Long-read RNA sequencing of Pacific abalone Haliotis discus hannai reveals innate immune system responses to environmental stress

Haliotis discus hannai is a commercially important mollusk species, and the abalone aquaculture sector has been jeopardized by deteriorating environmental circumstances such as bacterial infection and thermal stress during the hot summers. However, due to a paucity of genetic information, such as transcriptome resources, our understanding of their stress adaptation is restricted. In this research, using single-molecule long-read (SMRT) sequencing technology, a library composed of ten tissues (i.e., haemocytes, gills, muscle, hepatopancreas, digestive tract, mantle, mucous gland, ovary, testis and head) was constructed and sequenced. In all, 41,855 high-quality unique transcripts, among which 24,778 were successfully annotated. Additionally, 13,463 SSRs, 1,169 transcription factors, and 18,124 lncRNAs were identified in H. discus hannai transcriptome. Furthermore, multiple immune-related transcripts were identified according to KEGG annotation, and a portion of these transcripts were mapped into several classical immune-related pathways, including the PI3K-AKT signaling pathway and Toll-like receptor signaling pathway. Additionally, 24 typical sequences related to the immunity pathway were detected by RT-PCR; the results showed that most of the immune-related genes showed significantly high expression at 72 h after bacterial challenges and thermal stress, especially the expression level of genes in gills was significantly higher than that in haemocytes under V. parahaemolyticus stress at 24 h. At the same time. The analysis of alternative splicing identified several innate immunity-related functions genes, including CD109 and caspase 2. These results suggest that the complex immune system, particularly the powerful innate immunity system, was crucial for H. discus hannai response to numerous environmental challenges.