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

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.

Keywords: Liobagrus huaiheensis; genetic diversity; mitochondrial genome; phylogenetic analysis.

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 1

Detailed photograph of L. huaiheensis (photographed by Weizhao Zhang).

Figure 3

Relative synonymous codon usage (RSCU) of 13 PCGs in the mitogenome of L. huaiheensis.

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 5

The secondary structure predictions of tRNA of L. huaiheensis.

Figure 6

The Ka, Ks, and Ks/Ks values of 13 PCGs in L. huaiheensis.

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.