Shi Sheng-Lin, Jiang Yi-Ren, Yang Rui-Sheng, Wang Yong, Qin Li
Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
Infect Genet Evol. 2016 Oct;44:412-417. doi: 10.1016/j.meegid.2016.07.042. Epub 2016 Jul 30.
Mutations shape synonymous codon usage bias in certain organism genomes, while selection shapes it in others. Lepidopteran-specific Alphabaculovirus and Betabaculovirus are two large genera in the family of Baculoviridae. In this study, we analyzed the codon usage patterns in 17 baculoviruses, including 10 alphabaculoviruses and 7 betabaculoviruses, which were isolated from seven insect species, and we characterized the codon usage patterns between Alphabaculovirus and Betabaculovirus. Our results show that all the baculoviruses possessed a general weak trend of codon bias. The differences of ENc (effective number of codons) values, nucleotide contents and the impacts of nucleotide content on ENc value within alpha-/betabaculovirus pairs were independent of whether the host species are the same or different. Furthermore, the majority of amino acid sequences adopted codons unequally in all viruses, but the numbers of common preferred codons between alpha- and betabaculoviruses hosted by the same insect species were not significantly different from the differences observed between alpha- and betabaculoviruses hosted by different insect species. In addition, the amino acids that adopt the same synonymous codon composition between alpha- and betabaculoviruses hosted by the same insect species were statistically as few as those between alpha- and betabaculoviruses hosted by different insect species. Correspondence analysis revealed that no major factors resulted in the codon bias in these baculoviruses, implying multiple minor influential factors exist. Neutrality plot analysis indicated that selection pressure dominated mutations in shaping the codon usage. However, the levels of selection pressure were not significantly different among viruses hosted by the same insect species. We expect that evolution would cause the alpha- and betabaculoviruses hosted by the same insect species to share more patterns, but this effect was not observed.
突变塑造了某些生物体基因组中的同义密码子使用偏好，而选择则在其他生物体基因组中起到了塑造作用。鳞翅目特异性的甲型杆状病毒属和乙型杆状病毒属是杆状病毒科中的两个大属。在本研究中，我们分析了从七种昆虫物种中分离出的17种杆状病毒的密码子使用模式，其中包括10种甲型杆状病毒和7种乙型杆状病毒，并对甲型杆状病毒属和乙型杆状病毒属之间的密码子使用模式进行了特征描述。我们的结果表明，所有杆状病毒都呈现出一般较弱的密码子偏好趋势。甲型/乙型杆状病毒对之间的有效密码子数（ENc）值、核苷酸含量以及核苷酸含量对ENc值的影响差异，与宿主物种是否相同无关。此外，在所有病毒中，大多数氨基酸序列对密码子的使用并不均衡，但由相同昆虫物种携带的甲型和乙型杆状病毒之间的常见偏好密码子数量，与由不同昆虫物种携带的甲型和乙型杆状病毒之间的差异并无显著不同。此外，由相同昆虫物种携带的甲型和乙型杆状病毒之间采用相同同义密码子组成的氨基酸数量，在统计学上与由不同昆虫物种携带的甲型和乙型杆状病毒之间的数量一样少。对应分析表明，没有主要因素导致这些杆状病毒中的密码子偏好，这意味着存在多个次要影响因素。中性绘图分析表明，在塑造密码子使用方面，选择压力主导着突变。然而，在由相同昆虫物种携带的病毒之间，选择压力水平并无显著差异。我们预计进化会使由相同昆虫物种携带的甲型和乙型杆状病毒共享更多模式，但并未观察到这种效应。
