蓖麻蚕核型多角体病毒和柞蚕核型多角体病毒的密码子使用模式分析
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摘要
蓖麻蚕核型多角体病毒(Phcy NPV)是柞蚕核型多角体病毒(Anpe NPV)的变种,不能感染柞蚕。通过病毒基因组GC含量、GC3s含量、有效密码子数、相对同义密码子使用度、密码子偏好参数的计算及ENc-plot分析、中性绘图分析、对应分析等,比较Phcy NPV和Anpe NPV的密码子使用模式。Phcy NPV、Anpe NPV分别只有1个和4个ORF的密码子偏好性较强。与Anpe NPV比较,Phcy NPV少数ORF的GC含量、GC3s含量、有效密码子数量和密码子偏好参数变化较大,但2种病毒ORF组间的GC含量、GC3s含量、有效密码子数和密码子偏好参数均无统计学差异(P=0.135、P=0.189、P=0.192、P=0.200)。2种病毒ORF组间,由同义密码子编码的18种氨基酸的密码子使用均无统计学差异(P>0.05),鉴定的17种偏好性密码子也均相同。GC碱基组成是影响2种病毒ORF组密码子使用模式的主要因素,而自然选择对GC碱基组成的影响大于突变压力,但2种病毒间自然选择的影响程度无统计学差异(P=0.770)。Phcy NPV在适应新宿主蓖麻蚕的进化过程中密码子使用模式变化较小,尚不能通过密码子使用模式分析解释杆状病毒在不同宿主间的交叉感染机制。
Philosamia cynthia ricini nucleopolyhedrovirus( PhcyN PV) can not infect Antheraea pernyi though PhcyN PV is a variant of Antheraea pernyi nucleopolyhedrovirus( AnpeN PV). The codon usage of PhcyN PV was compared with that of AnpeN PV through examining the GC content,GC3 s content,effective number of codons( ENc),relative synonymous codon usage( RSCU),codon preference parameter( CPP),and through performing ENc-plot analysis,neutrality-plot analysis and corresponding analysis. PhcyN PV had only one ORF possessing strong codon bias,whereas AnpeN PV had four ORFs possessing strong codon bias. The GC contents,GC3 s contents,ENc values and CPP values of several ORFs in PhcyN PV changed greatly when compared with those of AnpeN PV; however,the four indices all had no statistical difference at ORFeome scale( P = 0. 135,P = 0. 189,P = 0. 192,and P = 0. 200). Between the two OR-Feomes,the codon usages of all the 18 amino acids encoded by synonymous codons were all statistically insignificant( P>0. 05),and the 17 identified preferred codons were all identical,too. GC base composition was the major factor influencing codon usage patterns of the two ORFemoes,and natural selection dominated mutational pressure in shaping GC base composition,but the influence degree of natural selection between the two viruses were not significantly different( P = 0. 770). The codon usage pattern of PhcyN PV changed in a small range when adapted to new host Philosamia cynthia ricini,hence it is impossible to explain the cross-infectivity mechanism through analysis of codon usage pattern.
Philosamia cynthia ricini nucleopolyhedrovirus( PhcyN PV) can not infect Antheraea pernyi though PhcyN PV is a variant of Antheraea pernyi nucleopolyhedrovirus( AnpeN PV). The codon usage of PhcyN PV was compared with that of AnpeN PV through examining the GC content,GC3 s content,effective number of codons( ENc),relative synonymous codon usage( RSCU),codon preference parameter( CPP),and through performing ENc-plot analysis,neutrality-plot analysis and corresponding analysis. PhcyN PV had only one ORF possessing strong codon bias,whereas AnpeN PV had four ORFs possessing strong codon bias. The GC contents,GC3 s contents,ENc values and CPP values of several ORFs in PhcyN PV changed greatly when compared with those of AnpeN PV; however,the four indices all had no statistical difference at ORFeome scale( P = 0. 135,P = 0. 189,P = 0. 192,and P = 0. 200). Between the two OR-Feomes,the codon usages of all the 18 amino acids encoded by synonymous codons were all statistically insignificant( P>0. 05),and the 17 identified preferred codons were all identical,too. GC base composition was the major factor influencing codon usage patterns of the two ORFemoes,and natural selection dominated mutational pressure in shaping GC base composition,but the influence degree of natural selection between the two viruses were not significantly different( P = 0. 770). The codon usage pattern of PhcyN PV changed in a small range when adapted to new host Philosamia cynthia ricini,hence it is impossible to explain the cross-infectivity mechanism through analysis of codon usage pattern.
引文
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[19]SHACKELTON L A,PARRISH C R,HOLMES E C.Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses[J].J Mol Evol,2006,62(5):551-563
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[21]石生林,李苗苗,姜义仁,等.5种家蚕病毒的密码子及密码对使用模式分析[J].蚕业科学,2012,38(2):273-280
[22]ARAGAO-SILVA C W,ANDRADE M S,ARDISSON-ARAUJO D M,et al.The complete genome of a baculovirus isolated from an insect of medical interest:Lonomia obliqua(Lepidoptera:Saturniidae)[J/OL].Sci Rep,2016,6:23127[2016-09-09].http://www.nature.com/srep/2016/160610/srep23127/pdf/srep23127.pdf.DOI:10.1038/srep23127
[23]WANG J,ZHU Z,ZHANG L,et al.Genome sequencing and analysis of Catopsilia pomona nucleopolyhedrovirus:a distinct species in groupⅠAlphabaculovirus[J/OL].PLOS ONE,2016,11(5):e0155134[2016-09-09].http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155134.DOI:10.1371/journal.pone.0155134
[24]THIEM S M,CHENG X W.Baculovirus host-range[J].Virol Sin,2009,24(5):436-457
[25]李京生,杨瑞生,贾萍,等.柞蚕核型多角体病毒和家蚕核型多角体病毒的同义密码子使用模式分析[J].蚕业科学,2011,37(2):266-271
[2]石生林,王学英,刘限,等.柞蚕核型多角体病毒研究进展[J].沈阳农业大学学报,2003,34(1):72-74
[3]QIAN H,ZHANG Y,WU Y,et al.Analysis of the genomic sequence of Philosamia cynthia nucleopolyhedrin virus and comparison with Antheraea pernyi nucleopolyhedrin virus[J].BMC Genomics,2013,14(1):1-6
[4]陈言,张月华,李兵,等.蓖麻蚕核型多角体病毒解旋酶基因的克隆和序列分析[J].蚕业科学,2008,34(1):65-71
[5]BEHURA S K,SEVERSON D W.Codon usage bias:causative factors,quantification methods and genome-wide patterns:with emphasis on insect genomes[J].Biol Rev Camb Philos Soc,2013,88(1):49-61
[6]SHAH P,GILCHRIST M A.Explaining complex codon usage patterns with selection for translational efficiency,mutation bias,and genetic drift[J].Proc Natl Acad Sci USA,2011,108(25):10231-10236
[7]石生林,姜义仁,杨瑞生,等.昆虫质型多角体病毒同义密码子使用模式分析[J].应用昆虫学报,2013,50(4):1020-1029
[8]BAHIR I,FROMER M,PRAT Y,et al.Viral adaptation to host:a proteome-based analysis of codon usage and amino acid preferences[J/OL].Mol Syst Biol,2009,5:311[2016-09-09].http://msb.embopress.org/content/5/1/311.DOI:10.1038/msb.2009.71
[9]SHI S L,JIANG Y R,LIU Y Q,et al.Selective pressure dominates the synonymous codon usage in parvoviridae[J].Virus Genes,2013,46(1):10-19
[10]FAN Q,LI S,WANG L,et al.The genome sequence of the multinucleocapsid nucleopolyhedrovirus of the Chinese oak silkworm Antheraea pernyi[J].Virology,2007,366(2):304-315
[11]何强,刘绍伦,马振刚,等.柞蚕核型多角体病毒(Anpe NPV)三地理株的全基因组比较分析揭示其遗传多样性[J].昆虫学报,2015,58(5):535-545
[12]WRIGHT F.The‘effective number of codons’used in a gene[J].Gene,1990,87(1):23-29
[13]SHI S L,JIANG Y R,YANG R S,et al.Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak,selection dominated and exhibits no more similar patterns than expected[J].Infect Genet Evol,2016,44:412-417
[14]WARRICK H M,SPUDICH J A.Codon preference in Dictyostelium discoideum[J].Nucleic Acids Res,1988,16(14A):6617-6635
[15]吴宪明,吴松锋,任大明,等.密码子偏性的分析方法及相关研究进展[J].遗传,2007,29(4):420-426
[16]SUEOKA N.Directional mutation pressure and neutral molecular evolution[J].Proc Natl Acad Sci USA,1988,85(8):2653-2657
[17]SUEOKA N.Two aspects of DNA base composition:G+C content and translation-coupled deviation from intra-strand rule of A=T and G=C[J].J Mol Evol,1999,49(1):49-62
[18]SUZUKI H,BROWN C J,FORNEY L J,et al.Comparison of correspondence analysis methods for synonymous codon usage in bacteria[J].DNA Res,2008,15(6):357-365
[19]SHACKELTON L A,PARRISH C R,HOLMES E C.Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses[J].J Mol Evol,2006,62(5):551-563
[20]JIANG Y,DENG F,WANG H,et al.An extensive analysis on the global codon usage pattern of baculoviruses[J].Arch Virol,2008,153(12):2273-2282
[21]石生林,李苗苗,姜义仁,等.5种家蚕病毒的密码子及密码对使用模式分析[J].蚕业科学,2012,38(2):273-280
[22]ARAGAO-SILVA C W,ANDRADE M S,ARDISSON-ARAUJO D M,et al.The complete genome of a baculovirus isolated from an insect of medical interest:Lonomia obliqua(Lepidoptera:Saturniidae)[J/OL].Sci Rep,2016,6:23127[2016-09-09].http://www.nature.com/srep/2016/160610/srep23127/pdf/srep23127.pdf.DOI:10.1038/srep23127
[23]WANG J,ZHU Z,ZHANG L,et al.Genome sequencing and analysis of Catopsilia pomona nucleopolyhedrovirus:a distinct species in groupⅠAlphabaculovirus[J/OL].PLOS ONE,2016,11(5):e0155134[2016-09-09].http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155134.DOI:10.1371/journal.pone.0155134
[24]THIEM S M,CHENG X W.Baculovirus host-range[J].Virol Sin,2009,24(5):436-457
[25]李京生,杨瑞生,贾萍,等.柞蚕核型多角体病毒和家蚕核型多角体病毒的同义密码子使用模式分析[J].蚕业科学,2011,37(2):266-271