Aerial exposure and seawater immersion induce distinct transcriptomic responses of the marine pulmonate gastropod, Siphonaria japonica (Donovan, 1824), as determined by Iso-seq and RNA-seq analysis.

Siphonariid limpets are a group of intertidal pulmonate snails that have undergone aquatic-terrestrial evolution followed by secondary recolonization of the marine environment. To elucidate the responses of Siphonaria japonica to extended aerial exposure and seawater immersion, we conducted comparative transcriptome analysis of three tissues (foot, gill, and mantle) using both next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq) methods. For Iso-seq, 448,457 reads representing a total length of 14,622,086 bp were obtained, which were assembled into 8072 unigenes. For RNA-seq, 867,101,624 clean reads were obtained with a total length of 130,390,993,290 bp. The Iso-seq and RNA-seq data were integrated to construct a comprehensive gene annotation across three tissues. Results showed that gill displayed the most extensive response with 252 differentially expressed genes (DEGs), whereas mantle exhibited the least with 121 DEGs. Gene Ontology enrichment analysis showed that the gill, mantle, and foot exhibited distinct gene regulatory profiles. The gill was involved in osmoregulatory and cell adhesion pathways, the mantle was implicated in metabolic processes, whereas in the foot transcripts associated with pathways related to epidermal cell differentiation, as well as serine-type endopeptidase inhibitor activity were prominent. Collectively, these findings suggest that S. japonica mounted a coordinated multi-tissue response, integrating metabolic modulation, osmoregulatory fine-tuning, and structural remodeling to optimize energy allocation under aquatic and terrestrial conditions.