Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV).
Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV).
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非典型猪瘟病毒（APPV）的系统发育和密码子使用分析
DOI：
10.1080/21505594.2020.1790282
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发表时间：
2020-12
期刊：
影响因子：
5.2
通讯作者：
Chen Z
中科院分区：
文献类型：
--
作者：
Pan S;Mou C;Wu H;Chen Z
非典型猪瘟病毒（APPV）是引起仔猪A-II型先天性震颤（CT）的主要病原，严重威胁着全球猪群的健康。然而，APPV的演变在很大程度上仍然是未知的。系统发育分析表明，APPV可分为三个类群（Ⅰ、Ⅱ、Ⅲ）。系统群I和II包括来自中国的病毒株，而系统群III包含来自欧洲、北美和亚洲的病毒株。系统群I和II被初步认为是中国起源。接下来，组成特性分析揭示了在APPV基因组中使用高频率的核苷酸A和A-末端密码子。有趣的是，对优选密码子的分析显示，阿加[Arg]和AGG[Arg]的代表性过高。二核苷酸CC被认为是代表性过高，和二核苷酸CG是代表性不足。此外，还发现APPV的弱密码子使用偏好主要受选择压力和突变力的影响。密码子适应指数（CAI）、相对密码子去优化指数（RCDI）和相似性指数（SiD）分析表明，与猪相比，猪的密码子使用模式更接近于猪的密码子使用模式，提示猪的密码子使用模式可能更适合于猪。总的来说，这项研究提供了深入了解APPV的进化，通过遗传学和密码子使用模式分析。
Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.
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影响因子：
5.5
作者：
Puigbo, Pere;Bravo, Ignacio G.;Garcia-Vallve, Santiago
通讯作者：
Garcia-Vallve, Santiago
影响因子：
4.6
作者：
Postel A;Hansmann F;Baechlein C;Fischer N;Alawi M;Grundhoff A;Derking S;Tenhündfeld J;Pfankuche VM;Herder V;Baumgärtner W;Wendt M;Becher P
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影响因子：
4.3
作者：
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通讯作者：
Postel, A.
DOI：
10.1016/j.bbrc.2004.03.138
发表时间：
2004-05-07
影响因子：
3.1
作者：
Fuglsang, A
通讯作者：
Fuglsang, A
影响因子：
2.6
作者：
Hu, Jianfei;Zhao, Xiaoqian;Yu, Jun
通讯作者：
Yu, Jun