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

中国畜牧兽医 ›› 2023, Vol. 50 ›› Issue (6): 2403-2413.doi: 10.16431/j.cnki.1671-7236.2023.06.025

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

孙守湖¹, 陈志飞^1,2, 郭智轩¹, 俞婷², 王修武¹, 李松倍¹, 魏文康², 贺东生^1,3

1. 华南农业大学兽医学院, 广东省动物源性人兽共患病预防与控制重点实验室, 广州 510642;
2. 广东省农业科学院农业生物基因研究中心, 广州 510640;
3. 岭南现代农业科学技术广东省实验室肇庆分中心, 肇庆 526238

收稿日期:2022-10-28 出版日期:2023-06-05 发布日期:2023-05-30
通讯作者: 魏文康, 贺东生 E-mail:3793433@qq.com;dhe@scau.edu.cn
作者简介:孙守湖,E-mail:13852134495@163.com;陈志飞,E-mail:3192682279@qq.com。
基金资助:
广东省科技计划（P20211154-0302）；广东省自然科学基金（2021A1515011072）；广东省农业科学院项目（202131TD）；广东省现代农业产业技术体系专项（2019KJ119）

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

SUN Shouhu¹, CHEN Zhifei^1,2, GUO Zhixuan¹, YU Ting², WANG Xiuwu¹, LI Songbei¹, WEI Wenkang², HE Dongsheng^1,3

1. Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agriculture University, Guangzhou 510642, China;
2. Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
3. Lingnan Modern Agricultural Science and Technology Guangdong Laboratory Zhaoqing Branch, Zhaoqing 526238, China

Received:2022-10-28 Online:2023-06-05 Published:2023-05-30

摘要/Abstract

摘要： 【目的】研究猪流行性腹泻病毒（PEDV）、猪传染性胃肠炎病毒（TGEV）、猪丁型冠状病毒（PDCoV）的N基因密码子偏好性差异及其影响因素。【方法】从GenBank数据库中下载上述3种猪冠状病毒（PoCoV）的全基因组序列，通过EMBOSS explorer、CALcal、DAMBE及CodonW等网站及软件计算有效密码子数（ENC）、相对同义密码子使用度（RSCU）等参数并进行ENC绘图、奇偶偏好性和中性绘图分析等。【结果】3种猪冠状病毒的N基因序列的ENC分布在48.99~54.96，其中PEDV、TGEV和PDCoV的ENC分别为53.74±0.61、50.09±0.88和0.72±0.65；RSCU分析显示，3种猪冠状病毒N基因偏好的密码子各不相同，但一般都偏好以U结尾；ENC绘图分析显示，3种猪冠状病毒的N基因数值点均位于标准曲线下方位置；奇偶偏好性分析显示全部散点位于y=0.5以下，且矢量向左下侧偏倚；中性绘图分析显示，3种病毒N基因绘图分析中回归曲线的斜率均接近0。3种猪冠状病毒的S和N基因在牛、猪、犬、人、鸡中的CAI值逐渐增高，RCDI值逐渐降低并接近于1。【结论】PEDV、TGEV、PDCoV的N基因密码子偏好性存在差异且密码子偏好性均较弱，3种猪冠状病毒的N基因表现为"CpG二核苷酸缺失"；自然选择作用是这3种猪冠状病毒N基因密码子偏好性形成的主要进化压力；人、猪、鸡3种宿主均适合3种猪冠状病毒的N基因表达，且PDCoV的S和N基因均更适合在鸡中表达。

关键词: 猪流行性腹泻病毒; 猪传染性胃肠炎病毒; 猪丁型冠状病毒; N基因; 密码子偏好性

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

中图分类号:

S852.65⁺9.6

孙守湖, 陈志飞, 郭智轩, 俞婷, 王修武, 李松倍, 魏文康, 贺东生. 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[J]. 中国畜牧兽医, 2023, 50(6): 2403-2413.

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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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

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

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