15个物种Toll样受体5基因密码子使用偏好性分析

doi:10.16431/j.cnki.1671-7236.2024.01.002

摘要/Abstract

摘要： 【目的】探究Toll样受体5（TLR5）基因的密码子使用模式，并分析TLR5基因密码子使用偏好性的影响因素。【方法】综合运用CodonW、BioEdit和R等软件对筛选的15个不同物种TLR5基因完整编码区（CDS）序列核苷酸组成和密码子使用模式进行计算和统计，再基于同义密码子相对使用度（RSCU）和CDS分别进行聚类分析，推测TLR5基因发挥相似生物学功能的物种，并通过ENC-plot、Neutrality-plot和PR2-plot 3种绘图分析造成密码子偏好性现象的可能因素。【结果】9个物种TLR5基因CDS密码子第3位碱基GC含量（GC3）>0.5，14个物种有效密码子数（ENC）值>35，15个物种密码子AU偏斜度（AU skew）和GC偏斜度（GC skew）值<0；不同物种TLR5基因CDS有31个高频密码子，其中21个以G或C结尾，此外GCC、AGA、AGG和CUG表现为较高的RSCU值，为优势密码子；RSCU层次聚类和系统发育聚类结果不完全相同，但两种聚类方法均提示猪、牛和羊TLR5基因的密码子使用特点相似，鸡和绿头鸭相似，虹鳟和鲫鱼相似；ENC-plot分析发现各物种TLR5基因均分布在标准曲线下方较远位置，Neutrality-plot显示密码子第1、2位GC含量的平均值（GC12）和GC3含量呈极显著正相关（P<0.01），PR2-plot则显示密码子第3位碱基使用频率不一致。【结论】不同物种TLR5基因密码子使用模式存在偏好性现象，该现象是物种进化过程中受碱基突变和翻译选择双重影响的结果，其中碱基突变是主要影响因素。研究结果可为后续TLR5基因的生物学功能挖掘提供新的角度和理论认识。

关键词: TLR5基因; 密码子使用偏好性; 碱基突变; 翻译选择

Abstract: 【Objective】 The codon usage pattern of Toll-like receptor 5 (TLR5) gene was intestigated, and the influencing factors of codon usage bias was analyzed.【Method】 The nucleotide composition and codon usage pattern of TLR5 gene complete coding (CDS) sequence in 15 different species were calculated and statistically analyzed by softwares such as CodonW, BioEdit and R, and then cluster analysis was conducted to infer species with similar biological functions of TLR5 gene based on relative synonymous codon usage (RSCU) and CDS, respectively.The possible factors responsible for the codon bias were analyzed by ENC-plot, Neutrality-plot and PR2-plot.【Result】 The GC content at the third base (GC3) of TLR5 gene CDS in 9 species was greater than 0.5, there were 14 species had the effective number of codon (ENC) values greater than 35, the AU skew (AU skew) and GC skew (GC skew) values of codons in 15 species were less than 0.The CDS of the TLR5 gene in different species had 31 high-frequency codons, of which 21 end in G or C.All of these species had four optimal codons, whose biased strongly codons were GCC, AGA, AGG and CUG.The results of RSCU hierarchical and phylogenetic clustering results were not exactly the same, but both two clustering methods suggested a similar pattern of codon usage of TLR5 gene in Sus scrofa, Capra hircus and Bubalus bubalis, with similar patterns in Gallus gallus and Anas platyrhynchos, Oncorhynchus mykiss and Carassius auratus.ENC-plot analysis found that TLR5 gene of all species were distributed far below the standard curve, and Neutrality plot showed a significant positive correlation between the average values of the first and second base (GC12) and GC3 (P<0.01), while PR2-plot showed an inconsistency usage of the third codon base.【Conclusion】 There was a bias in the codon usage pattern of TLR5 gene in different species, which was influenced by both base mutation and translational selection, of which base mutation was the main influencing factor.The findings would provide a new perspective and theoretical understanding for the subsequent biological function mining of TLR5 gene.

Key words: TLR5 gene; codon usage bias; base mutation; translational selection

中图分类号:

S813.3

戴开宇, 杨治风, 郭烨星. 15个物种Toll样受体5基因密码子使用偏好性分析[J]. 中国畜牧兽医, 2024, 51(1): 11-22.

DAI Kaiyu, YANG Zhifeng, GUO Yexing. Analysis of Codon Usage Bias of Toll-like Receptor 5 Gene in 15 Species[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(1): 11-22.

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