Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Mitochondrion. 2022 Jan;62:111-121. doi: 10.1016/j.mito.2021.11.004. Epub 2021 Nov 15.
The phenomenon of non-random occurrence of synonymous nucleotide triplets (codons) in the coding sequences of genes is the codon usage bias (CUB). In this study, we used bioinformatic tool kit to analyze the compositional pattern and CUB of mitogenes namely COI, COII and COIII across different orders of reptiles. Estimation of overall base composition in the protein-coding sequences of COI, COII and COIII genes of the reptilian orders revealed an uneven usage of nucleotides. The overall count of A nucleotide was found to be the highest while the overall count of G nucleotide was the least. The CO genes across the three reptilian orders were prominently AT biased. Comparison of the GC proportion at each codon position displayed that GC1 percentage ranked the highest in all the three CO genes of the reptilian orders. SCUO values indicated weaker CUB, while considerable variation of SCUO values existed in the three CO genes across the studied reptiles. Relative synonymous codon usage (RSCU) values indicated that mostly the A ending codons were preferred. Based on the parameters namely neutrality plot, mutational responsive index and translational selection, we could conclude that natural selection was the major evolutionary force in COI, COII and COIII genes in the studied reptilian orders. However, correspondence analysis, parity plot and correlation studies indicated the existence of mutation pressure as well on the CO genes.
基因编码序列中同义核苷酸三联体（密码子）非随机出现的现象称为密码子使用偏性（CUB）。在这项研究中，我们使用生物信息学工具包分析了不同爬行动物目下的线粒体基因 COI、COII 和 COIII 的组成模式和 CUB。对 COI、COII 和 COIII 基因编码序列中整体碱基组成的估计表明，核苷酸的使用不均匀。A 核苷酸的总数最高，而 G 核苷酸的总数最少。CO 基因在三个爬行动物目中明显呈 AT 偏倚。比较每个密码子位置的 GC 比例显示，GC1 百分比在三个爬行动物目的 CO 基因中均排名最高。SCUO 值表明 CUB 较弱，而在所研究的爬行动物中，三个 CO 基因的 SCUO 值存在相当大的变化。相对同义密码子使用（RSCU）值表明，大多数偏好 A 结尾的密码子。基于中性作图、突变响应指数和翻译选择等参数，我们可以得出结论，自然选择是研究爬行动物目中 COI、COII 和 COIII 基因的主要进化力量。然而，对应分析、奇偶校验图和相关性研究表明，CO 基因也存在突变压力。
