猪伪狂犬病病毒gE基因遗传变异及密码子使用偏好性分析

doi:10.16431/j.cnki.1671-7236.2025.07.027

中国畜牧兽医 ›› 2025, Vol. 52 ›› Issue (7): 3264-3275.doi: 10.16431/j.cnki.1671-7236.2025.07.027

猪伪狂犬病病毒gE基因遗传变异及密码子使用偏好性分析

陈志安^1,2,3, 章蓓雯^1,2,3, 何敏嘉^1,2,3, 陈美椿¹, 翁成桢^1,2,3, 黄欣欣^1,2,3, 李鸿喜^1,2,3, 曾仲文⁴, 陈宝良⁵, 邱龙新^1,2, 陈洪博^1,2, 李晓冰^1,2

1. 龙岩学院生命科学学院, 龙岩 364000;
2. 福建省预防兽医学与兽医生物技术重点实验室, 龙岩 364000;
3. 福建农林大学动物科学学院, 福州 350002;
4. 漳州大北农农牧科技有限公司, 漳州 363000;
5. 厦门辅农钧通管理咨询服务有限公司, 厦门 361024

收稿日期:2024-11-17 出版日期:2025-07-05 发布日期:2025-07-01
通讯作者: 陈洪博, 李晓冰 E-mail:lyxy_vet@163.com;924464270@qq.com
作者简介:陈志安，E-mail：3141079340@qq.com；章蓓雯，E-mail：1092796034@qq.com。
基金资助:
福建省自然科学基金(2024J01863)；福建省中青年教师教育科研重点项目(JZ230057)

Genetic Variation and Codon Usage Bias Analysis of Porcine Pseudorabies Virus gE Gene

CHEN Zhian^1,2,3, ZHANG Beiwen^1,2,3, HE Minjia^1,2,3, CHEN Meichun¹, WENG Chengzhen^1,2,3, HUANG Xinxin^1,2,3, LI Hongxi^1,2,3, ZENG Zhongwen⁴, CHEN Baoliang⁵, QIU Longxin^1,2, CHEN Hongbo^1,2, LI Xiaobing^1,2

1. School of Life Sciences, Longyan University, Longyan 364000, China;
2. Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Veterinary Biotechnology, Longyan 364000, China;
3. College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
4. Zhangzhou Dabei Agriculture and Animal Husbandry Technology Co., Ltd., Zhangzhou 363000, China;
5. Xiamen Funong Juntong Management Consulting Service Co., Ltd., Xiamen 361024, China

Received:2024-11-17 Online:2025-07-05 Published:2025-07-01

摘要/Abstract

摘要： 【目的】了解国内猪伪狂犬病病毒(Porcine pseudorabies virus，PRV)的流行现状、流行毒株的遗传情况以及PRV gE基因的密码子使用偏好性和影响因素。【方法】本研究针对2019—2023年中国分离到的106条PRV gE基因序列，利用Mega 7.0软件构建系统发育树，通过Launch DnaSP 6.0软件进行基因选择压力和基因流分析，采用CodonW 1.4.2和SPSS 27.0.1软件进行密码子分析。【结果】遗传进化分析结果表明，国内流行的PRV毒株为基因Ⅱ型，可进一步分为基因型2.1和基因型2.2。基因流分析显示，基因Ⅱ型中基因型2.1和2.2核苷酸多样性(Pi)分别为0.006和0.002；种群间遗传分化系数(Fst)为0.381，同义替换率(Ks)和基因流量化指标(Z)分别为1.353和6.637。基因选择压力分析显示，基因Ⅱ型中基因型2.1和2.2的非同义突变与同义突变比值(dN/dS)分别为1.808和1.362。密码子碱基分析结果表明，基因Ⅱ型的2个亚型中，GC3含量均>50%，基因型2.1和2.2的不同基因编码区有效密码子数(ENC)值分别为30.04和30.06。密码子使用偏好性分析显示，基因型2.1和2.2的相关系数分别为0.115和0.173。相对同义密码子使用度(RSCU)分析显示，基因型2.1和2.2中高表达的密码子第3位均为G/C碱基，低表达的密码子第3位主要为A/U碱基；共25个密码子的RSCU＞1，为优先使用密码子，其中13个具有高GC含量，16个以碱基C结尾。【结论】国内PRV流行株以基因Ⅱ型为主，其具有独特的碱基组成，GC含量较高、AU含量相对较低，表现出较低的偏好性，密码子使用受突变压力与自然选择的双重作用，其中自然选择起主导性作用。研究结果为国内猪伪狂犬病的流行趋势研判及防控策略制定提供了科学依据与技术支撑。

关键词: 猪伪狂犬病病毒(PRV); gE基因; 遗传多样性; 密码子; 偏好性

Abstract: 【Objective】 The purpose of this experiment was to understand the current epidemic status of Porcine pseudorabies virus (PRV) in China,the genetic status of the epidemic strain,the codon usage bias of PRV gE gene and the influencing factors. 【Method】 In this study,a phylogenetic tree was constructed using Mega 7.0 software for 106 PRV gE gene sequences isolated in China from 2019 to 2023.Launch DnaSP 6.0 software was used for gene selection pressure analysis and gene flow analysis.CodonW 1.4.2 and SPSS 27.0.1 software were used for codon analysis. 【Result】 The results of genetic evolution analysis showed that the PRV strains prevalent in China were genotype Ⅱ,which could be further divided into genotypes 2.1 and 2.2.Gene flow analysis showed that the nucleotide diversity (Pi) of genotypes 2.1 and 2.2 in genotype Ⅱ was 0.006 and 0.002,respectively.The coefficient of genetic differentiation (Fst) was 0.381,the synonymous substitution rate (Ks) and the quantitative index of gene flow (Z) were 1.353 and 6.637,respectively.Gene selection pressure analysis showed that the non-synonymous mutation to synonymous mutation ratio (dN/dS) of genotypes 2.1 and 2.2 was 1.808 and 1.362,respectively.The results of codon base analysis showed that the content of GC3 was more than 50% in the two subtypes of genotype Ⅱ,and the ENC values of different gene coding regions of genotypes 2.1 and 2.2 was 30.04 and 30.06,respectively.Codon usage bias analysis showed that the correlation coefficients of genotypes 2.1 and 2.2 was 0.115 and 0.173,respectively.Relative synonymous codon usage (RSCU) analysis showed that the third codon of high expression in genotypes 2.1 and 2.2 was G/C base,and the third codon of low expression was mainly A/U base.A total of 25 codons with RSCU ＞1 were used as preferred codons,of which 13 had high GC content and 16 ended with base C. 【Conclusion】 Genotype Ⅱ was the dominant PRV strain in China,which had a unique base composition,high GC content and relatively low AU content,showing a low preference.Codon usage was influenced by both mutation pressure and natural selection,in which natural selection played a dominant role.The results of this study provided scientific basis and technical support for the study of the epidemic trend of porcine pseudorabies in China and the formulation of prevention and control strategies.

Key words: Porcine pseudorabies virus (PRV); gE gene; genetic diversity; codon; bias

中图分类号:

S852.65^＋9.1

陈志安, 章蓓雯, 何敏嘉, 陈美椿, 翁成桢, 黄欣欣, 李鸿喜, 曾仲文, 陈宝良, 邱龙新, 陈洪博, 李晓冰. 猪伪狂犬病病毒gE基因遗传变异及密码子使用偏好性分析[J]. 中国畜牧兽医, 2025, 52(7): 3264-3275.

CHEN Zhian, ZHANG Beiwen, HE Minjia, CHEN Meichun, WENG Chengzhen, HUANG Xinxin, LI Hongxi, ZENG Zhongwen, CHEN Baoliang, QIU Longxin, CHEN Hongbo, LI Xiaobing. Genetic Variation and Codon Usage Bias Analysis of Porcine Pseudorabies Virus gE Gene[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(7): 3264-3275.

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猪伪狂犬病病毒gE基因遗传变异及密码子使用偏好性分析

Genetic Variation and Codon Usage Bias Analysis of Porcine Pseudorabies Virus gE Gene

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