Abstract：To explore the codon usage bias of the emerging bat SARS-related coronavirus (SARSr-CoV) in Yunnan Province and its evolutionary relationship with SARS-CoVs and other SARSr-CoVs, we used Lasergene, EMBOSS, CodonW and other biological information software to analyze codon usage bias and cluster analysis of the protein coding sequences of the emerging bat SARSr-CoVs in Yunnan Province, SARS-CoVs, and other SARSr-CoVs. Results showed that the number of effective codons (ENC) of these emerging bat SARSr-CoVs proteins were close to 61, their codon usage bias were weak. The Relative Synonymous Codon Usage (RSCU) analysis showed that the preferred codons of each protein were different, but tending to use the codons ending with A or U. In the choice of preferred codons, these new emerging bat SARSr-CoVs were highly consistent with SARS-CoVs. ENC-Plot, neutral plot analysis and PR2 rule analysis indicated that the natural selection factors mainly influenced the evolution of these emerging bat SARSr-CoVs. Clustering analysis based on codon usage bias indicated that the emerging bat SARSr-CoVs were closely related to SARS-CoVs. In addition, these emerging bat SARSr-CoVs were dispersedly clustered with SARSr-CoVs found in other regions. All of these shown that the new emerging bat SARSr-CoVs in Yunnan have higher degree of similarity to SARS-CoVs and have higher risks of cross species transmission. This further indicated that the bat SARSr-CoVs in Yunnan may be the natural gene reservoir of SARS-CoVs and SARSr-CoVs for other regions from the perspective of codon usage preference.
田明明, 魏雪玲, 杨兴, 宋秀锋, 李光华, 刘奇. 云南新现蝙蝠SARS样冠状病毒密码子偏性及其聚类分析[J]. 中国人兽共患病学报, 2018, 34(12): 1079-1086.
TIAN Ming-ming, WEI Xue-ling, YANG Xing, SONG Xiu-feng, LI Guang-hua, LIU Qi. Codon usage bias studies and cluster analysis on emerging bat SARS-related coronaviruses in Yunnan Province, China. Chinese Journal of Zoonoses, 2018, 34(12): 1079-1086.
[1] Ji H, Song W, Gao Z, et al. SARS-CoV proteins decrease levels and activity of human ENaC via activation of distinct PKC isoforms[J]. Am J Physiol Lung Cell Mol Physiol, 2009, 296(3):L372-L383. DOI:10.1152/ajplung.90437.2008 [2] Monagin C, Paccha B, Liang N, et al. Serologic and behavioral risk survey of workers with wildlife contact in China[J]. PLoS One,2018,13(4):e194647. DOI:10.1371/journal.pone.0194647 [3] Hu B, Zeng L, Yang X, et al. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus[J]. PLoS Pathog, 2017,13(11):e1006698. DOI:10.1371/journal.ppat.1006698 [4] Lau SKP, Woo PCY, Li KSM, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats[J]. Proc Natl Acad Sci U S A,2005,102(39):14040-14045. DOI:10.1073/pnas. 0506735102 [5] Nasrullah I, Butt A M, Tahir S, et al. Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution[J]. BMC Evol Biol, 2015, 15(1):174. DOI:10.1186/s12862-015-0456-4 [6] Wei L, He J, Jia X, et al. Analysis of codon usage bias of mitochondrial genome in Bombyx moriand its relation to evolution[J]. BMC Evol Biol, 2014,14(1):262. DOI:10.1186/s12862-014-4 [7] Song H, Liu J, Song Q, et al. Comprehensive analysis of codon usage bias in seven epichlo species and their peramine-coding genes[J]. Front Microbiol,2017,8:1419. DOI:10.3389/ fmicb.2017. 01419 [8] Mazumder TH, Chakraborty S. Gaining insights into the codon usage patterns of TP53 gene across eight Mammalian Species[J]. PLoS One,2015,10(3):e121709. DOI:10.1371/journal.pone.0121709 [9] Marra MA. The genome sequence of the SARS-associated coronavirus[J]. Science,2003,300(5624): 1399-1404. DOI:10.1126/science.1085953 [10] Castells M, Victoria M, Colina R, et al. Genome-wide analysis of codon usage bias in Bovine Coronavirus[J]. Virol J,2017,14(1):115. DOI:10.1186/s12985-017-0780-y [11] Wright F. The 'effective number of codons' used in a gene[J]. Gene,1990,87(1):23-29. DOI:10.1016/0378-1119(90)90491-9 [12] Bae Y. Codon usage patterns of tyrosinase genes in clonorchis sinensis[J]. Korean J Parasitol, 2017,55(2):175. DOI:10.3347/kjp.2017.55.2.175 [13] Sharp PM, Li W. Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’codons[J]. Nucleic Acids Res,1986,14(19):7737-7749. DOI:10.1093/nar/14.19.7737 [14] Kumar N, Bera BC, Greenbaum BD, et al. Revelation of influencing factors in overall codon usage bias of equine influenza viruses[J]. PLoS One,2016,11(4):e154376. DOI:10.1371/journal.pone.0154376 [15] Huang X, Xu J, Chen L, et al. Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps[J]. BMC Genomics,2017,18(1):308. DOI:10.1186/s12864-017-3704-8 [16] Sueoka N. Translation-coupled violation of parity rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position[J]. Gene,1999,238(1):53-58. DOI:10.1016/s0378-1119(99)00320-0 [17] Sueoka N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons[J]. J Mol Evol,1995,40(3):318-325. DOI:10.1007/bf02198860 [18] Rota PA. Characterization of a Novel Coronavirus associated with severe acute respiratory syndrome[J]. Science,2003,300(5624):1394-1399. DOI:10.1126/science.1085952 [19] 赵建岚,胡莎莎,罗洪,等. 中东呼吸综合征冠状病毒结构蛋白与附属蛋白编码基因密码子偏爱性分析[J]. 病毒学报,2016(04):404-410. DOI:10.13242/j.cnki.bingduxuebao.002978
2018, Vol. 34 
