Genome-level identification, gene expression, and comparative analysis of porcine [beta]-defensin genes

Beta-defensins ([beta]-defensins) are innate immune peptides with evolutionary conservation across a wide range of species and has been suggested to play important roles in innate immune reactions against pathogens. However, the complete [beta]-defensin repertoire in the pig has not been fully addressed. A BLAST analysis was performed against the available pig genomic sequence in the NCBI database to identify [beta]-defensin-related sequences using previously reported [beta]-defensin sequences of pigs, humans, and cattle. The porcine [beta]-defensin gene clusters were mapped to chromosomes 7, 14, 15 and 17. The gene expression analysis of 17 newly annotated porcine [beta]-defensin genes across 15 tissues using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) showed differences in their tissue distribution, with the kidney and testis having the largest pBD expression repertoire. We also analyzed single nucleotide polymorphisms (SNPs) in the mature peptide region of pBD genes from 35 pigs of 7 breeds. We found 8 cSNPs in 7 pBDs. We identified 29 porcine [beta]-defensin (pBD) gene-like sequences, including 17 unreported pBDs in the porcine genome. Comparative analysis of [beta]-defensin genes in the pig genome with those in human and cattle genomes showed structural conservation of [beta]-defensin syntenic regions among these species.