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

Abstract

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

CLC Number:

S813.3

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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Analysis of Codon Usage Bias of Toll-like Receptor 5 Gene in 15 Species

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