Codon usage bias (CUB) is a universal feature in both mitochondrial and ribosomal genes, shaped by the combined forces of mutation and selection, and serves as a valuable indicator of evolutionary processes and phylogenetic signals. However, comprehensive analysis of CUB is lacking in the Leuciscinae family. We sequenced and annotated the complete mitochondrial genome of Abramis brama orientalis and examined codon usage patterns in all Leuciscinae species, subsequently finding the dominant evolutionary forces and phylogenetic relationships. We performed a PR2 bias plot, neutrality plot, effective number of codons (ENC) vs. GC3, relative synonymous codon use (RSCU) clustering and Ka/Ks calculations for 22 Leuciscinae species. We constructed the phylogenetic trees of Leuciscinae using Bayesian inference and maximum likelihood on concatenated mitochondrial sequences. The complete mitochondrial genome of Abramis brama orientalis was 16,607 bp, with typical vertebrate structure and high A + T bias. The codons of protein-coding genes in Leuciscinae have a preference for ending in A/C. All protein-coding genes were under strong purifying selection (Ka/Ks < 1). RSCU patterns and phylogenetic analyses showed two lines of Leuciscinae in the RSCU, with A. brama orientalis being a monophyletic group with A. brama. The results demonstrate the strong role for selection in shaping mitochondrial codon usage in Leuciscinae, despite mutational biases. The study clarified the taxonomic status of A. brama orientalis and provided a framework for understanding molecular evolution in this ecologically important freshwater fish family.
Hao et al. (Fri,) studied this question.
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