Analysis of Codon Usage Bias in Mitochondrial Whole Genome of Pinctada margaritifera
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摘要: 【目的】探究珠母贝（Pinctada margaritifera）线粒体全基因组密码子的使用偏好性，明确密码子偏好性的影响因素，为提高珠母贝外源基因表达效率及种质资源保护与遗传育种的研究提供理论依据。【方法】选取珠母贝线粒体基因组中大于300 bp的10条非重复编码序列，利用CodonW 1.4.2、Excel、SPSS 22.0等软件分析序列的密码子偏好性参数，以同义密码子相对使用度差值（△RSCU）> 0.08以及在高表达基因库中RSCU值>1.00为标准筛选最优密码子。【结果】珠母贝线粒体基因组密码子第1位GC（GC1）比例为35.2%~51.8%，平均值为45.6%；第2位GC （GC2）比例为35.8%~46.8%，平均值为40.0%；第3位GC （GC3）比例为37.7%~51.8%，平均值为44.1%；总GC比例为41.1%~47.5%，平均值为34.9%。密码子的适应指数（CAI）为0.119~0.181，平均值为0.151。密码子的偏好性指数（CBI）为-0.184~-0.04，平均值为-0.1048。最优密码子使用频率（FOP）为0.259~0.359，平均值为0.322。有效密码子数（ENC）为39.72~54.35，平均值为47.46。总平均亲水性Gravy）为0.216 6~1.038 5，平均值为0.7412。相对密码子使用度（RSCU）> 1.00的密码子数目为26个，主要以U （T）/G结尾。中性绘图、ENC-plot绘图和对应性分析均表明，珠母贝线粒体基因组密码子偏好更多受选择压力的影响。AGG、AUU、CCU、GAG、GCU、UGA等6个密码子为最优密码子。【结论】珠母贝线粒体基因组密码子偏好以U（T）/G结尾，筛选的6个最优密码子主要以U（T）/G结尾。珠母贝线粒体全基因组密码子的偏好性为弱偏好性，自然选择是偏好性形成的主要影响因素。Abstract: 【Objective】The codon use bias of mitochondrial whole genome of Pinctada margaritifer was investigated, and the factors affecting codon bias were analyzed to raise gene expression efficiency, promote germplasm resources protection and genetic breeding of P. margaritifera. 【Method】In this study, we screened out 10 CDs (Coding DNA Sequence) from the whole genome sequence of P. margaritifera mitocondria, which were more than 300 bp non-repeated sequences and started from ATG, and optimal codons were selected with Relative Synonymous Codon Usage (RSCU) Variation (ΔRSCU) > 0.08 and RSCU >1.00 in highly expressed gene bank by using the software of CodonW 1.4.2 and SPSS 22.0. 【Results】The GC content in different codons of different genes was different. GC1 ranged from 35.2% to 51.8% with an average of 45.57%. GC2 ranged from 35.8% to 46.8% with an average of 40.01%. GC3 ranged from37.7% to 51.8% with an average of 44.14%. Total GC content ranged from 41.1% to 47.5% with an average of 34.89%. Codon adaption index (CAI) ranged from 0.119 to 0.181 with an average of 0.151. Codon bias index (CBI) ranged from -0.184 to -0.04 with an average of -0.105. Frequency of optimal codon (FOP) ranged from 0.259 to 0.359 with an average of 0.322. Effective Number of Codon (ENC) ranged from 39.72 to 54.35 with an average of 47.46. Grand average of hydrophilia (Gravy) ranged from 0.216 6 to 1.038 5 with an average of 0.741 2. Neutrality plots, ENC-plot and correspondence analysis results showed that the codon bias of mitochondrial genome in P. margaritifera was affected by mutation but more by selection. 6 codons, i. e., AGG, AUU, CCU, GAG, GCU and UGA, were identified as the optimal codons in the mitochondrial genome of P. margaritifera. 【Conclusion】 The mitochondrial whole genome codon of P. margaritifera mainly end with U(T)/G, and the six selected optimal codons end with U(T)/G. The codons in mitochondrial whole genome of P. margaritifera show weak bias. Natural selection plays a leading role in the formation of codon usage bias.
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Key words:
- Pinctada margaritifera /
- codon bias /
- optimal codons /
- mitochondrial genome
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