Journal of Taiwan Agricultural Research

Author:Meng-Li Wei, Yi-Han Chung, Chun-Tang Lu, and Hsiu-Ying Lu*

Abstract:

    Codon usage bias varied among genes (Xa) conferring resistance of rice (Oryza sativa) to bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae.  This study was conducted to elucidate the evolution of synonymous codon usage by analysis of factors influencing the synonymous codon usage pattern of Xa genes.  A total of 17 coding domain sequences (CDS) of the completely sequenced genes, Xa1, xa5, xa13, Xa13, Xa21, Xa26, and Xa27, were obtained through the access of the GenBank database of National Center for Biotechnology Information (NCBI) and they were used to unravel the main factors influencing codon usage bias.  The length of CDS and indices of synonymous condon usage bias such as relative synonymous codon usage (RSCU), codon adaption index (CAI), effective number of codons (ENC), frequency of G or C nucleotides present at the third position of synonymous codons (GC3), and mean frequencies of G or C nucleotides present at the first and second positions of synonymous codons (GC12) were estimated to examine relationships among them.  The length of CDS and level of gene expression were highly correlated to codon usage bias in Xa genes; the Xa genes with shorter CDS (xa5, xa13, Xa13, and Xa27) had higher gene expression and higher codon usage bias.  The GC3 compositional constraints also affected the codon usage in Xa genes.  Moreover, the GC12 had a direct effect on GC3 mutation bias, leading to further high codon usage bias in Xa genes.

Key words:Synonymous codon usage bias, Gene expression level, GC3 content, Mutation bias, Molecular evolution, Bacterial leaf blight, Xanthomonas oryzae

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