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Simple Summary: Sipunculus nudus is a species of significant economic importance because of its high nutritional and medicinal value. It is widely distributed along coastlines worldwide, particularly in China, where a comprehensive industry exists encompassing breeding, farming, processing, and sale. Traditionally, S. nudus is cultured on sandy beaches without the need for artificial diets. The organisms rely on nutrients from the surface sediment, including microalgae and other organic matter. These worms inhabit both the intertidal and subtidal zones, enduring varying immersion periods throughout their growth process. As a result, they are exposed to different abiotic factors, such as varying irradiation times, oxygen availability, and others. In our study, we investigated the transcriptomic response of S. nudus across high, middle, and low tidal flats. We analyzed and compared the differential gene expression and relevant metabolic pathways in S. nudus from different habitats. This analysis aimed to shed light on the molecular mechanisms underpinning physiological responses to diverse environments in burrowing species. Interestingly, we observed that the differential gene expression of S. nudus primarily involved metabolic pathways associated with disease and immune responses rather than thermal stress, calcification, and pH regulation. This finding highlights the close relationship between gene expression and S. nudus' unique living habits The peanut worm (Sipunculus nudus) is an important intertidal species worldwide. Species living in the same aquaculture area might suffer different environmental impacts. To increase knowledge of the molecular mechanisms underlying the response to environmental fluctuations, we performed a transcriptome analysis of S. nudus from different intertidal zones using a combination of the SMRT platform and the Illumina sequencing platform. (1) A total of 105,259 unigenes were assembled, and 23,063 unigenes were perfectly annotated. The results of the PacBio Iso-Seq and IIIumina RNA-Seq enriched the genetic database of S. nudus. (2) A total of 830 DEGs were detected in S. nudus from the different groups. In particular, 33 DEGs had differential expression in the top nine KEGG pathways related to pathogens, protein synthesis, and cellular immune response and signaling. The results indicate that S. nudus from different zones experience different environmental stresses. (3) Several DEGs (HSPA1, NFKBIA, eEF1A, etc.) in pathways related to pathogens (influenza A, legionellosis, measles, and toxoplasmosis) had higher expression in groups M and L. HSPA1 was clearly enriched in most of the pathways, followed by NFKBIA. The results show that the peanut worms from the M and L tidal flats might have suffered more severe environmental conditions. (4) Some DEGs (MKP, MRAS, and HSPB1) were upregulated in peanut worms from the H tidal flat, and these DEGs were mainly involved in the MAPK signaling pathway. These results indicate that the MAPK pathway may play a vital role in the immune response of the peanut worm to the effects of different intertidal flats. This study provides a valuable starting point for further studies to elucidate the molecular basis of the response to different environmental stresses in S. nudus. [ABSTRACT FROM AUTHOR]

Simple Summary: The interactions between parasitoids and their host have always attracted much attention, and parasitoids manipulate the host physiology to benefit the survival and development of their offspring. It is critical to analyze these physiological regulatory mechanisms. In this study, using RNA-sequencing analysis, we clarified the effects of parasitization on host gene expression of Microplitis manilae, a dominant larval parasitoid of Spodoptera frugiperda. Several differentially expressed genes were identified in S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization. Among these, many genes were implicated in host metabolism and immunity. Further qPCR results involving 20 differentially expressed metabolism, and immune-related genes were consistent with the expression profiles of the RNA-seq data, which confirmed the physiological manipulation of M. manilae on host S. frugiperda. These results contribute to defining the molecular basis of wasps' successful parasitization and facilitate their application. It has been extensively found that parasitoids manipulate host physiology to benefit the survival and development of their offspring. However, the underlying regulatory mechanisms have not received much attention. To reveal the effects of parasitization of the larval solitary endoparasitoid Microplitis manilae (Hymenoptera: Braconidae) on host Spodoptera frugiperda (Lepidoptera: Noctuidae), one of the most destructive agricultural pests in China, deep-sequencing-based transcriptome analysis was conducted to compare the host gene expression levels after 2 h, 24 h, and 48 h parasitization. A total of 1861, 962, and 108 differentially expressed genes (DEGs) were obtained from the S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization, respectively, compared with unparasitized controls. The changes in host gene expressions were most likely caused by the injection of wasp parasitic factors, including PDVs, that were injected along with the eggs during oviposition. Based on the functional annotations in GO and KEGG databases, we revealed that most DEGs were implicated in host metabolism and immunity. Further analysis of the common DEGs in three comparisons between the unparasitized and parasitized groups identified four genes, including one unknown and three prophenoloxidase (PPO) genes. Moreover, 46 and 7 common DEGs involved in host metabolism and immunity were identified at two or three time points after parasitization, respectively. Among these, most DEGs showed increased expressions at 2 h post-wasp parasitization while exhibiting significantly decreased expression levels at 24 h post-parasitization, demonstrating the expression regulations of M. manilae parasitization on host metabolism and immune-related genes. Further qPCR verification in 20 randomly selected DEGs confirmed the accuracy and reproducibility of the gene expression profiles generated from RNA-seq. This study reveals the molecular regulatory network about how host insects respond to wasp parasitism, laying a solid foundation for revealing the physiological manipulation of wasp parasitization on host insects, which facilitates the development of biological control practices for parasitoids. [ABSTRACT FROM AUTHOR]