Abstract
Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples.
Highlights
Pigs (Sus scrofa) were domesticated in multiple geographic regions of Asia and Europe through artificial and natural selections about 10 000 years ago
The results revealed that chromosome 1 contains the coding genes for carbonic anhydrase (CA) IX and CA XII; chromosome 4 contains the coding genes for CA I–III, CA XIII, CAXIV and CA-related proteins (CARPs) VIII; chromosome 6 contains the coding genes for CA VA, CA VI, CA VII and CARP XI; chromosome 12 contains the coding genes for CA IV and CARP X and chromosome X contains the coding gene for CA VB
Scrofa predicted that CA I–III, CA VII, CA XIII and CARP VIII are cytoplasmic; CA VA and CA VB are mitochondrial; CA VI, CARP X and CARP XI are secretory; CA IX, CA XII, and CA XIV are transmembrane and CA IV is membrane-bound (Table 1)
Summary
Pigs (Sus scrofa) were domesticated in multiple geographic regions of Asia and Europe through artificial and natural selections about 10 000 years ago. The whole genome sequences (WGS) of pig models and minipig varieties are important in biomedical studies, such as generation of porcine-induced pluripotent stem cells for the treatment of human diseases including diabetes and cancer as well as ophthalmic, neurodegenerative and cardiovascular diseases [4, 5]. Wuzhishan pig (WZSP) is a Chinese inbred miniature minipig, which is characterized by its small size, approximately weight of 30 kg, homozygosis, genetic stability and good predictability in in vivo studies [6]. WZSP was developed in the Institute of Animal Science of the Chinese Academy of Agriculture Science in 1987. The WGS of WZSP, completed by the researchers from Beijing Genomics Institute, provided pivotal data for the use of this minipig model in biological, medical and veterinary medicine studies
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