Analysis of synonymous codon usage patterns in the genus Rhizobium |
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Authors: | Xinxin Wang Liang Wu Ping Zhou Shengfeng Zhu Wei An Yu Chen Lin Zhao |
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Affiliation: | 1. School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, People’s Republic of China 2. China Offshore Environmental Service Co. Ltd., Tianjin, 300452, People’s Republic of China 3. College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, Shandong, People’s Republic of China 4. China National Offshore Oil Corporation, Beijing, 100010, People’s Republic of China
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Abstract: | The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman’s rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium. |
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