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

The genus <i>Pseudobagrus</i> 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 <i>Pseudobagrus</i> 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 <i>COI</i> (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 <i>P. albomarginatus</i>. The phylogenetic trees based on concatenated PCGs revealed two major clades. Clade I contained 14 species. Within this clade, <i>P. albomarginatus</i>, <i>P. tenuis</i>, and <i>P. brevicorpus</i> clustered together first, and then this trio grouped with <i>P. ussuriensis</i>. <i>Pseudobagrus trilineatus</i> formed the separate Clade II. These results provide a molecular foundation for species delimitation and systematic revision within <i>Pseudobagrus</i>, supporting the monophyly of the genus while highlighting cryptic diversity and taxonomic complexity.