Identification and Analysis of Alternative Splicing Events in <italic>Sus Scrofa</italic> Using RNA-Seq Data

Abstract

Alternative splicing has been widely found in the eukaryotic gene transcription and serves as an important mechanism to enrich the genomic and proteomic diversity. In the current study, we sequenced the transcriptomic profiling of pig testes at four representative stages: 60 dpc (days post coitus, E60), 90 dpc (E90), 30-day-old (D30) and 180-day-old (DM) using Illumina Hiseq 2500 technology. Then, RNA-seq data were further used to identify the alternative splicing events referring the Sus Scrofa genome. The results showed that 92738 alternative splicing events were observed from Sus Scrofa genome corresponding to 20398 genes (80.6%). Alternative 5 first exon (TSS), alternative 3 last exon (TTS), skipped exon (SKIP) and alternative exon ends (AE) were the highest frequency events with 41.0%, 32.9%, 7.6% and 7.4% of total alternative splicing events, respectively. GO enrichment analysis showed that the alternative splicing genes were mainly enriched in metabolic process, molecular binding and enzyme activity. The alternative splicing events in different developmental stage seemed to preferentially occur in genes with physiological state. Genes in E60 were associated with enzyme activity and tissue formation. Genes in D30 were connected in response to environmental stress and ion channel activity. The genes of DM were involved in circulatory system. In addition, 64 testosterone related genes were selected and 63 genes of them were detected alternative splicing events. Alternative 5 first exon (TSS) and alternative 3 last exon (TTS) were the most frequency events, which revealed that these two alternative splicing events had a crucial role in the metabolic process of testosterone. Through the genome-wide analysis of alternative splicing in Sus scrofa , our results will provide insight into further research on the biological function and the molecular breeding in pigs.