State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
Virol J. 2011 Jun 27;8:325. doi: 10.1186/1743-422X-8-325.
Cardioviruses are positive-strand RNA viruses in the Picornaviridae family that can cause enteric infection in rodents and also been detected at lower frequencies in other mammals such as pigs and human beings. The Cardiovirus genus consists two distinct species: Encephalomyocarditis virus (EMCV) and Theilovirus (ThV). There are a lot differences between the two species. In this study, the differences of codon usage in EMCV and ThV were compared.
The mean ENC values of EMCV and ThV are 54.86 and 51.08 respectively, higher than 40.And there are correlations between (C+G)₁₂% and (C+G)₃% for both EMCV and ThV (r = -0.736; r = 0.986, P < 0.01, repectively). For ThV the (C+G)₁₂%, (C+G)₃%, axis f'₁ and axis f'₂ had a significant correlations respectively but not for EMCV. According to the RSCU values, the EMCV species seemed to prefer U, G and C ending codon, while the ThV spice seemed to like using U and A ending codon. However, in both genus AGA for Arg, AUU for Ile, UCU for Ser, and GGA for Gly were chosen preferentially. Correspondence analysis detected one major trend in the first axis (f'₁) which accounted for 22.89% of the total variation, and another major trend in the second axis (f'₂) which accounted for 17.64% of the total variation. And the plots of the same serotype seemed at the same region at the coordinate.
The overall extents of codon usage bias in both EMCV and ThV are low. The mutational pressure is the main factor that determines the codon usage bias, but the (C+G) content plays a more important role in codon usage bias for ThV than for EMCV. The synonymous codon usage pattern in both EMCV and ThV genes is gene function and geography specific, but not host specific. Maybe the serotype is one factor effected the codon bias for ThV, and location has no significant effect on the variations of synonymous codon usage in these virus genes.
小 RNA 病毒科的正链 RNA 病毒是心肌病毒科，可引起啮齿动物的肠道感染，也在其他哺乳动物如猪和人类中以较低频率检测到。心肌病毒属由两个不同的种组成：脑炎心肌炎病毒（EMCV）和泰利病毒（ThV）。这两个物种之间有很多差异。在这项研究中，比较了 EMCV 和 ThV 密码子使用的差异。
EMCV 和 ThV 的平均 ENC 值分别为 54.86 和 51.08，高于 40。并且 EMCV 和 ThV 的（C+G）₁₂%和（C+G）₃%之间存在相关性（r=-0.736；r=0.986，P<0.01）。对于 ThV，（C+G）₁₂%、（C+G）₃%、轴 f'₁和轴 f'₂分别有显著相关性，但对于 EMCV 则没有。根据 RSCU 值，EMCV 种似乎更喜欢 U、G 和 C 结尾的密码子，而 ThV 种似乎更喜欢使用 U 和 A 结尾的密码子。然而，在这两个属中，AGA 优先用于 Arg、AUU 用于 Ile、UCU 用于 Ser 和 GGA 用于 Gly。对应分析在第一轴（f'₁）上检测到一个主要趋势，占总变异的 22.89%，在第二轴（f'₂）上检测到另一个主要趋势，占总变异的 17.64%。并且同一血清型的图谱似乎位于坐标的同一区域。
EMCV 和 ThV 的密码子使用偏好总体程度较低。突变压力是决定密码子使用偏好的主要因素，但（C+G）含量对 ThV 的密码子使用偏好的影响大于对 EMCV 的影响。EMCV 和 ThV 基因中的同义密码子使用模式是基因功能和地理位置特异性的，但不是宿主特异性的。也许血清型是影响 ThV 密码子偏倚的一个因素，而位置对这些病毒基因中同义密码子使用的变化没有显著影响。
