Mazumder Gulshana A, Uddin Arif, Chakraborty Supriyo
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Acta Parasitol. 2017 Dec 20;62(4):748-761. doi: 10.1515/ap-2017-0090.
Schistosoma japonicum and Ascaris suum are considered as the major parasites of human which cause various life threatening diseases such as schistomiasis and ascariasis. The codon usage bias (CUB) is known as the phenomenon of more usage of a specific codon than the other synonymous codons for an amino acid. The factors that influence the codon usage bias are mutation pressure, natural selection, gene expression, gene length, GC content, RNA stability, recombination rates, codon position etc. Here we had used various bioinformatic tools and statistical analyses to understand the compositional features, expression level and codon usage bias in the genes of these two species.After estimating the effective number of codon (ENC) in both the species, codon usage bias was found to be low and gene expression was high. The nucleobase A and T were used most often than C and G. From neutrality plot and correspondence analysis it was found that both natural selection and mutation pressure played an important role in shaping the codon usage pattern of both species. Moreover, natural selection played a major role while mutation pressure played a minor role in shaping the codon usage bias in S. japonicum and A.suum. This is the first report on the codon usage biology in S. japonicum and A.suum, and the factors influencing their codon usage bias. These results are expected to be useful for genetic engineering and evolutionary studies.
日本血吸虫和猪蛔虫被认为是人类的主要寄生虫，可引发诸如血吸虫病和蛔虫病等各种危及生命的疾病。密码子使用偏好（CUB）是指对于一种氨基酸，特定密码子的使用频率高于其他同义密码子的现象。影响密码子使用偏好的因素包括突变压力、自然选择、基因表达、基因长度、GC含量、RNA稳定性、重组率、密码子位置等。在此，我们运用了各种生物信息学工具和统计分析方法，以了解这两个物种基因的组成特征、表达水平和密码子使用偏好。在估算了这两个物种的有效密码子数（ENC）后，发现密码子使用偏好较低，而基因表达较高。核碱基A和T的使用频率高于C和G。从中性绘图和对应分析发现，自然选择和突变压力在塑造这两个物种的密码子使用模式中均发挥了重要作用。此外，在塑造日本血吸虫和猪蛔虫的密码子使用偏好方面，自然选择起主要作用，而突变压力起次要作用。这是关于日本血吸虫和猪蛔虫密码子使用生物学以及影响其密码子使用偏好因素的首篇报道。这些结果有望对基因工程和进化研究有所帮助。
