摘要
本研究以猪苓转录组数据(SRP058382)为基础,利用BLASTx和ESTScan对猪苓的CDS进行预测,共筛选出332条unigenes,再利用CodonW分析这些基因密码子使用偏向性。结果显示,猪苓基因密码子GC含量范围在44.51%~64.6%,平均含量为53.57%, GC3平均含量为57.98%,说明猪苓基因偏向使用以G或C结尾的密码子;ENC值在38.46到61之间,说明其密码子偏向性较弱;中性绘图分析及ENC-plot曲线分析显示,猪苓基因GC12与GC3的回归系数为0.075,说明GC12和GC3的相关性微弱,并且大部分基因ENC值偏离了理论值。这些分析表明在猪苓基因的密码子使用偏向性的形成过程中,突变和选择压力等诸多因素都发挥着重要作用。通过高表达优越密码子分析确定了猪苓基因中22个最优密码子,多以G或C结尾。研究结果为猪苓的转基因研究中载体的选择及分子进化研究提供理论依据。
We obtained 332 coding sequences from the Polyporus umbellatus transcriptome based on the BLASTx and ESTScan analyses. The codon usage patterns of P. umbellatus were calculated and statistically analyzed using CodonW. The results showed that the average GC content of genes was 53.57% and the average GC3 content was 57.98%, suggesting that genes favored codons ending with G or C. The effective number of codons(ENC) value range from 38.46 to 61, which indicates that these genes have low codon usage bias. The neutrality plot and ENC-plot analysis revealed that many factors such as mutation and selective pressure play an important role in shaping codon usage bias in P. umbellatus genes. Twenty-two optimal codons were identified as being biased toward codons ending with G or C using the high expression superior codon analysis method. This study will lay a foundation for future research on genetic engineering and molecular evolution in P. umbellatus.
作者
刘蒙蒙
邢咏梅
郭顺星
LIU Meng-meng;XING Yong-mei;GUO Shun-xing(Institute of Medicinal Plant Development,Chinese Academy of Medical Sciences and Peking Union Medical College,Beijing 100193,China;College of Traditional Chinese Medicine,Hebei University,Baoding 071002,China;Institute of Bioinformatics and Medical Engineering,School of Electrical and Information Engineering,Jiangsu University of Technology,Changzhou 213001,China)
出处
《药学学报》
CAS
CSCD
北大核心
2020年第5期1050-1055,共6页
Acta Pharmaceutica Sinica
基金
国家自然科学基金资助项目(81773843,81973425)
河北省教育厅基金资助项目(QN2018128)
北京协和医学院学科建设项目(201920100901).
关键词
猪苓
转录组
密码子偏向性
最优密码子
Polyporus umbellatus
transcriptome
codon usage bias
preferred codon
