# Identified Optimal Codons and Phylogenetic Relationship in Pseudobagrus Species Based on Complete Mitogenomes

## TL;DR

This study analyzed the mitochondrial genomes of 15 Pseudobagrus fish species to clarify their evolutionary relationships and identify optimal codons, revealing two main groups and aiding in species classification.

## Contribution

The study identifies optimal codons and clarifies phylogenetic relationships in Pseudobagrus species using complete mitogenomes.

## Key findings

- Pseudobagrus species have conserved mitochondrial gene structures with significant AT bias.
- Two major evolutionary clades were identified, supporting the genus' unity while revealing hidden diversity.
- 12 optimal codons were identified in P. albomarginatus, providing a genetic basis for species classification.

## Abstract

The classification of Pseudobagrus, a group of valuable East Asian freshwater fishes, has long been unclear. This study aimed to clarify their evolutionary relationships and identify optimal genetic codes by analyzing the complete mitochondrial genes of 15 species. Results showed these genes have a stable structure with more A/T bases, and 12–15 optimal genetic codes were found in different species. The fishes fell into two main evolutionary groups, supporting the genus’ unity while revealing hidden diversity. These findings provide a genetic basis for accurate species identification and classification revision, which will aid sustainable aquaculture development and aquatic ecosystem protection.

The genus Pseudobagrus represents a group of economically and ecologically significant freshwater bagrid catfishes in East Asia, yet its taxonomy remains contentious. This study employed the complete mitochondrial genomes of 15 Pseudobagrus species to clarify their phylogenetic relationships. The mitogenomes ranged from 16,526 to 16,647 bp, exhibiting a conserved gene order and significant AT bias (average A + T = 57.85%). All genomes contained 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and a control region. Start codons were predominantly ATG, except for COI (GTG), while stop codons varied among TAA, TAG, and incomplete T--. Codon usage bias favored NNU and NNA codons, and 12 optimal codons were identified in P. albomarginatus. The phylogenetic trees based on concatenated PCGs revealed two major clades. Clade I contained 14 species. Within this clade, P. albomarginatus, P. tenuis, and P. brevicorpus clustered together first, and then this trio grouped with P. ussuriensis. Pseudobagrus trilineatus formed the separate Clade II. These results provide a molecular foundation for species delimitation and systematic revision within Pseudobagrus, supporting the monophyly of the genus while highlighting cryptic diversity and taxonomic complexity.