De novo whole transcriptome sequencing reveals differentially expressed messenger RNA and MicroRNA in hepatopancreas of <i>Pandalus hypsinotus</i>

Pandalus hypsinotus (P. hypsinotus), also known as coonstripe shrimp, has high economic value and is widely distributed in Alaska, the Bering Sea and the East Sea of Korea. However, owing to the low catch rates and patchy spatial distribution, transcriptome-based studies on this species remain limited. Transcriptome analyses using PacBio Iso-Seq and Illumina RNA sequencing techniques were performed to establish a de novo unigene set of P. hypsinotus and identify differentially expressed genes (DEGs) in the hepatopancreas compared to the tail muscle. A search of all the unigenes against Gene Ontology (GO), KEGG, Pfam, BLASTN, and UniProt resulted in 46,703 annotated unigenes. A comparison of the sequences in the two tissue-derived libraries revealed 9,429 DEGs in the hepatopancreas. We also investigated the small RNAomes of P. hypsinotus using the Illumina small RNA sequencing technology. Because miRNAs are highly sensitive to stress responses and pathogen infections, they serve as effective indicators of the immune status, thereby acting as crucial tools for enhancing productivity and disease control in the aquaculture industry. The 130 identified microRNA (miRNA) candidates were classified into 32 orthologous and 98 novel miRNAs using BLASTN and miRBase. Through GO analysis and direct interactions between miRNAs and genes, the differentially expressed miRNAs (DEMs) and DEGs related to immune responses showed regulatory relationships based on their sequences. These findings provide a valuable resource for future studies on novel gene detection, gene mapping and biological pathways that may be regulated by miRNAs unique to P. hypsinotus.