Department of Biotechnology, Assam University, Silchar, 788011 Assam, India.
Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150 Assam, India.
Mol Biochem Parasitol. 2020 Jul;238:111294. doi: 10.1016/j.molbiopara.2020.111294. Epub 2020 Jun 24.
Codon usage bias (CUB) is the nonrandom usage of synonymous codons in which some codons are more preferred to others.CUB can be determined by mutation pressure and selection. Various approaches have been used to understand the pattern of CUB in the mitochondrial ND (MT-ND or ND) genes involved in complex I of respiratory chain in five different classes of Platyhelminthes as no work was reported yet. The present study revealed that the CUB varies across MT-ND genes and the coding sequences showed the richness of A and T. Correspondence analysis implied the effect of mutational pressure and also the pattern of codon usage was different in different classes of platyhelminthes for MT-ND genes. Highly significant correlation was observed between overall nucleotide composition and its 3rd codon position in most of the homogeneous nucleotides such as A% and A3%, T% and T3%, G% and G3%, C% and C3%, GC% and GC3% and also some significant correlations observed among heterogeneous nucleotides in all the five classes for MT-ND genes suggested the role of mutational pressure as well as natural selection in affecting the CUB. Neutrality plot suggested that the contributions of natural selection and mutational pressure varied across different classes of platyhelminthes and also differed in different MT-ND genes.
密码子使用偏性（CUB）是指同义密码子的非随机使用，其中一些密码子比其他密码子更受欢迎。CUB 可以通过突变压力和选择来确定。目前还没有报道过关于五门扁形动物复合体 I 呼吸链中参与的线粒体 ND（MT-ND 或 ND）基因的 CUB 模式的研究，因此我们采用了各种方法来了解这一情况。本研究表明，CUB 在 MT-ND 基因中存在差异，并且编码序列显示出 A 和 T 的丰富性。对应分析表明，突变压力的影响以及不同扁形动物类群中 MT-ND 基因的密码子使用模式也存在差异。在大多数同质核苷酸中，如 A%和 A3%、T%和 T3%、G%和 G3%、C%和 C3%、GC%和 GC3%，整体核苷酸组成与其第三密码子位置之间存在高度显著的相关性，而且在所有五类 MT-ND 基因的异质核苷酸中也观察到一些显著的相关性，这表明突变压力以及自然选择在影响 CUB 方面发挥了作用。中性绘图表明，自然选择和突变压力的贡献在不同的扁形动物类群中有所不同，而且在不同的 MT-ND 基因中也存在差异。
