Genome-Wide Patterns of Codon Usage in the Pacific Oyster Genome

The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same genome.Mutational processes or natural selective pressures affect this bias.However,a systematic investigation of codon usage pattern for molluscan species and its association with the two factors hasn’t been conducted.In this study,the whole genome codon usage patterns in oyster genome is investigated using the relative synonymous codon usage(RSCU)method,and 17 putative optimal codons were identified,wherein most had either a cytosine(C)or guanine(G)residue at the third position.Results showed that codon bias was positively associated with gene expression levels and breadth.Optimal codons had different mutational bias patterns compared with nonoptimal codons.Moreover,the results show that codon bias is negatively associated with nucleotide diversity.In the oyster genome,the fourfold degenerate codons are affected by different selective pressures,which can be regarded as an evidence that natural selection shapes codon usage patterns.This research will help to understand how natural selection and mutation bias affect codon usage in Mollusca genomes.