Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakand 788150, Assam, India.
Gene. 2020 Aug 15;751:144762. doi: 10.1016/j.gene.2020.144762. Epub 2020 May 11.
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.
我们描绘了不同两栖动物类群（即目蛙类、有尾目和蚓螈目）呼吸链中线粒体 CYB 基因同义密码子使用偏好（CUB）及其决定因素的模式。我们观察到，两栖动物的 CYB 基因中的 CUB 较低。蚓螈目具有相对较高的偏好，其次是有尾目和蛙目。TCA、CCA、CAA、CGA、TGA、AAA 和 ACA 等密码子在所有三个目都有过表达。GCC 和 TCC 等密码子在蛙目过表达，而在有尾目，过表达的密码子是 TTA、CTA、ATA、GTA、GAA、GGA 和 GCA。在蚓螈目，GCC、TTA、CTA、ATA、GTA、GAA 和 GGA 等密码子过表达。ENC 与 3' 位核碱基之间的回归分析表明，在蛙目，核碱基 A 和 C 对 CUB 有积极影响，而在有尾目和蚓螈目，核碱基 A 和 T 对 CUB 有积极影响。相关性分析表明，蛙目呼吸链中线粒体 CYB 基因（复合物 III 基因）的 CUB 受突变压力和自然选择的相互影响，然而，中性分析表明，自然选择是 CUB 的主要进化因素。
