Abstract:

To elucidate the codon usages bias in pomegranate（Punica granatum），the transcriptome was assembled de novo to generate a transcript，and all putative complete CDSs in the transcript were identified. The relative synonymous codon usage（RSCU）patterns were compared among pomegranate and other 8 species of the Rosides. Functional evolution and RSCU models of the PgWRKY subfamilies were analyzed，and which of PgMYB subfamilies were performed likewise. The results showed as followed：(1) Under the natural selection pressure，the most genes in pomegranate had a small codon usage bias. The genes with strong bias functionally involved in the cell. By contrast，genes with none bias linked to maintaining the basic life. (2) During translating amino acids，differential high expression affected the RSCU，and high ratio of CG dinucleotides influenced the codon adaptation index. (3) The RSCU in one species was similar to that in the other species related closely. Pomegranate and eucalypt（Eucalyptus  grandis）are species of the order Myrtales，and had the same RSCU patterns. (4) Functional evolution of subfamily affected the codon usage bias. Groups 1，4 and 13 of PgWRKY family formed a disease- resistance clade. Genes in this clade preferred to use AGG to translate arginine and use CUC to translate leucine，indicating that the ongoing development of resistance to disease affected the codon usage bias. Genes of PgMYB subfamily 8 tended to use ACA to translate threonine，revealing that the expansion of woody in genome influenced the codon usage bias.

Key words: pomegranate, codon usage bias, transcriptome, gene family