Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library

• Published in: PloS one 2016-10, Vol.11 (10), p.e0163295
• Main Authors: Zhou, Qiongqiong, Sun, Wenjuan, Liu, Xiyan, Wang, Xiliang, Xiao, Yuncai, Bi, Dingren, Yin, Jingdong, Shi, Deshi
• Format: Article
• Language: English
• Subjects: Agriculture; Amplification; Analysis; Animal genetic engineering; Animal sciences; Animals; Artificial chromosomes; Bacterial artificial chromosomes; Bioinformatics; Biology and Life Sciences; Carboxylesterase; Carboxylesterase - genetics; Carboxylesterase - isolation & purification; Chromosomes, Artificial, Bacterial - genetics; Cloning; Cloning, Molecular; Complement component C4; Esterase; Exons; Exons - genetics; Gene expression; Gene sequencing; Genes; Genetic structure; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Homology; Hydrolases; Introns; Introns - genetics; Laboratories; Liver; Liver - enzymology; Medical screening; Metabolism; Molecular Sequence Annotation; Multigene Family; Physiology; Pichia pastoris; Ple gene; Polymerase chain reaction; Primers; Regulatory mechanisms (biology); Regulatory sequences; Regulatory Sequences, Nucleic Acid - genetics; Research and Analysis Methods; Sequence Analysis, DNA; Structure-function relationships; Sus scrofa - genetics; Veterinarians; Veterinary colleges; Veterinary medicine; Zoology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0163295

Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for investigation of the genetic structure, function, and regulatory mechanisms of the PLE gene family.