猪Claudin家族基因密码子使用偏好性分析

doi:10.3969/j.issn.1004-1524.2018.12.04

浙江农业学报 ›› 2018, Vol. 30 ›› Issue (12): 2007-2017.DOI: 10.3969/j.issn.1004-1524.2018.12.04

猪Claudin家族基因密码子使用偏好性分析

宗秋芳¹, 黄焱杰¹, 吴丽思¹, 吴圣龙^1,2, 包文斌^1,2,*

1.扬州大学江苏省动物遗传繁育与分子设计重点实验室,江苏扬州 225009;
2.扬州大学教育部农业与农产品安全国际合作联合实验室,江苏扬州 225009

收稿日期:2018-04-16 出版日期:2018-12-25 发布日期:2018-12-28
通讯作者: 包文斌,E-mail: wbbao@yzu.edu.cn
作者简介:宗秋芳(1994—),女,河南济源人,硕士研究生,研究方向为猪抗病育种。E-mail: zongqiufang@163.com
基金资助:
国家自然科学基金(31572360,31372285);江苏省农业三新工程(SXGC〔2017〕302);江苏高校优势学科建设工程(PAPD)

Analysis of genetic codon usage preference in pig Claudin family

ZONG Qiufang¹, HUANG Yanjie¹, WU Lisi¹, WU Shenglong^1,2, BAO Wenbin^1,2,*

1. Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China;
2. Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China

Received:2018-04-16 Online:2018-12-25 Published:2018-12-28

摘要/Abstract

摘要： 猪流行性腹泻病毒(PEDV)可通过感染猪肠道上皮细胞引起仔猪腹泻。紧密连接蛋白是肠道黏膜屏障的重要组成部分,而Claudin家族作为重要的紧密连接蛋白之一,是组成肠道黏膜屏障完整性、决定肠道通透性的重要蛋白分子。研究密码子的使用特性有助于进一步了解某一特定基因的分子机制和进化关系。为了揭示Claudin家族基因密码子使用模式,本研究对Claudin家族22个基因编码序列进行分析,利用CodonW和在线网站EMBOSS Explore计算核苷酸组成、相对同义密码子使用度(RSCU)和密码子使用偏性参数,同时分析了Claudin家族基因密码子使用偏好性的影响因素。结果表明:Claudin家族基因主要偏好以G/C结尾的密码子;RSCU值分析发现,11个密码子CUG、AUC、GUG、UCC、CCC、ACC、GCC、CAG、CGC、CGG、GGC偏好性较强,为优势密码子;聚类结果显示,Claudin-3和Claudin-4较为接近,Claudin-10和Claudin-11较为接近;此外,Claudin家族基因密码子偏好性主要受到突变压力影响。分析Claudin家族基因密码子使用模式,旨在揭示这些基因之间的遗传和进化关系,为今后从密码子优化途径提高外源基因的表达水平提供一定的理论依据。

关键词: Claudin家族, 密码子偏好性, 猪, 紧密连接蛋白

Abstract: Porcine epidemic diarrhea virus (PEDV) can cause diarrhea in piglets by infecting pig intestinal epithelial cells. The tight junction protein is an important part of the intestinal mucosal barrier. As one of the important tight junction proteins, the Claudin family constitutes the integrity of the intestinal mucosal barrier and determines intestinal permeability. Studying the use of codons can help to further understand the molecular mechanisms and evolutionary relationships of a particular gene. In order to reveal the Claudin family gene codon usage patterns, we analyzed the coding sequences of 22 genes in Claudin family and calculated nucleotide composition, relative synonymous codon usage (RSCU) and the codon bias parameters by using CodonW and the online website EMBOSS Explore. At the same time, the influence factors of the codon usage preference of the Claudin family were analyzed. The results showed that Claudin family genes mainly prefer codons ending in G/C; RSCU value analysis showed that the 11 codons CUG, AUC, GUG, UCC, CCC, ACC, GCC, CAG, CGC, CGG, GGC had a strong preference and were dominant codons. The clustering results showed that Claudin-3 and Claudin-4 were closer, and Claudin-10 and Claudin-11 were closer. In addition, Claudin family gene codon bias was mainly affected by mutational pressure. This study analyzed the codon usage pattern of Claudin family genes, to reveal the genetic and evolutionary relationship between these genes, and provide some theoretical guidance for improving the expression level of foreign genes from the codon optimization approach in the future.

Key words: Claudin family, codon preference, pig, tight junction protein

中图分类号:

S828

宗秋芳, 黄焱杰, 吴丽思, 吴圣龙, 包文斌. 猪Claudin家族基因密码子使用偏好性分析[J]. 浙江农业学报, 2018, 30(12): 2007-2017.

ZONG Qiufang, HUANG Yanjie, WU Lisi, WU Shenglong, BAO Wenbin. Analysis of genetic codon usage preference in pig Claudin family[J]. , 2018, 30(12): 2007-2017.

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猪Claudin家族基因密码子使用偏好性分析

Analysis of genetic codon usage preference in pig Claudin family

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