the whole genome, PCGs, rRNAs, or tRNAs. This region showed great variability between the species of Channidae. The D-loop region is the most rapidly evolving part of the mitogenome [40].

3.4. Phylogenetic Relationships within the Genus Channa

As shown in Figure 7, the trees generated by BI and ML had identical topology and nodal support. The two species in this study showed a close relationship. C. burmanica first clustered into one branch with C. stewartii and then with C. aurantimaculata. The two species also showed a close relationship with C. andrao and C. bleheri. The existence of distinct phylogenetic groups has been proposed by the putative C. gachua species assemblage described by Britz [41], which contains C. orientalis, C. gachua, C. bleheri, C. burmanica, C. barca, C. aurantimaculata, and C. stewartii. The current study partly supported this point. However, according to the phylogenetic analysis, C. burmanica and C. aurantimaculata show a close relationship. The adult sizes of these two species differ greatly. C. burmanica is one of several genus members that lacks pelvic fins, while C. aurantimaculata has pelvic fin. C. asiatica, which also lacks pelvic fins, was slightly farther in the phylogenetic context from C. burmanica. Thus, some studies suggest that the lack of a pelvic fin is hypothesized to occur independently in the evolution of Channidae [12,42]. In the future, more research is needed to clarify the mechanisms behind these phenomena.

4. Conclusions

In this study, two mitochondrial genomes from Channa were sequenced and added to the existing data; we sequenced and analyzed the mitogenomes of C. burmanica and C. aurantimaculata. The two mitogenomes are conserved in genomic structure, base composition, and codon usage. All tRNAs were of the standard cloverleaf structure, except trnS1. Cox1 is the most conserved mitochondrial protein gene of Channa, and atp8 has the fastest evolutionary rate. We performed a phylogenetic analysis based on the sequences of thirteen PCGs genes. Our result showed that C. burmanica and C. aurantimaculata are closely related and supports the sister relationship between C. burmanica and C. stewartii. Our results provide a valuable resource for further phylogenetic and evolutionary analyses of the Channa. However, they have many morphological differences. In the future, the complex relationships among Channa fish should be elucidated based on comprehensive evidence including molecular characteristics, morphological characteristics, and geographical distribution.

Author Contributions

Conceptualization, H.L.; methodology, T.X.; software, T.X. and W.Z.; validation, H.L. and Y.L.; formal analysis, H.L. and Y.L.; resources, J.W. and Y.B.; writing—original draft preparation, T.X.; writing—review and editing, H.L.; visualization, Y.L.; project administration, H.L.; funding acquisition, W.Z. and J.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Biodiversity Investigation, Observation, and Assessment Program (2019–2023) of the Ministry of Ecology and Environment of China, grant number 2110404, and the Innovation and Entrepreneurship Training Program for College Students of China, grant number 202210298070Z.

Institutional Review Board Statement

This research has been conducted with the Experimental Animal Welfare and Ethics Committee, Nanjing Forestry University (No. 2022001).

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of the NCBI at https://www.ncbi.nlm.nih.gov (accessed on 5 December 2022) under accession no. OP954106 and OQ134162.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Gene map of the two sequenced mitogenomes of Channa species. Genes encoded by the J-chain are shown outside the circle, and those encoded by the N-chain are shown inside the circle. Different gene types are shown as filled boxes in different colors.
Figure 1. Gene map of the two sequenced mitogenomes of Channa species. Genes encoded by the J-chain are shown outside the circle, and those encoded by the N-chain are shown inside the circle. Different gene types are shown as filled boxes in different colors.
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Figure 2. The codon distribution and RSCU of the mitogenomes of the two Channa species.
Figure 2. The codon distribution and RSCU of the mitogenomes of the two Channa species.
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Figure 3. The number of amino acids coded in mitogenomes of the Channa species. (A) Mean value of amino acid number of 15 Channa mitogenomes. (B) Amino acid number of C. aurantimaculata mitogenome. (C) Amino acid number of C. burmanica mitogenome.
Figure 3. The number of amino acids coded in mitogenomes of the Channa species. (A) Mean value of amino acid number of 15 Channa mitogenomes. (B) Amino acid number of C. aurantimaculata mitogenome. (C) Amino acid number of C. burmanica mitogenome.
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Figure 4. Ka/Ks values for the 13 PCGs of 17 Channa mitogenomes.
Figure 4. Ka/Ks values for the 13 PCGs of 17 Channa mitogenomes.
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Figure 5. Secondary structures of the 22 transfer RNA of two Channa species.
Figure 5. Secondary structures of the 22 transfer RNA of two Channa species.
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Figure 6. Secondary structures of the rRNA of two Channa species.
Figure 6. Secondary structures of the rRNA of two Channa species.
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Figure 7. Phylogenetic tree based on 13 PCGs of 18 Channidae species. Numbers at nodes represent the posterior probability and bootstrap values for the BI and ML analyses, respectively. Underlines indicate sequences obtained in this study.
Figure 7. Phylogenetic tree based on 13 PCGs of 18 Channidae species. Numbers at nodes represent the posterior probability and bootstrap values for the BI and ML analyses, respectively. Underlines indicate sequences obtained in this study.
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Table 1. List of the mitogenomes analyzed in this study.
Table 1. List of the mitogenomes analyzed in this study.
FamilySpeciesAccession No.Length (bp)
ChannaChanna diplogrammaMG986721.116,571
Channa luciusMF804538.116,570
Channa maruliusKF420268.116,569
Channa micropeltesKX129904.116,567
Channa gachuaMK371068.116,561
Channa argusMG751766.116,558
Channa maculataKC823606.116,559
Channa asiaticaKJ930190.116,550
Channa striataKX177965.116,509
Channa punctataMK007075.116,409
Channa ornatipinnisOP271694.116,866
Channa pulchraOP271693.116,895
Channa stewartiiOP402840.116,765
Channa andraoOP402839.116,729
Channa bleheriOP186040.116,714
Channa burmanicaOP954106.116,953
Channa aurantimaculataOQ134162.116,897
ParachannaParachanna insignisAP006042.116,607
Table 2. General features of the mitogenomes. Channa burmanica is in front, Channa aurantimaculata is behind.
Table 2. General features of the mitogenomes. Channa burmanica is in front, Channa aurantimaculata is behind.
GeneLocationIntergenic NucleotidesSizeCodonStand
FromToStartStop
tRNA-Phe1/169/690/069/69 H
12S rRNA70/701017/10170/0948/948 H
tRNA-Val1018/10181089/10890/072/72 H
16S rRNA1113/11132768/276523/231656/1653 H
tRNA-Leu22769/27662842/28390/074/74 H
ND12843/28403817/38140/0975/975ATG/ATGTAA/TAAH
tRNA-Ile3822/38193891/38884/470/70 H
tRNA-Gln3889/38883959/3958−3/−171/71 L
tRNA-Met3959/39584028/4027−1/−170/70 H
ND24029/40285075/50740/01047/1047ATG/ATGTAA/TAAH
tRNA-Trp5075/50745144/5143−1/−170/70 H
tRNA-Ala5146/51455214/52131/169/69 L
tRNA-Asn5216/52155288/52871/173/73 L
tRNA-Cys5327/53265391/539038/3865/65 L
tRNA-Tyr5392/53915461/54600/070/70 L
COI5463/54627004/70031/11542/1542GTG/GTGTAA/TAAH
tRNA-Ser27013/70127083/70828/871/71 L
tRNA-Asp7086/70867157/71572/272/72 H
COII7165/71657855/78557/7691/691ATG/ATGT/TH
tRNA-Lys7856/78567930/79300/075/75 H
ATP87932/79328099/80991/1168/168ATG/ATGTAA/TAAH
ATP68090/80908773/8773−10/−10684/684ATG/ATGTAA/TAAH
COIII8773/87739558/9558−1/−1786/786ATG/ATGTAA/TAAH
tRNA-Gly9558/95589626/9626−1/−169/69 H
ND39627/96279975/99750/0349/349ATA/ATAT/TH
tRNA-Arg9976/997610,044/10,0440/069/69 H
ND4L10,045/10,04510,341/10,3410/0297/297ATG/ATGTAA/TAAH
ND410,335/10,33511,715/11,715−7/−71381/1381ATG/ATGT/TH
tRNA-His11,716/11,71611,784/11,7840/069/69 H
tRNA-Ser111,785/11,78511,852/11,8520/068/68 H
tRNA-Leu111,855/11,85511,927/11,9272/273/73 H
ND511,928/11,92813,766/13,7660/01839/1839ATG/ATGTAA/TAAH
ND613,763/13,76314,284/14,284−4/−4522/522ATG/ATGTAG/TAGL
tRNA-Glu14,285/14,28514,353/14,3530/069/69 L
Cyt b14,358/14,35815,498/15,4984/41141/1141ATG/ATGT/TH
tRNA-Thr15,499/15,49915,570/15,5700/072/72 H
tRNA-Pro15,570/15,57015,639/15,639−1/−170/70 L
D-loop15,640/15,64016,953/16,8970/01314/1258
Table 3. Base compositions of the complete genomes, PCGs, rRNAs, tRNAs, and D-loop regions of the 18 Channidae mitogenomes.
Table 3. Base compositions of the complete genomes, PCGs, rRNAs, tRNAs, and D-loop regions of the 18 Channidae mitogenomes.
SpeciesWhole MitogenomeAT SkewGC SkewPCGstRNAsrRNAsD-Loop
Size (bp)AT (%)Size (bp)AT (%)Size (bp)AT (%)Size (bp)AT (%)Size (bp)AT (%)
C. burmanica16,95353.670.030−0.31211,42252.50155055.16260452.69131465.14
C. aurantimaculata16,89755.680.024−0.31511,42054.40155056.97260153.94125870.03
C. diplogramma16,57153.530.102−0.33711,43052.35155754.66262754.0591865.14
C. lucius16,57054.000.084−0.33511,42952.70156055.13263354.5890967.55
C. marulius16,56952.750.077−0.32511,43051.56155655.21263154.2491560.00
C. micropeltes16,56753.340.102−0.33311,43052.32155855.13260253.6592163.52
C. gachua16,56155.160.028−0.30611,42954.72154855.36262954.4390863.66
C. argus16,55851.430.059−0.30111,42649.91155654.37263253.1290761.30
C. maculata16,55951.860.041−0.36011,42651.30155855.39263154.1290863.66
C. asiatica16,55055.750.055−0.31011,42655.30155556.01263654.7489663.73
C. striata16,50954.980.055−0.29611,42254.31155455.47262555.0187063.56
C. punctata16,40953.670.026−0.30811,42852.63154954.74262354.0277466.41
C. ornatipinnis16,86653.710.035−0.33611,41252.83154755.07262453.24124462.14
C. pulchra16,89553.900.045−0.35011,41152.97155054.39263053.54126363.66
C. stewartii16,76553.300.017−0.29711,42051.78155055.81262553.14112666.43
C. andrao16,72956.550.022−0.30711,42056.26155056.52262855.06108663.90
C. bleheri16,71453.080.012−0.30211,42051.74154955.78262053.59108163.09
P. insignis16,60752.880.058−0.32511,42651.98155254.96266053.0892361.00
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Xu, T.; Zhang, W.; Li, Y.; Wang, J.; Bai, Y.; Liu, H. The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis. Diversity 2024, 16, 346. https://doi.org/10.3390/d16060346

AMA Style

Xu T, Zhang W, Li Y, Wang J, Bai Y, Liu H. The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis. Diversity. 2024; 16(6):346. https://doi.org/10.3390/d16060346

Chicago/Turabian Style

Xu, Tangjun, Wenwen Zhang, Yao Li, Jiachen Wang, Yawen Bai, and Hongyi Liu. 2024. "The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis" Diversity 16, no. 6: 346. https://doi.org/10.3390/d16060346

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