基于转录组的大头金蝇密码子的偏好性分析
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摘要
使用Codon W软件分析大头金蝇[Chrysomya megacephala(Fabricius,1794)]转录组10 923条全长转录序列的密码子偏好性。结果表明,大头金蝇转录组中的AT含量(61.81%)远大于GC含量(38.19%);PR2(parity rule 2,即密码子偏好性)绘图结果显示,密码子第3位碱基A的使用频率大于碱基T,碱基G的使用频率大于碱基C;中性绘图结果显示,该序列密码子的使用更多地受到选择压力的影响;有效密码子数(effective number of codons,简称ENC)在25.17～61.00个之间,均值为43.16个;密码子适应指数(codon adaptation index,简称CAI)在0.099～0.554之间,均值为0.215 8。结果共筛选出29个同义密码子相对使用度(relative synonymous codon usage,简称RSCU)>1的密码子和28个最优密码子。
引文
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[2]Margulies M,Egholm M,Altman W E,et al.Genome sequencing in microfabricated high-density picolitre reactors[J].Nature,2005,437(757):376-380.
[3]张棋麟,袁明龙.基于新一代测序技术的昆虫转录组学研究进展[J].昆虫学报,2013,56(12):1489-1508.
[4]Olejniczak M,Uhlenbeck O C.tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition[J].Biochimie,2006,88(8):943-950.
[5]Campos J L,Zeng K,Parker D J,et al.Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster[J].Molecular Biology and Evolution,2013,30(4):811-823.
[6]时慧,王玉,杨路成,等.茶树抗寒调控转录因子ICE1密码子偏性分析[J].园艺学报,2012,39(7):1341-1352.
[7]Quax T E F,Claassens N J,S9ll D,et al.Codon bias as a means to fine-tune gene expression[J].Molecular Cell,2015,59(2):149-161.
[8]薛万琦,赵建铭.中国蝇类(下册)[M].沈阳:辽宁科学技术出版社,1998:1438-1452.
[9]Wright F.The‘effective number of codons’used in a gene[J].Gene,1990,87(1):23-29.
[10]Sharp P M,Li W H.The codon adaptation index-a measure of directional synonymous codon usage bias,and its potential applications[J].Nucleic Acids Research,1987,15(3):1281-1295.
[11]Bellgard M,Schibeci D,Trifonov E,et al.Early detection of G+Cdifferences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains[J].Journal of Molecular Evolution,2001,53(4/5):465-468.
[12]Sueoka N.Directional mutation pressure and neutral molecular evolution[J].Proceedings of the National Academy of Sciences of the United States of America,1988,85(8):2653-2657.
[13]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].Journal of Molecular Evolution,1999,49(1):49-62.
[14]Nie X J,Deng P C,Feng K W,et al.Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family[J].Plant Molecular Biology Reporter,2014,32(4):828-840.
[15]Comeron J M,AguadéM.An evaluation of measures of synonymous codon usage bias[J].Journal of Molecular Evolution,1998,47(3):268-274.
[16]Rai A,Yamazaki M,Takahashi H,et al.RNA-seq transcriptome analysis of Panax japonicus,and its comparison with other panax species to identify potential genes involved in the saponins biosynthesis[J].Frontiers in Plant Science,2016,7:481.