蒙古韭叶绿体基因组密码子使用偏好性分析

为分析蒙古韭叶绿体基因组密码子的使用模式,本研究通过高通量测序获得了蒙古韭叶绿体基因组序列,从中筛选出52条蛋白编码序列(codingsequence,CDS),利用CodonW 1.4.2和在线软件CUSP进行密码子使用模式及偏好性成因分析.结果显示,蒙古韭叶绿体基因组的有效密码子数(effective number...

Analysis of the Codon Usage Bias in the Chloroplast Genome of Allium mongolicum Regel

In order to analyze the codon usage bias in the chloroplast genome of Allium mongolicum Regel,the whole chloroplast genome sequence was obtained by high-throughput sequencing.And then we selected 52 protein coding sequence(CDS)for exploring the usage pattern of codon and the main factors affecting codon usage bias by using CodonW 1.4.2 and CUSP.The results showed:The effective number of codons(ENC)ranged from 36.94 to 52.61 in the chloroplast genome of A.mongolicum,indicating that the codon bias was weak;the average GC content in the third codon position(GC₃)was 27.63%,suggesting that the third positions for all codons prefers A and U,which was consistent with that of relative synonymous codon usage(RSCU)analysis.Correlation analysis showed significant positive correlation was found between ENC and GC₃,implying that the third base composition had a great influence on the codon bias.In addition,7 codons(UUG,GGA,CCA,UAU,AAU,CGA,UCA)were determined to be the optimal codons for the chloroplast genome of A.mongolicum.Neutrality plot,ENC-plot and PR2-plot analysis showed that codon preference might be determined by both mutation and selection,mainly due to the effect of selection.