Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia,Journal of Cellular Physiology

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Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia
Journal of Cellular Physiology ( IF 4.5 ) Pub Date : 2020-09-22 , DOI: 10.1002/jcp.30050
Parvin A Barbhuiya ₁ , Arif Uddin ₂ , Supriyo Chakraborty ₁

Affiliation

In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.

中文翻译：

两栖纲目线粒体ND基因密码子使用模式及进化力

在这项研究中，我们使用生物信息学方法分析了三个两栖动物群（即 Anura、Caudata 和 Gymnophiona）的线粒体 ND 基因中同义密码子使用的核苷酸组成和模式，以确定密码子使用的共性和差异为尚未报告任何研究工作。密码子有效数的高值表明，各目中线粒体ND基因的密码子使用偏差（CUB）较低。核苷酸组成分析表明，对于每个基因，Anura、Caudata 和 Gymnophiona 的组成特征不同，GC 含量低于 AT 含量。此外，一个非常显着的差异（p <.05) 在订单中的每个基因中都发现了 GC 含量。热图显示了不同 ND 基因之间密码子使用的对比模式。GC12 对 GC3 的回归表明 GC3 分布范围很窄，并且一些点位于对角线上，表明突变压力和自然选择都可能影响 CUB。此外，所有目间 ND 基因的回归线斜率小于 0.5，表明自然选择可能起主导作用，而突变压力在形成跨目 ND 基因的 CUB 中起次要作用。

更新日期：2020-09-22

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