Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India.
Infect Genet Evol. 2018 Jan;57:128-137. doi: 10.1016/j.meegid.2017.10.018. Epub 2017 Oct 21.
Codon usage bias refers to the phenomenon where synonymous codons are used with unequal frequencies. To understand the patterns of codon usage in mitochondrial cytochrome B (MT-CYB) gene of phylum platyhelminthes we used bioinformatic approaches to analyze the protein coding sequences of five different classes - cestoda, monogenea, rabditophora, trematoda and turbellaria. It was found from nucleotide composition analysis that in all the classes, A/T-ended codons were preferred to G/C -ended codons. From box plot analysis GC1 was found to have highest response to codon usage bias. Correspondence analysis indicated that besides mutation other factors such as natural selection might also affect the codon usage pattern. Neutrality plot reveals that both mutation and natural selection played role in codon usage pattern in five classes of MT-CYB gene. Various factors namely nucleotide composition, natural selection and mutation pressure affected the codon usage pattern.
密码子使用偏好是指同义密码子使用频率不同的现象。为了了解扁形动物门线粒体细胞色素 B（MT-CYB）基因的密码子使用模式，我们使用生物信息学方法分析了五个不同类群的蛋白质编码序列 - 绦虫、单殖吸虫、腹足类、吸虫和涡虫。从核苷酸组成分析中发现，在所有类群中，A/T 结尾的密码子比 G/C 结尾的密码子更受欢迎。从箱线图分析中发现，GC1 对密码子使用偏好的反应最高。对应分析表明，除了突变，其他因素如自然选择也可能影响密码子使用模式。中性分析表明，突变和自然选择都在五个类群的 MT-CYB 基因的密码子使用模式中发挥了作用。核苷酸组成、自然选择和突变压力等各种因素影响了密码子使用模式。
