We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.

中文翻译：

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分析无脊椎动物，无尾熊和裸露线虫中线粒体CYB基因的组成特性和密码子使用偏向。

我们在不同的两栖动物群（即无序动物，无尾熊和裸露纲动物）的呼吸链线粒体CYB基因中描绘了同义密码子使用偏向（CUB）及其决定因素。我们观察到两栖动物的CYB基因中CUB较低。体操运动员具有相对较高的偏见，其次是urodeles和anurans。TCA，CCA，CAA，CGA，TGA，AAA和ACA的密码子在这三个顺序中均过分代表。诸如GCC和TCC的密码子在无尾动物中被过度代表，而在urodela中，被过度代表的密码子是TTA，CTA，ATA，GTA，GAA，GGA和GCA。在裸藻纲中，GCC，TTA，CTA，ATA，GTA，GAA和GGA密码子被过度代表。有效密码子（ENC）与第3位核碱基之间的回归分析表明，核碱基A和C对先祖顺序的CUB产生了积极影响，而在urodela和Gymnophiona中，核碱基A和T对CUB产生了积极影响。突变压力和自然选择相互说明了两栖动物CYB基因（复杂III基因）的CUB，通过密码子中第3个核苷酸与该基因总核苷酸含量之间的相关性分析得以阐明。然而，中性图表明，自然选择是CUB的主要进化因子。