Genomic Landscape of Rare Codon Usage at Start Region in the Pacific Oyster Genome

Synonymous codons have different frequencies of usage in many species.Based on the frequency of usage,the codons can be divided into two groups,rare codons and abundant codons.Rare codons are found to be enriched at the start regions of genes,and it is assumed that these codons can reduce elongation speed of genes.However,the rare codon usage in different genomic regions of mollusks and their relationship with selective pressure has not been systematically investigated.In this study,the patterns of rare codon usage are characterized at whole genome level,and their relationship with selective pressures is investigated in Crassostrea gigas.The rare codons are enriched at the start regions of genes with high and medium expression levels,and their proportion is higher than those in the genes with low expression level.The genes with longer coding sequences and more exon numbers have lower fraction of rare codons at start regions.Rare codons have lower level of nucleotide diversity and higher frequency of rare mutations at start regions.This work is the first comprehensive investigation of the relationships between rare codon usage and some intrinsic genetic factors in mollusca species.The results suggest that the selective pressures play an important role in shaping the rare codon usage in the C.gigas genome.

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.