Selection shapes the patterns of codon usage in three closely related species of genus Misgurnus.

Abstract Neutrality plots revealed that selection probably dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in three loaches, Misgurnus anguillicaudatus , M. mohoity , and M. bipartitus. These three species also clearly showed similar tendencies in the preferential usage of codons. Nineteen, nine, and 14 preferred codon pairs and 179, 182, and 173 avoided codon pairs were also detected in M. anguillicaudatus , M. bipartitus , and M. mohoity , respectively, and the most frequently avoided type of cP3-cA1 dinucleotide in these species was nnUAnn. The expression-linked patterns of codon usage revealed that higher expression was associated with higher GC 3 , lower ENC, and a smaller proportion of amino acids with high size/complexity (S/C) scores in these three species. These results elucidate selectively driven codon bias in Misgurnus species, and reveal the potential importance of expression-mediated selection in shaping the genome evolution of fish. Highlights • Selection dominates codon bias, whereas mutation plays only a minor role, in shaping the codon bias in the loaches. • Three loach species clearly show similar tendencies in the preferential usage of codons. • Higher expression was associated with higher GC3, lower ENC (effective number of codons) in the loaches. • Highly expressed gene was linked to a higher frequency of amino acids with low metabolic costs in the loaches. [ABSTRACT FROM AUTHOR]