Analysis of codon usage in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.)
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摘要: 密码子使用偏性（CUB）是生物体重要的进化特征，对研究物种进化、基因功能以及外源基因表达等具有重要科学意义。本研究利用糜子（Panicum miliaceum L.）叶绿体基因组中筛选出的53条蛋白编码序列，对其密码子使用模式及偏性进行了分析。结果表明，糜子叶绿体基因的有效密码子数（ENC）在37.14~61之间，多数密码子的偏性较弱。相对同义密码子使用度（RSCU）分析发现，RSCU > 1的密码子有32个，其中28个以A、U结尾，表明第3位密码子偏好使用A和U碱基。中性分析发现，GC3与GC12的相关性不显著，回归曲线斜率为0.2129，表明密码子偏性主要受到自然选择的影响；而ENC-plot分析发现大部分基因落在曲线的上方及周围，表明突变也影响了密码子偏性的形成。进一步的对应性分析发现，第1轴为主要影响因素，解释了17.92%的差异，其与ENC、GC3S值的相关性均达到显著水平，但与CBI、GCall不相关。最后，9个密码子被鉴定为糜子叶绿体基因组的最优密码子，糜子叶绿体基因组的密码子使用偏性可能受选择和突变共同作用。Abstract: Codon usage bias (CUB) is an important evolutionary feature in a genome,which provides important information for studying organism evolution,gene function,and exogenous gene expression.The CUB and its influencing factors in the chloroplast genome of Broomcorn millet (Panicum miliaceum L.) were preliminarily analyzed in this study based on 53 length-filtered CDS sequences.Results showed that the effective number of codons (ENC) ranged from 37.14 to 61,indicating that codon bias was weak.Relative synonymous codon usage (RSCU) analysis found 32 codons with a RSCU value of more than 1,of which 28 ended with A or T,suggesting that the third codon preferred A or U.Neutrality analysis showed no significant correlation between GC12 and GC3,and the regressive slope was 0.2129,suggesting natural selection mainly contributed to the CUB.ENC-plot (ENC vs GC3S) analysis showed that most genes followed the parabolic line of trajectory,but several genes with low ENC values below the expected curve were also observed.Furthermore,correspondence analysis of RSCU demonstrated that the first axis could explained 17.92% of variation,which was the major factor influencing codon bias.The first axis showed a significant correlation between ENC and GC3S,whereas no significant correlation was found for CBI and GC.Finally,nine codons were identified as optimal codons.We concluded that both natural selection and mutation have impacted the formation of CUB in the Broomcorn millet chloroplast genome.
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Keywords:
- Broomcorn millet /
- Chloroplast /
- Codon usage bias /
- Optimal codons
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