罗雪莲, 王海印, 叶长芸. 单增李斯特菌EGD-e基因组的密码子使用分析[J]. 疾病监测, 2011, 26(4): 290-294.
引用本文: 罗雪莲, 王海印, 叶长芸. 单增李斯特菌EGD-e基因组的密码子使用分析[J]. 疾病监测, 2011, 26(4): 290-294.
LUO Xue-lian, WANG Hai-yin, YE Chang-yun. Codon usage in genome of Listeria monocytogenes EGD-e[J]. Disease Surveillance, 2011, 26(4): 290-294.
Citation: LUO Xue-lian, WANG Hai-yin, YE Chang-yun. Codon usage in genome of Listeria monocytogenes EGD-e[J]. Disease Surveillance, 2011, 26(4): 290-294.

单增李斯特菌EGD-e基因组的密码子使用分析

Codon usage in genome of Listeria monocytogenes EGD-e

  • 摘要: 目的 以单增李斯特菌EGD-e为研究对象,分析其密码子使用模式及影响因素。 方法 利用Codon W在线工具分析单增李斯特菌EGD-e基因组的密码子使用情况;利用对应分析、ENC绘图(Nc-plot)等推测影响单增李斯特菌EGD-e密码子偏性的因素;利用高表达优越密码子分析法确定单增李斯特菌EGD-e基因组的主要偏爱密码子。 结果 单增李斯特菌EGD-e基因组中G+C含量仅为37%,偏爱使用以U或A结尾的密码子;对应分析显示第1条向量轴与G+C(R=-0.182, P0.01)、CAI(R=-0.740, P0.01)呈显著相关,且与后者的相关程度明显高于前者。 结论 单增李斯特菌EGD-e基因组的密码子使用具有一定的偏性;推测基因的表达水平是影响单增李斯特菌EGD-e基因组密码子使用的主要因素。同时,基因组密码子使用偏性还受到碱基组成的影响,而基因长度对密码子的使用偏性影响不大。最后确定了UUC、UUA等27个密码子为单增李斯特菌EGD-e的最优密码子。这些结果将为进一步研究单增李斯特菌的基因组学提供基础。

     

    Abstract: Objective To analyze the codon usage patterns and related factors by taking Listeria monocytogenes EGD-e as subject. Methods The codon usage patterns of Listeria monocytogenes was analyzed with EGD-e Online Codon W software; the factors in codon usage of Listeria monocytogenes EGD-e was presumed by using correspondence analysis and Nc-plot; the major preference codons in genome of Listeria monocytogenes EGD-e was defined by using high-expression codon. Results The GC content in the genome of Listeria monocytogenes EGD-e was only 37%, and the codon ended with U or A was used frequently; correspondence analysis showed that there was a significant correlation (R=-0.182, P0.01) between the gene position on the first axis and G+C content and a significant correlation (R=-0.740, P0.01) between the gene position on the first axis and CAI. Moreover, the correlation with the latter was significantly higher than the former. Conclusion The codon usage pattern in the genome of Listeria monocytogenes EGD-e had certain bias; the gene expression level of genes in Listeria monocytogenes EGD-e might be the main factor influencing codon usage bias. The codon usage bias was also affected by base composition, and gene length had little effect on codon usage bias. Finally, 27 codons were defined as the major preference codons in Listeria monocytogenes EGD-e, which provided a basis for genomics study of Listeria monocytogenes in the future.

     

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