3种猪冠状病毒N基因密码子偏好性及宿主适应机制研究

doi:10.16431/j.cnki.1671-7236.2023.06.025

Abstract

Abstract: 【Objective】 The purpose of this study was to study the differences and influencing factors of N gene codon usage bias of Porcine epidemic diarrhea virus (PEDV), Porcine transmissible gastroenteritis virus (TGEV) and Porcine deltacoronavirus (PDCoV).【Method】 The whole genome sequences of the above three PoCoVs were downloaded from GenBank database.The effective codon number (ENC) and relative synonymous codon usage (RSCU) were calculated through websites and software such as EMBOSS explorer, CALcal, DAMBE and CodonW, and the ENC mapping analysis, parity preference analysis and neutral mapping analysis were performed.【Result】 The ENC of N gene sequences of the three PoCoVs ranged from 48.99 to 54.96.The ENC of PEDV, TGEV and PDCoV were 53.74±0.61, 50.09±0.88 and 50.72±0.65, respectively.RSCU analysis showed that the codons of N gene of the three PoCoVs were different, but they generally preferred to end with U.ENC mapping analysis showed that the N gene values of the three PoCoVs were below the standard curve.The parity bias analysis showed that all scatter points were below y=0.5, and the vector was biased to the lower left.Neutral mapping analysis showed that the slope of regression curves in N gene mapping analysis of the PoCoVs was close to 0.The CAI values of S and N genes of the three PoCoVs in Bos taurus, Sus scrofa, Canis lupus familiaris, Homo sapiens and Gallus gallus increased gradually, and the RCDI values decreased gradually and approached 1.【Conclusion】 The codon usage bias of N gene of PEDV, TGEV and PDCoV were different and weak.The N gene of three PoCoVs showed "CpG di-nucleotide deficiency".Natural selection was the main evolutionary pressure for the formation of codon preference for N genes in PEDV, TGEV and PDCoV.Homo sapiens, Sus scrofa and Gallus gallus were suitable to express the N gene of PEDV, TGEV and PDCoV, and the S and N genes of PDCoV were more easily expressed in Gallus gallus.

Key words: PEDV; TGEV; PDCoV; N gene; codon usage bias

CLC Number:

S852.65⁺9.6

SUN Shouhu, CHEN Zhifei, GUO Zhixuan, YU Ting, WANG Xiuwu, LI Songbei, WEI Wenkang, HE Dongsheng. Study on Codon Usage Bias of N gene of Three Porcine Coronaviruses and Their Host Adaptive Mechanism[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(6): 2403-2413.

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Study on Codon Usage Bias of N gene of Three Porcine Coronaviruses and Their Host Adaptive Mechanism

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