猪蛋白质二硫化物异构酶A4基因克隆及密码子偏好性分析

doi:10.16431/j.cnki.1671-7236.2019.04.014

Abstract

Abstract:

The objective of the study was to explore the codon usage feature of protein disulfide isomerase A4 (PDIA4) gene in pig,the codon usage differences and evolutionary relationship between pig and other reference species.In this research,the coding region of the PDIA4 gene was amplified by RT-PCR using the uterus of pig as experimental material.The PDIA4 gene sequences of 18 species were downloaded as conferences from NCBI database.At the same time,the differences of codon usage bias between pig and four different kinds of model organisms were compared.The results showed that the complete coding region of PDIA4 gene of pig was 1 941 bp in length,which coded 646 amino acid residues.The results of molecular identification showed that the identity between PDIA4 gene cloned in this study with the known sequences of Sus scrofa in NCBI database (GenBank accession No.:NM_001267834.1) was 99%.The PDIA4 in pig preferred to use G-or C-ending codons and had 27 preferred codons (RSCU>1).Moreover,the three codons with the highest frequency were CTG (RSCU=3.69),GCC (RSCU=2.31) and CGC (RSCU=2.29),respectively.Comparing the codon usage feature of the PDIA4 gene among 19 species,there were significant differences in the related data and most of them tended to use G/C-ending codons.These related data included the effective number of codons (ENc),codon adaptation index (CAI),GC contents,contents of T,C,A,G and GC on the 3rd site (T3s,C3s,A3s,G3s and GC3s).Although there were differences between cluster analysis based on the relative synonymous codon usage and the results of phylogeny derived from coding region,and the molecular phylogenetic tree rooted in the PDIA4 CDS region was more consistent with the true classification system of the 19 species.The differences in codon usage frequency between pig PDIA4 gene and genome of Mus musculus were less than those in other three kinds model organisms' genome.Mus musculus might be the best receptors for genetic transformation and heterologous expression of PDIA4 gene in pig.

Key words: pig; PDIA4 gene; cloning; condon usage bias

CLC Number:

Q755

ZHANG Xiaodan, NIU Xi, XU Yao, RUAN Yiqi, LI Dapeng, RAN Xueqin, WANG Jiafu, WU Juan, YANG Jing, TIAN Lan, LONG Yanxia. Cloning and Codon-preference Analysis of Protein Disulfide Isomerase A4 Gene in Pig[J]. , 2019, 46(4): 1074-1085.

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Cloning and Codon-preference Analysis of Protein Disulfide Isomerase A4 Gene in Pig

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