Analysis of genetic codon usage preference in pig Claudin family

doi:10.3969/j.issn.1004-1524.2018.12.04

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

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S828

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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Analysis of genetic codon usage preference in pig Claudin family

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