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. 2024 Jul 8;15(7):893.
doi: 10.3390/genes15070893.

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

Li-Min Yang  1 , Jing-Feng Xue  2 , Xiao-Man Zhao  2 , Ke Ding  3   4 , Zhao-Wen Liu  1   2 , Zhou-Si-Yu Wang  1 , Jian-Bing Chen  1 , You-Kun Huang  2
Affiliations

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

Li-Min Yang et al. Genes (Basel). .

Abstract

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms.

Keywords: divergence time; evolutionary pressure; mitogenome; phylogenetic construction.

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Conflict of interest statement

The authors declare that no conflicts of interest.

Figures

Figure 1
Figure 1
Gene map of A. nadeshnyi mitogenome.
Figure 2
Figure 2
The relative synonymous codon usage (RSCU) in the mitogenome of A. nadeshnyi (A). (The y-axis represents the usage frequency of the corresponding amino acid codons in 13 PCGs. Different colors represent the different codons in the amino acids.) The amino acid composition in the mitogenome of A. nadeshnyi (B). (The x- and y-axis refer to the amino acid composition and the number of each amino acid in 13 PCGs, respectively.)
Figure 3
Figure 3
The relative evolutionary pressure index of species based on the mitochondrial genome model of Pleuronectidae (A). The ratio (Ks/Ks) of synonymous substitution (Ka) and synonymous substitution (Ks) calculated using amino acids as data points indicates the mutation pressure index of the mitochondrial genome (B).
Figure 4
Figure 4
Nucleotide substitution saturation plots for all 13 PCGs of Pleuronectidae. First codon positions (A); second codon positions (B); third codon positions (C); and first codon and second codon positions (D). Plots in blue and green indicate transition and transversion, respectively.
Figure 5
Figure 5
The divergence time and geological scale of species mitochondrial genomes of Pleuronectidae. The life evolution scale of this chart is based on the relative divergence time of two outer groups E. pelecanoides and S. lavenbergi as a unit. Among them, the divergence time between E. pelecanoides and S. lavenbergi is 25.9–118.3 Mya, and 39 Mya is selected as the unit scale based on species affinity (https://timetree.org).
See this image and copyright information in PMC

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