Reference-guided detection of the transcriptome reveals circular RNA-related competing endogenous RNA networks in response to three respiration pathogens in pig lungs

The porcine reproductive and respiratory syndrome virus (PRRSV), African swine fever virus (ASFV), and Mycoplasma hyopneumoniae (Mhp) have been found to injure pig lungs and lead to enormous economic losses in the global pig industry. Circular RNAs (circRNAs) play crucial roles in immune response and viral infection. However, the roles of circRNAs during the three pathogens infecting lungs remain largely unknown in pigs. In this study, we utilized RNA-seq reads from 91 datasets of pig lungs to reference-guided detection of transcriptome reconstruct circRNAs and further construct circRNA-related competing endogenous RNA (ceRNA) networks in pig lungs using bioinformatics approaches. Our results identified 72,203 known and 14,344 novel circRNAs and showed that 66, 67, and 197 circRNAs were differentially expressed when lungs were infected by PRRSV, ASFV, and Mhp, respectively. Most differentially expressed circRNAs were up- and down-regulated in response to specific pathogens among PRRSV, ASFV, and Mhp. The functional annotation showed that ceRNA networks of the circRNAs that were specifically up-regulated in response to Mhp and ASFV were significantly enriched in humoral immunity-related functions and reactive oxygen species-related signal pathways, respectively. The ceRNA networks of the circRNAs that were down-regulated in response to PRRSV were significantly enriched in the functions involved in the RNA splicing. Further analysis of down-regulated circRNAs revealed that circular ratios of circRNAs were broadly decreased after PRRSV infection, which might form feedback via the RNA splicing-related target genes. Our study provided a comprehensive circRNA catalog of circRNAs in pig lungs and might facilitate potential insights into understanding the infection mechanism of lung damage. Key points: 1. Our study provided a comprehensive circRNA catalog of circRNAs in pig lungs and revealed the differences of circRNAs in response to three major respiration pathogens. 2. The ceRNA networks of the circRNAs that were specifically up-regulated in response to Mhp and ASFV were significantly enriched in humoral immunity-related functions and reactive oxygen species-related signal pathways, respectively. 3. A broad decrease in the circular ratio of circRNA loci might be a key process during PRRSV infection. 4. Our data facilitated potential insights into understanding the mechanism of lung damage during the virus challenge.