›› 2019, Vol. 46 ›› Issue (5): 1263-1272.doi: 10.16431/j.cnki.1671-7236.2019.05.002

• Biotechnology • Previous Articles     Next Articles

Cloning and Bioinformatics Analysis of SPDEF Gene in Saba Pigs

YUAN Hemei1, LI Mingli1, MA Li2, LAN Guoxiang1, CUI Yijia1, ZHOU Xiaoxia1, ZENG Weizhi1, YAN Dawei1, LU Shaoxiong1, DONG Xinxing1   

  1. 1. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
    2. Yunnan Vocational and Technical College of Agricultural, Kunming 650212, China
  • Received:2018-11-05 Online:2019-05-20 Published:2019-05-20

Abstract:

In order to identify the genetic characteristics of the SPDEF gene,the CDS of different pig breeds were amplified,sequenced,spliced,and the CDS of Saba pigs were analyzed by bioinformatics.The exon sequence of pigs were detected by direct sequencing after PCR,and sequence splicing were performed using SeqMan.The open reading frame (ORF) of SPDEF gene,and basic physicochemical properties,hydrophobicity,signal peptide,transmembrane region,subcellular localization,phosphorylation site,glycosylation site,secondary structure,tertiary structure,functional domain of SPDEF protein were predicted,and phylogenetic tree was constructed using bioinformatics software.The results showed that only 2 synonymous SNPs were detected in exon 1 (C13971T) and exon 2 (C16541T) of SPDEF gene in different pigs,respectively,indicating that the coding region of SPDEF gene was highly conserved among the tested herds.SPDEF gene had a complete ORF at length of 1 092 bp.The Ser content was the highest,which accounted for 10.7%.SPDEF was an unstable hydrophilic protein with an estimated half-life of 30 h in vitro.The SPDEF protein has no signal peptide and transmembrane structure,and had 39 potential phosphorylation sites and 1 glycosylation site.The protein located the cytoplasm in analysis of subcellular localization.In the secondary structure prediction,the amino acids involved in the random coil were the most,accounting for 55.10%,followed by the α-helix region,accounting for 28.37%.Functional domain predictions revealed the existence of an ETS functional domain and an SAM-PNT functional domain.Sequence homology analysis showed that pig has higher homology with Bos taurus,Ovis aries and Capra hircus.This study could provide references for further analysis of the function of SPDEF gene in Saba pigs.

Key words: Saba pigs; SPDEF gene; cloning; bioinformatics analysis

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