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Article

The Complete Mitochondrial Genome of Liobagrus huaiheensis (Teleostei: Siluriformes: Amblycipitidae): Characterization, Phylogenetic Placement, and Insights into Genetic Diversity

by
Chaoqun Su
1,2,
Chenxi Tan
1,2,
Liangjie Zhao
1,2,
Jiahui Liu
1,2,
Xusheng Guo
1,2,
Gaoyou Yao
1,2,
Weizhao Zhang
1,2 and
Tiezhu Yang
1,2,*
1
School of Fisheries, Xinyang Agriculture and Forestry University, Xinyang 464000, China
2
Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang 464000, China
*
Author to whom correspondence should be addressed.
Genes 2025, 16(8), 977; https://doi.org/10.3390/genes16080977
Submission received: 22 July 2025 / Revised: 17 August 2025 / Accepted: 18 August 2025 / Published: 19 August 2025
(This article belongs to the Section Animal Genetics and Genomics)
Browse Figures
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Abstract

Background/Objectives: Liobagrus huaiheensis, an endemic fish in the Huaihe River basin, is a newly described species with limited molecular genetic research, hindering understanding of its evolutionary status, population structure, and genetic diversity. This study aimed to characterize its complete mitochondrial genome, clarify its phylogenetic position within Liobagrus, and assess its population genetic diversity. Methods: We obtained the complete mitogenome of L. huaiheensis (sourced from the Zhugan River) through sequencing, followed by detailed annotation of this genomic sequence. We analyzed its genomic structure, nucleotide composition, codon usage, and base asymmetry. Selection pressure on 13 protein-coding genes (PCGs) was evaluated using Ka/Ks ratios. Phylogenetic trees were generated by means of Bayesian inference (BI) and maximum likelihood (ML), using a dataset composed of 13 protein-coding genes (PCGs) from 37 species. Population genetic diversity was assessed using the cox1 gene. Results: The mitogenome is a 16,512 bp circular molecule encoding 37 genes and one control region, with a conserved structure typical of Liobagrus. It has high A + T content (55.74%) with A-preference and C-enrichment. All PCGs undergo purifying selection (Ka/Ks < 1). Phylogenetic analyses revealed L. huaiheensis is closest to L. obesus (100% support), with Liobagrus divided into three clades. The cox1 gene analysis showed low diversity (Hd = 0.656, π = 0.00171) and neutral evolution. Conclusions: This study fills the mitogenome data gap for L. huaiheensis, clarifies its evolutionary characteristics and phylogenetic position, and provides a basis for conservation genetics of Huaihe endemic fishes and molecular evolution research on Amblycipitidae.

1. Introduction

The genus Liobagrus (Amblycipitidae) comprises freshwater catfishes widely distributed in freshwater ecosystems across central and southern China, Japan, and the Korean Peninsula, with their taxonomic status and evolutionary history being focal points of ichthyological research [1]. L. huaiheensis, a newly described species in 2021, was initially discovered in the Shiguan River (a tributary of the Huaihe River), and subsequent surveys have expanded its known distribution to the main stream of the Huaihe River and other tributaries (e.g., Zhugan River, Shi River). It represents the only endemic fish among 73 recorded species in the Huaihe River basin [2]. Distinguished by unique morphological traits (e.g., the posterior margin of the pectoral-fin spine is equipped with two to three serrations, while the anal fin contains 15 to 17 rays in total) and its biogeographic position, this species serves as a key taxon linking Liobagrus populations in China and the Korean Peninsula [3,4,5].
Mitochondrial genomes (mitogenomes) are valuable molecular markers in phylogenetic reconstruction, population genetics, and species delimitation due to their conserved structure, moderate evolutionary rate, and maternal inheritance [6,7]. Despite progress in the taxonomic study of Liobagrus (e.g., morphological classification and distribution mapping), molecular genetic research on L. huaiheensis remains limited. The lack of complete mitogenome data for this species hinders insights into its evolutionary status, population structure, and genetic diversity. Additionally, phylogenetic relationships within Liobagrus remain unresolved, highlighting the need for mitogenome-based analyses to clarify evolutionary affinities [8].
This research represents the first attempt to determine the complete mitogenome of L. huaiheensis, with a subsequent detailed characterization of its genomic features. We systematically analyzed its genomic structure, nucleotide composition, codon usage patterns of protein-coding genes (PCGs), features of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), and assessed base asymmetry via AT/GC skew. Furthermore, we conducted selection pressure analyses on 13 PCGs, reconstructed the phylogeny of Liobagrus species, and evaluated the genetic diversity of the Huaihe River population. The objectives were to (1) fill the gap in molecular data for L. huaiheensis and provide genetic markers for species identification; (2) elucidate the evolutionary characteristics and adaptive selection mechanisms of its mitogenome; and (3) clarify its phylogenetic position within Liobagrus to enhance understanding of the genus’ biogeographic evolution. This research will lay a foundation for the conservation genetics of endemic fishes in the Huaihe River and molecular evolution studies of Amblycipitidae.

2. Materials and Methods

2.1. Sample Collection and Processing

Adult specimens of L. huaiheensis (Figure 1) in this study were collected using cage traps in August 2024 from the Zhugan River, a tributary of the Huaihe River in Luoshan County, Xinyang City, Henan Province (geographic coordinates: 114°37′4″ E, 32°4′21″ N). Samples were initially identified morphologically on-site and immediately preserved in 100% ethanol. Upon returning to the laboratory, specimens were further confirmed as L. huaiheensis through morphological examination and stored at −80 °C until DNA extraction. All experimental procedures were conducted in strict compliance with international guidelines governing the care and handling of laboratory animals. Some individuals were prepared as vouchers and deposited in the Herbarium of Xinyang Agriculture and Forestry University under the accession number XYAFU-Mo-240811630.

2.2. DNA Extraction, Library Construction, and Sequencing

The Tissue DNA Extraction Kit (DP304, Tiangen Biochemical Technology (Beijing) Co., Ltd., Beijing, China) was employed to extract total genomic DNA from the muscle tissue of L. huaiheensis. Subsequently, the purity and concentration of the obtained DNA were determined with a NanoDrop 2000 instrument (Thermo Fisher Scientific, Waltham, MA, USA). DNA libraries were prepared with the TIANSeq Fast DNA Library Prep Kit (Illumina) (NG102-01; Tiangen Biochemical Technology (Beijing) Co., Ltd., Beijing, China). The concentrations of the libraries were measured with a Qubit 4 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), and the fragment sizes of the libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) was then utilized for library sequencing, yielding 150 bp paired-end reads.

2.3. Assembly and Annotation of the Mitochondrial Genome

Quality control and filtering of raw sequencing data were performed using Fastp v0.36 [9]. Second-generation sequencing data were assembled with SPAdes v3.15 [10], and gaps in the resulting contigs were filled using GapFiller v 2.1.2 [11]. Base errors and small indels in the assembly were corrected with Pilon v 1.24 [12]. Coding sequence (CDS) boundaries were determined by combining tblastn and genewise v 2.2.0 [13] against a closely related reference genome. Transfer RNA (tRNA) sequences were predicted using MitoFinder v 1.4.2 [14] and tRNAscan-SE 2.0 search server [15], and ribosomal RNA (rRNA) elements were identified via CMsearch [16] against the Rfam database [17]. Additionally, the mitochondrial genome sequence was automatically annotated using the MITOS2 de novo annotation tool on the Galaxy Web Server [18].

2.4. Analysis of Mitochondrial Genome Sequence Characteristics

MEGA v 11.0 [19] software was employed to analyze both the base composition and codon usage patterns of the L. huaiheensis mitochondrial genome, while the relative synonymous codon usage (RSCU) for each protein-coding gene (PCG) was analyzed using CodonW v 1.4.2 [20]. The A + T skew value was derived using (A% − T%)/(A% + T%), whereas the G + C skew value was calculated with (G% − C%)/(G% + C%) [21]. Substitution rates, encompassing both nonsynonymous (Ka) and synonymous (Ks) rates, among closely related species were determined using KaKs Calculator v3.0 [22].

2.5. Phylogenetic Analysis Methods

A total of 37 complete mitochondrial sequences of 37 species from 15 genera of 5 families were downloaded from NCBI data, including 13 species belonging to the genus Liobagrus (Table 1). Nucleotide sequences of the 13 protein-coding genes (PCGs) from all species were aligned and format-converted using AliView v 1.2.6 [23]. Information and accession numbers of the species used in this study are listed in Table 1. Kryptopterus vitreolus and Kryptopterus bicirrhis from the family Siluridae were selected as outgroups for phylogenetic tree construction [24]. PartitionFinder v 2.1.1 was used to identify the most suitable evolutionary models for the analysis [25]. After organizing and concatenating the 13 PCGs’ nucleotide sequences in a specific order, we analyzed phylogenetic relationships using the ML and BI approaches. IQ-TREE v 2.3.6 [26] was used to build the ML tree with 1000 bootstrap replicates. BI analysis was conducted in MrBayes v 3.2.7a [27], with four MCMC chains running for 200,000 generations (sampled every 1000 generations) and a 25% burn-in applied to the initial dataset. The resulting phylogenetic trees were generated and visualized using FigTree v 1.4.4 and Adobe Illustrator 2020.

2.6. Population-Level Genetic Diversity Analysis

This research involved the collection and storage of DNA samples from 30 adult L. huaiheensis specimens. For the assessment of population genetic diversity, the mitochondrial cytochrome b (cyt b) gene of L. huaiheensis was selected as the molecular marker [44]. Specific primers for the cox1 gene were used for amplification: Lh-cox1-F (5′-GACTTGAAAAACCACCGTTG-3′) and Lh-cox1-R (5′-CTCCGATCTCCGGATTACAAGAC-3′), targeting a 1150 bp fragment [45,46]. PCR reactions were performed using TaKaRa Taq™ HS Perfect Mix (Cat. No. R300A; Takara Biomedical Technology (Beijing) Co., Ltd., Shiga, Japan) following the manufacturer’s instructions. PCR amplicons were subjected to bidirectional sequencing services provided by Sangon Biotech (Shanghai, China), and sequences were assembled using DNAstar v 7.1.0 software [47]. Population genetic diversity was analyzed using DnaSP v 6.12.03 software [48].

3. Results and Discussion

3.1. Overall Characteristics of the Mitochondrial Genome of L. huaiheensis

Following de novo assembly and subsequent annotation of high-throughput sequencing data (with 100% assembly coverage), the mitochondrial genome of L. huaiheensis was characterized as a double-stranded circular molecule. This genome has a total length of 16,512 bp and harbors 37 annotated genes, along with one control region (Table 2). The 37 encoded genes consist of 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. Most PCGs are located on the heavy strand (H-strand), with only the nad6 gene on the light strand (L-strand). Among the 22 tRNA genes, 14 are on the H-strand (tRNAPhe, tRNAVal, tRNALeu(tta), tRNAIle, tRNAMet, tRNATrp, tRNAAsp, tRNALys, tRNAGly, tRNAArg, tRNAHis, tRNASer(gct), tRNALeu(tag), tRNAThr), and the remaining 8 are on the L-strand (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer(tga), tRNAGlu, tRNAPro) (Figure 2). These structural features are not only highly similar to those of other species in the genus Liobagrus but also consistent with the mitochondrial genome structures of Amphilius and even Cyprininae species, reflecting the stability of mitochondrial genomes in terms of structure and gene order [49,50].
Genes 16 00977 g002
Figure 2. Circos plot of the mitochondrial genome of L. huaiheensis. In the outermost gene elements, the inner circle shows genes transcribed in the forward direction, and the outer circle shows genes transcribed in the reverse direction; light green bars in the middle ring indicate the sequencing depth of the corresponding regions.
Figure 2. Circos plot of the mitochondrial genome of L. huaiheensis. In the outermost gene elements, the inner circle shows genes transcribed in the forward direction, and the outer circle shows genes transcribed in the reverse direction; light green bars in the middle ring indicate the sequencing depth of the corresponding regions.
Genes 16 00977 g002

3.2. Nucleotide Composition and Base Bias Analysis

The mitochondrial genome of L. huaiheensis exhibits an overall base composition characterized by A (30.87%) > T (24.87%) > C (28.85%) > G (15.41%). The A + T content accounts for 55.74%, significantly higher than the 44.26% G + C content. Additionally, the positive AT skew (0.10764) and negative GC skew (−0.30366) reflect a typical pattern of A-base preference and relative C-base enrichment (Table 3). Integrating comparative data of 13 Liobagrus species’ mitochondrial genomes (Table 4), the whole-genome A + T content (55.74%) of L. huaiheensis is moderately high within the genus (e.g., 56.19% in L. stuarti, 57.07% in L. anguillicauda). However, its GC skew (−0.3037) has a significantly higher absolute value than most species (e.g., −0.2797 in L. marginatus, −0.2796 in L. mediadiposalis), indicating stronger C-base enrichment. The PCGs’ A + T content (54.88%) aligns with the genus-wide average (53.44–56.73%), yet the more negative GC skew (−0.3264) suggests unique base composition in protein-coding regions. The rRNA genes’ A + T content (55.53%) shows minor differences from other genus species (54.08–56.74%), but the high AT skew (0.2401) reflects enhanced A-base preference in the rRNA region [51].
From the functional element perspective, most PCGs in L. huaiheensis show significant A-preference and C-enrichment. The atp8 gene has a 37.58% A content and the highest genome-wide AT skew (0.26532), indicating strong A-preference. The light-strand nad6 gene, due to strand localization, has a 40.74% T content (significantly higher than 14.04% A) and a negative AT skew (−0.48740), presenting a unique base distribution. At codon sites, the third site has the highest A (39.22%) and lowest G (7.41%) content, an extreme skew pattern related to mitochondrial energy metabolism functional requirements, potentially reflecting adaptive codon usage optimization for efficient transcription and translation [52,53,54]. tRNA genes have a 56.09% A + T content and a positive GC skew (0.03667, unique genome-wide), suggesting G-base preference, likely related to tRNA secondary structure stability [55]. The D-loop has the highest genome-wide A + T content (66.07%), with near-zero AT skew and negative GC skew, indicating high and balanced A/T content, associated with mitochondrial replication–transcription regulation [52]. The mitochondrial genome of L. huaiheensis presents core characteristics of high A + T content, A-base preference, and C-base enrichment. Compared to other Liobagrus species, it shows uniqueness in GC skew pattern and PCG base composition, reflecting functional adaptation in energy metabolism and genetic information transfer, and providing molecular evidence for resolving Liobagrus phylogenetic relationships.

3.3. Protein-Coding Genes and Codon Usage Characteristics

Among the 13 PCGs present in L. huaiheensis’ mitochondrial genome, ATG serves as the start codon for all, while cox1 is an exception, initiating with GTG—a feature consistent with most fish species [56]. In contrast, stop codon usage is more diverse: nad1, nad2, cox1, and nad6 employ the complete stop codon TAG; atp8, atp6, nad4l, and nad5 use TAA as the complete stop codon; cox3 has the incomplete stop codon TA-; and the remaining genes (cox2, nad3, nad4, and cyt b) terminate with the incomplete stop codon T- (Table 2). For genes with incomplete stop codons, mitochondria can dynamically form complete termination signals by adding adenines to the 3′ end of mRNA via polyadenylase, ensuring translational accuracy [57].
Statistics on codon counts and relative synonymous codon usage (RSCU) (Figure 3, Table 5, Figure 4) revealed that the preferred codons for most amino acids are NNA- or NNC-type, except for Tyr and Ile, which favor NNT-type codons—this differs significantly from the pattern observed in Aloa lactinea [58]. Additionally, the three codons with the highest RSCU values are CUA (RSCU = 2.68, encoding Leu), CGA (RSCU = 2.50, encoding Arg), and CCC (RSCU = 2.07, encoding Pro). In terms of amino acid usage frequency, Leu is the most abundant, followed by Ala and Thr; notably, the number of amino acids encoded by the heavy strand is significantly higher than that encoded by the light strand.

3.4. Characteristics of Ribosomal RNA and Transfer RNA Genes

In the mitochondrial genome of L. huaiheensis, the two ribosomal RNA (rRNA) genes located on the heavy strand, crucial for ribosome assembly and protein synthesis, are, respectively, transcribed into 12S rRNA, with a length of 956 bp, and 16S rRNA, which is 1666 bp in length. These rRNA genes exhibit a combined AT content of 55.54% and a pronounced A-base preference (AT skew = 0.24019). The encoded tRNA genes average approximately 71 bp in length, with tRNACys being the shortest (67 bp) and tRNALeu(tta) the longest (75 bp) (Table 2 and Table 3). Collectively, the tRNA genes span 1560 bp, with an AT content of 56.09%—significantly lower than that reported for Aloa lactinea [58]. Notably, both the AT skew and GC skew of the tRNA genes in L. huaiheensis are positive, a characteristic distinct from the findings of Yang et al. in their study of Arius maculatus [59]. All tRNA genes can fold into the typical cloverleaf secondary structure (Figure 5). Specifically, there are eight pairs of unpaired bases in the amino acid acceptor arm, seven pairs of incorrectly paired bases in the TΨC stem and loop, and two pairs of unpaired bases in the DHU arm. The amino acid acceptor arm of all tRNAs is 6 bp in length, with the TΨC stem and loop ranging from 3 to 4 bp, the DHU arm from 2 to 3 bp, and the anticodon arm from 3 to 4 bp. Notably, the DHU arm of tRNACys exhibits an indistinct loop formation, and no obvious variable loop structure is observed in any of the tRNA secondary structures.

3.5. Selection Pressure Analysis

To quantitatively assess the evolutionary significance of variable protein-coding sequences across divergent species, nonsynonymous (Ka) and synonymous (Ks) substitution rates are powerful metrics. The number of substitutions per nonsynonymous site is denoted by Ka, while that per synonymous site is denoted by Ks, and their ratio (Ka/Ks) classifies sequence evolution into three scenarios: negative (purifying) selection (Ka/Ks < 1), positive (adaptive) selection (Ka/Ks > 1), and neutral evolution (Ka/Ks = 1) [60,61,62]. The Ka, Ks, and Ka/Ks values of the 13 protein-coding genes in L. huaiheensis are presented in Figure 6. Genes with relatively high Ka values include atp8 (0.0370), atp6 (0.0337), and nad5 (0.0384), whereas nad4 exhibits the highest Ks value (0.3800). For Ka/Ks ratios, the atp8 gene shows a significantly higher value (0.2476) compared to other genes, with the cyt b gene having the lowest (0.0293). Since all Ka/Ks ratios are less than 1, this indicates that all protein-coding genes in L. huaiheensis have undergone purifying selection, which helps maintain the stability of mitochondrial genes.

3.6. Results of Phylogenetic Analysis

The optimal evolutionary models selected via PartitionFinder partitioning were as follows: the GTR + I + G model for nad1, nad2, cox1, cox2, atp6, cox3, nad3, nad4, nad5, and cyt b; and the GTR + G model for atp8, nad4l, and nad6. On the basis of these results, phylogenetic trees were constructed via BI and ML methods, using the nucleotide sequences of 13 PCGs derived from the mitochondrial genomes of 37 species (covering 14 genera and five families) (Figure 7). The trees showed that L. huaiheensis is most closely related to L. obesus, with a 100% posterior probability for this clade in both analyses. Based on the inferred tree topology, the currently recognized Liobagrus species can be clustered into three distinct clades, each with a posterior probability of 100%: (1) L. huaiheensis, L. obesus, and L. andersoni; (2) L. anguillicauda, L. styani, L. marginatoides, L. nigricauda, L. kingi, and L. marginatus; and (3) L. reinii, L. geumgangensis, L. hyeongsanensis, L. mediadiposalis, and L. somjinensis. The results of this study are consistent with those of Philjae Kim, who used unpartitioned mitochondrial genome data, and those of Chen Chongguang, who constructed trees based on partial cyt b sequences [24,63].

3.7. Population Genetic Diversity Analysis

Genetic diversity underpins a species’ survival, evolution, and adaptability to environmental alterations: typically, greater genetic diversity is associated with heightened adaptability and evolutionary potential. The cox1 gene sequence, which exhibits high genetic polymorphism, has been widely utilized in studies on the genetic diversity of various fish species [64]. In our current study, we retrieved most of the cox1 gene sequence from L. huaiheensis. After alignment and refinement, it reached a total length of 1150 bp, with only four distinct haplotypes identified. For the population of L. huaiheensis from the Huai River, the haplotype diversity (Hd) was 0.656 and the nucleotide diversity (π) was 0.00171. Both low values (Hd < 0.5 and π < 0.005, as shown in Table 6) suggest that this population may be at risk of genetic deterioration. Moreover, the results of Tajima’s D and Fu’s Fs tests indicated that this gene likely follows a neutral evolution model within the population, with no evident signals of strong impacts—such as natural selection or population expansion—on its genetic structure detected [65].

4. Conclusions

This study determined the complete mitochondrial genome of L. huaiheensis, a 16,512 bp circular molecule encoding 37 genes, with a conserved structure consistent with other Liobagrus species. Its mitogenome exhibits high A + T content (55.74%) with A-preference and C-enrichment, and unique base skew patterns in PCGs and tRNAs linked to functional adaptation. All 13 PCGs undergo purifying selection (Ka/Ks < 1), ensuring mitochondrial stability. Phylogenetic analyses (BI/ML) show L. huaiheensis is closest to L. obesus (100% support), with Liobagrus divided into three clades, consistent with prior studies. Population analysis of the cox1 gene reveals low diversity (Hd = 0.656, π = 0.00171), indicating potential genetic deterioration, with neutral evolution supported by Tajima’s D and Fu’s Fs.
These results not only address existing data gaps regarding L. huaiheensis (a Huaihe endemic species), clarify its phylogenetic position within the genus, and provide foundational support for its conservation, but also lay a solid basis for subsequent research and applications. Specifically, they can be further leveraged to investigate the species’ geographical dispersal history, develop its DNA barcode for accurate species identification, explore the evolutionary mechanisms underlying its adaptation to specific environments, and screen potential genetic markers to facilitate marker-assisted breeding in aquaculture.

Author Contributions

Conceptualization, C.S. and T.Y.; methodology, C.S., X.G. and G.Y.; software, C.S. and T.Y.; validation, C.S., T.Y. and L.Z.; formal analysis, C.S., C.T. and L.Z.; investigation, C.S. and J.L.; resources, W.Z., J.L. and X.G.; data curation, W.Z., T.Y. and C.T.; writing—original draft preparation, C.S. and T.Y.; writing—review and editing, C.S. and T.Y.; visualization, C.S. and G.Y.; supervision, T.Y.; project administration, C.S. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the Youth Fund Project of Xinyang Agriculture and Forestry University (Grant No. QN2021020); the Natural Science Foundation of Henan Province (Grant Nos. 232300421273, 242300420175, 252102110075); the Key Scientific Research Projects of Colleges and Universities in Henan Province (Grant Nos. 23B240003, 24B240001); and the Science and Technology Research Project of Henan Province (Grant No. 252102110075).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data supporting the findings of this study are openly available in the National Center for Biotechnology Information (NCBI) database, accessible at https://www.ncbi.nlm.nih.gov (accessed on 22 July 2025) under the accession number PV953861.

Acknowledgments

We appreciate the anonymous reviewers for providing valuable comments on this study.

Conflicts of Interest

The authors declare no conflicts of interest.

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Genes 16 00977 g001
Figure 1. Detailed photograph of L. huaiheensis (photographed by Weizhao Zhang).
Figure 1. Detailed photograph of L. huaiheensis (photographed by Weizhao Zhang).
Genes 16 00977 g001
Genes 16 00977 g003
Figure 3. Relative synonymous codon usage (RSCU) of 13 PCGs in the mitogenome of L. huaiheensis.
Figure 3. Relative synonymous codon usage (RSCU) of 13 PCGs in the mitogenome of L. huaiheensis.
Genes 16 00977 g003
Genes 16 00977 g004
Figure 4. Mitochondrial genome codon usage of L. huaiheensis. Amino acids are displayed on the X-axis, and the Y-axis presents both the number of amino acids and gene direction. The H strand appears in orange, with the L strand in gray.
Figure 4. Mitochondrial genome codon usage of L. huaiheensis. Amino acids are displayed on the X-axis, and the Y-axis presents both the number of amino acids and gene direction. The H strand appears in orange, with the L strand in gray.
Genes 16 00977 g004
Genes 16 00977 g005
Figure 5. The secondary structure predictions of tRNA of L. huaiheensis.
Figure 5. The secondary structure predictions of tRNA of L. huaiheensis.
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Genes 16 00977 g006
Figure 6. The Ka, Ks, and Ks/Ks values of 13 PCGs in L. huaiheensis.
Figure 6. The Ka, Ks, and Ks/Ks values of 13 PCGs in L. huaiheensis.
Genes 16 00977 g006
Genes 16 00977 g007
Figure 7. Phylogenetic analyses of L. huaiheensis based on 13 PCG nucleotide sequences from its mitogenome. Posterior probabilities from the BI and ML methods are shown on branch labels, and different families are distinguished by unique colors.
Figure 7. Phylogenetic analyses of L. huaiheensis based on 13 PCG nucleotide sequences from its mitogenome. Posterior probabilities from the BI and ML methods are shown on branch labels, and different families are distinguished by unique colors.
Genes 16 00977 g007
Table 1. Detailed information of mitogenome sequences analyzed in this study, including NCBI accession numbers.
Table 1. Detailed information of mitogenome sequences analyzed in this study, including NCBI accession numbers.
FamilyGenusSpeciesGenbank Accession NoResource
AmblycipitidaeLiobagrusLiobagrus andersoniKX767082.1[28]
Liobagrus anguillicaudaJQ026256.1Unpublished
Liobagrus geumgangensisNC_088753.1[29]
Liobagrus hyeongsanensisMZ066608.1[24]
Liobagrus kingiKC193779.1[30]
Liobagrus marginatoidesKC473938.1[31]
Liobagrus marginatusKC757128.1[32]
Liobagrus mediadiposalisKR075136.1[33]
Liobagrus nigricaudaKC316116.1[34]
Liobagrus obesusJQ714035.1[35]
Liobagrus somjinensisMN756661.1[36]
Liobagrus styaniKX096605.1[37]
Liobagrus reiniiAP012015.1Unpublished
Liobagrus huaiheensisPV953861 This study
XiurenbagrusXiurenbagrus dorsalisMN308285.1Unpublished
SisoridaeBagariusBagarius yarrelliJQ026260.1[38]
GagataGagata dolichonemaJQ026250.1Unpublished
CreteuchiloglanisCreteuchiloglanis kamengensisMN396886.1Unpublished
Creteuchiloglanis gongshanensisKP872697.1Unpublished
Creteuchiloglanis macropterusKP872682.1Unpublished
EuchiloglanisEuchiloglanis davidiMK181572.1[39]
Euchiloglanis kishinouyeiJQ026252.1Unpublished
GlyptosternonGlyptosternon maculatumJQ026251.1Unpublished
PseudexostomaPseudexostoma yunnanensisJQ026258.1Unpublished
PangasiidaePangasianodonPangasianodon gigasAY762971.1[40]
PangasiusPangasius nasutusOQ078746.1[41]
Pangasius sanitwongseiMN809630.1[42]
Pangasius conchophilusOQ078745.1[41]
Pangasius pangasiusKC572135.1Unpublished
Pangasius larnaudiiAP012018.1Unpublished
SiluridaeKryptopterusKryptopterus vitreolusKY710750.1Unpublished
Kryptopterus bicirrhisKY569440.1Unpublished
IctaluridaeNoturusNoturus tayloriKP013089.1Unpublished
AmeiurusAmeiurus catusMG570433.1Unpublished
Ameiurus natalisMG570406.1Unpublished
IctalurusIctalurus furcatusKM576102.1Unpublished
Ictalurus priceiKJ496298.1[43]
Table 2. Annotation of the mitochondrial genome genes in L. huaiheensis.
Table 2. Annotation of the mitochondrial genome genes in L. huaiheensis.
GeneLocationStrandGene Length (bp)Intergenic NucleotidesOverlapping NucleotidesCodons
FromToStartStop
tRNAPhe169H69-   
12S rRNA701025H956    
tRNAVal10261097H72    
16S rRNA10982763H1666    
tRNALeu(tta)27642838H75    
nad128393810H9725 ATGTAG
tRNAIle38163887H72 1  
tRNAGln38873957L71 1  
tRNAMet39574025H69    
nad240265072H1047 2ATGTAG
tRNATrp50715139H692   
tRNAAla51425210L691   
tRNAAsn52125284L7329   
tRNACys53145380L67    
tRNATyr53815451L711   
cox154537003H1551  GTGTAG
tRNASer(tga)70047074L714   
tRNAAsp70797150H7213   
cox271647854H691  ATGT-
tRNALys78557928H741   
atp879308097H168 10ATGTAA
atp680888771H684 1ATGTAA
cox387719555H785 1ATGTA-
tRNAGly95559627H73    
nad396289976H349  ATGT-
tRNAArg997710,046H70    
nad4l10,04710,343H297 7ATGTAA
nad410,33711,717H1381  ATGT-
tRNAHis11,71811,787H70    
tRNASer(gct)11,78811,856H692   
tRNALeu(tag)11,85911,931H73    
nad511,93213,755H1824 4ATGTAA
nad613,75214,267L516  ATGTAG
tRNAGlu14,26814,336L692   
cyt b14,33915,476H1138  ATGT-
tRNAThr15,47715,548H72 2  
tRNAPro15,54715,616L70    
CR15,61716,512H896    
Table 3. Base composition characteristics of the mitogenome in L. huaiheensis.
Table 3. Base composition characteristics of the mitogenome in L. huaiheensis.
Gene/RegionSize (bp)Base Composition (%) AT SkewGC Skew
ATCGA + TG + C
Genome16,51230.8724.8728.8515.4155.7444.260.10764−0.30366
PCGs11,37328.5626.3329.9215.1954.8845.120.04069−0.32645
nad196927.9725.3932.9213.7353.3646.650.04835−0.41136
nad2104432.9522.5132.2812.2655.4644.540.18824−0.44948
cox1154826.1628.1028.2317.5154.2645.74−0.03575−0.23437
cox269030.8726.0927.9715.0756.9643.040.08392−0.29972
atp816537.5821.8229.0911.5259.4040.610.26532−0.43265
atp668132.0124.9629.6613.3656.9743.020.12375−0.37889
cox378325.6725.8031.0317.5051.4748.53−0.00253−0.27880
nad334826.1527.3032.4714.0853.4546.55−0.02152−0.39506
nad4l29423.4724.4935.0317.0147.9652.04−0.02127−0.34627
nad4138030.3624.7831.3813.4855.1444.860.10120−0.39902
nad5182130.7525.6531.3012.3056.4043.600.09043−0.43578
nad651314.0440.749.9435.2854.7845.22−0.487400.56037
cyt b113728.4126.8231.1313.6355.2344.760.02879−0.39097
First site379127.6420.1827.2024.9847.8252.180.15600−0.04255
Secondary site379118.8140.6027.4113.1959.4140.60−0.36677−0.35025
Tertiary site379139.2218.2035.167.4157.4242.570.36607−0.65187
tRNA gene156028.6527.4421.1522.7656.0943.910.021570.03667
rRNA gene260234.4421.1024.4420.0255.5444.460.24019−0.09942
D-loop zone89633.3732.7020.6513.2866.0733.930.01014−0.21721
Table 4. Comparative analysis of the complete mitochondrial genomes of 13 Liobagrus species.
Table 4. Comparative analysis of the complete mitochondrial genomes of 13 Liobagrus species.
SpeciesWhole GenomePCGsrRNA
SizeA + TGC SkewAT SkewSizeA + TGC SkewAT SkewSizeA + TGC SkewAT Skew
(bp)(%)(bp)(%)(bp)(%)
Liobagrus andersoni16,51455.42−0.29040.096211,37354.63−0.30850.0246262055.11−0.09860.2396
Liobagrus anguillicauda16,53657.07−0.28130.083611,38256.73−0.30030.0150262255.95−0.08920.2243
Liobagrus geumgangensis16,52255.93−0.28730.089411,37755.10−0.30190.0190262455.34−0.10580.2383
Liobagrus hyeongsanensis16,52955.41−0.28060.087711,37654.22−0.29450.0156262656.02−0.10480.2373
Liobagrus kingi16,48354.10−0.28220.096711,37653.02−0.29130.0211260954.08−0.11350.2417
Liobagrus marginatoides16,49855.67−0.28700.095511,37354.95−0.30200.0186260255.00−0.09650.2383
Liobagrus marginatus16,49754.53−0.27970.094411,37653.47−0.29420.0212257054.09−0.10000.2388
Liobagrus mediadiposalis16,53455.17−0.27960.090711,37653.89−0.29010.0183262655.98−0.10380.2367
Liobagrus nigricauda16,50955.93−0.28520.092911,37155.29−0.30250.0189261855.42−0.09680.2378
Liobagrus obesus16,50654.42−0.27510.106911,37653.46−0.29200.0276261955.25−0.09730.2440
Liobagrus somjinensis16,52655.58−0.28240.088311,37654.34−0.29800.0194262456.10−0.09720.2323
Liobagrus styani16,51556.19−0.28860.092811,37355.61−0.30640.0212262155.67−0.09980.2378
Liobagrus huaiheensis16,51255.74−0.30370.107611,37354.88−0.32640.0407260255.53−0.09940.2401
Table 5. Codon number and RSCU of 13 PCGs in the mitogenome of L. huaiheensis.
Table 5. Codon number and RSCU of 13 PCGs in the mitogenome of L. huaiheensis.
Amino AcidCodonCountRSCUAmino AcidCodonCountRSCU
PheUUU900.82TyrUAU621.07
Phe UUC 1301.18TyrUAC540.93
LeuUUA920.86stop codonUAA41.00
LeuUUG160.15stop codonUAG41.00
LeuCUU810.76HisCAU160.30
LeuCUC1081.01HisCAC921.70
LeuCUA2872.68GlnCAA911.80
LeuCUG580.54GlnCAG100.20
IleAUU1501.05AsnAAU460.69
IleAUC1350.95AsnAAC871.31
MetAUA1331.49LysAAA721.76
MetAUG460.51LysAAG100.24
ValGUU531.00AspGAU200.57
ValGUC430.81AspGAC501.43
ValGUA911.71GluGAA861.67
ValGUG260.49GluGAG170.33
SerUCU290.81CysUGU50.37
SerUCC701.96CysUGC221.63
SerUCA641.79TrpUGA1071.75
SerUCG90.25TrpUGG150.25
ProCCU250.46ArgCGU20.11
ProCCC1122.07ArgCGC170.94
ProCCA731.35ArgCGA452.50
ProCCG60.11ArgCGG80.44
ThrACU440.54SerAGU90.25
ThrACC1291.58SerAGC330.93
ThrACA1491.82stop codonAGA00
ThrACG50.06stop codonAGG00
AlaGCU340.42GlyGGU240.41
AlaGCC1672.06GlyGGC841.42
AlaGCA1091.35GlyGGA881.49
AlaGCG140.17GlyGGG410.69
Table 6. cox1 gene genetic diversity parameters in L. huaiheensis from the Huaihe River basin population.
Table 6. cox1 gene genetic diversity parameters in L. huaiheensis from the Huaihe River basin population.
PopulationGeneNumber of HaplotypesHaplotype (Gene) DiversityAverage Number of Nucleotide DifferenceNucleotide DiversityTajima’s DFu’s Fs
Huai Rivercox140.6561.8880.001710.021951.899
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Su, C.; Tan, C.; Zhao, L.; Liu, J.; Guo, X.; Yao, G.; Zhang, W.; Yang, T. The Complete Mitochondrial Genome of Liobagrus huaiheensis (Teleostei: Siluriformes: Amblycipitidae): Characterization, Phylogenetic Placement, and Insights into Genetic Diversity. Genes 2025, 16, 977. https://doi.org/10.3390/genes16080977

AMA Style

Su C, Tan C, Zhao L, Liu J, Guo X, Yao G, Zhang W, Yang T. The Complete Mitochondrial Genome of Liobagrus huaiheensis (Teleostei: Siluriformes: Amblycipitidae): Characterization, Phylogenetic Placement, and Insights into Genetic Diversity. Genes. 2025; 16(8):977. https://doi.org/10.3390/genes16080977

Chicago/Turabian Style

Su, Chaoqun, Chenxi Tan, Liangjie Zhao, Jiahui Liu, Xusheng Guo, Gaoyou Yao, Weizhao Zhang, and Tiezhu Yang. 2025. "The Complete Mitochondrial Genome of Liobagrus huaiheensis (Teleostei: Siluriformes: Amblycipitidae): Characterization, Phylogenetic Placement, and Insights into Genetic Diversity" Genes 16, no. 8: 977. https://doi.org/10.3390/genes16080977

APA Style

Su, C., Tan, C., Zhao, L., Liu, J., Guo, X., Yao, G., Zhang, W., & Yang, T. (2025). The Complete Mitochondrial Genome of Liobagrus huaiheensis (Teleostei: Siluriformes: Amblycipitidae): Characterization, Phylogenetic Placement, and Insights into Genetic Diversity. Genes, 16(8), 977. https://doi.org/10.3390/genes16080977

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