Transcriptome Analysis of Hepatopancreas from the Cr (VI)-Stimulated Mantis Shrimp ( Oratosquilla oratoria) by Illumina Paired-End Sequencing: Assembly, Annotation, and Expression Analysis

Transcriptomic insights into the resistance mechanism of Penaeus vannamei against highly lethal Vibrio parahaemolyticus

Highly lethal Vibrio disease (HLVD) caused by a virulent strain of Vibrio parahaemolyticus (VpHLVD), which poses a significant threat to Penaeus vannamei post-larvae, leads to substantial mortality and economic losses. To address this challenge, researchers have recently isolated a highly disease-resistant strain of P. vannamei shrimp. However, the underlying mechanisms that could improve disease resistance require further investigation. Our study found that disease-resistant shrimp exhibited a remarkable ability to prevent VpHLVD invasion effectively. To unravel the genetic basis of this resistance, we conducted a transcriptomic analysis with susceptible and disease-resistant shrimp at various time points (0, 6, and 12 h) post-infection with VpHLVD. Differential gene expression (DEGs) analysis of uninfected shrimp revealed that disease-resistant individuals displayed higher expression of immune-related genes and pathways compared to their susceptible counterparts. Simultaneously, they exhibited lower expression of Vibrio toxin-binding genes and Vibrio colonization gene, indicating enhanced defense mechanisms in the resistant shrimp. Upon VpHLVD infection, DEGs analysis also showed that susceptible shrimp attempt to mount a similar immune response as the disease-resistant shrimp during the early stages of infection. However, as the infection progresses, the defense strategies diverge between the two groups, with the peak of gene response occurring later in the disease-resistant shrimp. Our findings indicated that disease-resistant shrimp did not experience significant stress during the early stages of infection and are capable of effectively enhancing their immune response in the middle and late stages of the infection. In summary, our study enhanced the understanding of the mechanisms employed by disease-resistant shrimp to combat Vibrio, and would help to develop effective strategies for disease prevention and control, ultimately reducing the impact of HLVD on shrimp aquaculture.

Transcriptome analysis provides new insight into the mechanism of Bombyx mori under zinc exposure

Zinc is a significant source of heavy metal pollution that poses risks to both human health and biodiversity. Excessive concentrations of zinc can hinder the growth and development of insects and trigger cell death through oxidative damage. The midgut is the main organ affected by exposure to heavy metals. The silkworm, a prominent insect species belonging to the Lepidoptera class and widely used in China, serves as a model for studying the genetic response to heavy metal stress. In this study, high-throughput sequencing technology was employed to investigate detoxification-related genes in the midgut that are induced by zinc exposure. A total of 11,320 unigenes and 14,723 transcripts were identified, with 553 differentially expressed genes (DEGs) detected, among which 394 were up-regulated and 159 were down-regulated. The Gene Ontology (GO) analysis revealed that 452 DEGs were involved in 18 biological process subclasses, 14 cellular component subclasses and 8 molecular functional subclasses. Furthermore, the KEGG analysis demonstrated enrichment in pathways such as Protein digestion, absorption and Lysosome. Validation of the expression levels of 9 detoxification-related DEGs through qRT-PCR confirmed the accuracy of the RNA-seq results. This study not only contributes new insights into the detoxification mechanisms mechanism of silkworms against zinc contamination, but also serves as a foundation basis for understanding the molecular detoxification processes in lepidopteran insects.

Transcriptome Analysis Reveals Antioxidant Defense Mechanisms in the Silkworm Bombyx mori after Exposure to Lead

Lead (Pb) is a major source of heavy metal contamination, and poses a threat to biodiversity and human health. Elevated levels of Pb can hinder insect growth and development, leading to apoptosis via mechanisms like oxidative damage. The midgut of silkworms is the main organ exposed to heavy metals. As an economically important lepidopteran model insect in China, heavy metal-induced stress on silkworms causes considerable losses in sericulture, thereby causing substantial economic damage. This study aimed to investigate Pb-induced detoxification-related genes in the midgut of silkworms using high-throughput sequencing methods to achieve a deeper comprehension of the genes' reactions to lead exposure. This study identified 11,567 unigenes and 14,978 transcripts. A total of 1265 differentially expressed genes (DEGs) were screened, comprising 907 upregulated and 358 downregulated genes. Subsequently, Gene Ontology (GO) classification analysis revealed that the 1265 DEGs were distributed across biological processes, cellular components, and molecular functions. This suggests that the silkworm midgut may affect various organelle functions and biological processes, providing crucial clues for further exploration of DEG function. Additionally, the expression levels of 12 selected detoxification-related DEGs were validated using qRT-PCR, which confirmed the reliability of the RNA-seq results. This study not only provides new insights into the detoxification defense mechanisms of silkworms after Pb exposure, but also establishes a valuable foundation for further investigation into the molecular detoxification mechanisms in silkworms.

RNA-seq analysis revealing the immune response of Neocaridina denticulata sinensis gill to Vibrio parahaemolyticus infection

Vibrio parahaemolyticus causes serious economic losses to the shrimp farming industry. There is still a lack of adequate understanding of the changes in the overall response of N. denticulata sinensis caused by V. parahaemolyticus, particularly with respect to gill tissue, which is severely damaged by the pathogen. In this study, a total of 1358 differentially expressed genes were identified between the PBS control and Vibrio stimulation groups using transcriptome sequencing techniques. After further screening and analysis, many immune-related genes were obtained, involving lysosome pathway, metabolic process, chitin-binding protein, and serine protease family members. In addition, we randomly selected six DEGs in the lysosome pathway for qRT-PCR verification, and the results showed that their expression patterns were consistent with the RNA-seq. The results demonstrate the molecular regulation of the gill tissue response to V. parahaemolyticus infection in N. denticulata sinensis, contributing to the understand of the complex and efficient innate immune system and defense mechanisms in crustaceans.

Transcriptome analysis reveals antioxidant defense mechanisms in the red swamp crayfish Procambarus clarkia after exposure to chromium

Chromium (Cr) as a chromate anion has a strong redox capacity that seriously threatens the ecological environment and human health. Cr can contaminate water and impart toxicity to aquatic species. Procambarus clarkii is an important food source that once represented a large proportion of the aquaculture industry due to its rapid reproduction and high economic value. However, there have been reports on the death of P. clarkii due to heavy metal pollution. The underlying mechanism regarding heavy metal toxicity was studied in this paper. The transcriptome data of hemocytes extracted from P. clarkii injected with Cr were analyzed by high-throughput sequencing and compared to the control group. In total, 48,128,748 clean reads were obtained in the treatment group and 56,480,556 clean reads were obtained in the control group. The reads were assembled using Trinity and the identified unigenes were then annotated. Then, 421 differentially-expressed genes (DEGs) were found, 170 of which were upregulated and 251 downregulated. Many of these genes were found to be related to glutathione metabolism and transportation. The glutathione metabolic pathway of P. clarkii was thus activated by Cr exposure to detoxify and maintain body function. Validation of DEGs with quantitative real-time PCR confirms the changes in gene expression. Thus, this study provides data supporting a glutathione-focused response of P. clarkii to exposure to heavy metals.

Transcriptome Analysis of the Hepatopancreas in the Litopenaeus vannamei Responding to the Lead Stress

Lead (Pb) is one of the most hazardous pollutants and toxic heavy metal in marine environment. The molecular mechanisms of Pb toxicity in aquatic organism are not well understood. In this study, hepatopancreas transcriptome of Litopenaeus vannamei (L. vannamei) was characterized by a comparison between control and Pb exposure samples using RNA-Seq approach. Hepatopancreas morphology of L. vannamei was also assessed. The result reveals that compared with the control group, an increase in the number of B cells was observed following Pb exposure in L. vannamei. Transcriptome data showed that a total of 1593 genes were recognized to be differentially expressed including 1278 up-regulated and 315 down-regulated genes. These genes were mainly associated with energy metabolism, cell apoptosis, exogenous microbial infection, cell junction, and cell adhesion. Fifteen ribosomal protein genes (RPS3, RPS13, RPSA, RPL11, RPS2, RPL8, RPS23, RPL3, RPL5, RPS6, RPS4X, RPS18, RPL19, RPL9, RPL6) were identified as the common hubs of protein-protein interaction (PPI) networks, as well as part of modules of the PPI network. Besides ribosomal protein, we identified differential expression genes (DEGs) including GAPDH, EEF1A1, HSPA8, UBC, and EEF1G as the common hubs of PPI networks. These findings may have important implications for understanding the adverse biological effects of Pb and its toxic mechanisms, as yet not clearly defined, and provide potential biomarkers of Pb exposure in hepatopancreas of L. vannamei, which might be useful for monitoring aquatic environments and assessing the health of the marine ecosystem.

New insight into the molecular basis of chromium exposure of Litopenaeus vannamei by transcriptome analysis

Heavy metal pollution arising from agricultural and industrial activities poses a significant threat to the aquatic environment, especially the increasing levels of chromium (Cr) that is exacerbating marine pollution. Given the economic importance of the Pacific white shrimp Litopenaeus vannamei (L. vannamei), understanding the impact of marine Cr pollution is deemed to be significant. In this study, we used the transcriptome sequencing (RNA-seq) technique to characterize the molecular mechanism of Cr exposure in L. vannamei. Gene ontology enrichment analysis showed substrate-specific and ion transport-related functions were mainly influenced by Cr exposure. We further identified genes involved in protein digestion and absorption (PEPT1, BAT1, MDU1), chemical carcinogenesis (GST and UGTs), ABC transporters (ABCC2), apoptosis (CAPN1, CASP10, PARP), implying the potentially Cr disintoxication mechanisms in L. vannamei. Genes within pancreatic secretion (ALT, LDH), lysosome (CTSL and HEXB), and peroxisome (ACOX1, ECI2, NUDT12) pathways implied the potentially Cr toxicity mechanisms in L. vannamei.

Comparative accumulation and transcriptomic analysis of juvenile Marsupenaeus japonicus under cadmium or copper exposure

Waterborne metals may be hazardous to aquatic organisms and trigger stress responses. The present study aimed to assess the effect of exposure to 100 μg/L cadmium (Cd) or copper (Cu) for 48 h on juvenile Marsupenaeus japonicus, in terms of bioaccumulation and the whole body transcriptome. The results demonstrated that Cu accumulation in M. japonicas was much higher than that of Cd. Meanwhile, transcriptome analysis identified 1802 and 2670 differentially expressed genes (DEGs) after 48 h exposure to 100 μg/L Cd and Cu, respectively. Among them, 851 DEGs responded to both metals. Cd and Cu stress shared genes were related to the cytoskeleton, immunity, antioxidation, and detoxification. Metallothionein 1 (MT1) was specifically induced in the Cd-stress response, while glycometabolism, heat shock protein 90 (HSP90), metallothionein 2 (MT2), apoptosis, and iron transport-related genes were changed specifically in response to Cu stress. In addition, real-time PCR was used to verify the expression patterns of 28 randomly selected DEGs. The sequencing and real-time PCR results were consistent. Moreover, based on the number of significantly modulated genes and their expression levels, we deduced that Cu acts as a stronger stress inducer than Cd in M. japonicus. The identified Cd and Cu stress related genes and pathways will provide new insights into the common and different molecular mechanisms underlying Cd and Cu toxicity effects in M. japonicus.

Sulforaphane prevents chromium-induced lung injury in rats via activation of the Akt/GSK-3β/Fyn pathway

Chromium (Cr) is an internationally recognized carcinogenic hazard that causes serious pulmonary toxicity. However, Cr-induced pulmonary toxicity lacks effective treatment to date. Sulforaphane (SFN), a well-known organosulfur compound, has gained increasing attention because of its unique biological function. This study investigates if SFN could decrease K₂Cr₂O₇-induced pulmonary toxicity and a potential mechanism involved using a rat 35-day Cr-induced pulmonary toxicity model and the mouse alveolar type II epithelial cell line (MLE-12). The results showed that SFN prevented Cr-induced oxidative stress, histopathological lesions, inflammation, apoptosis, and changes in protein kinase B (Akt) and glycogen synthase kinase 3 beta (GSK-3β) levels in vivo and in vitro. However, SFN can not play the protective effect against K₂Cr₂O₇-induced cell injury after treating by an Akt-specific inhibitor (MK-2206 2HCl) in MLE-12 cells. Furthermore, SFN increased the expression of nuclear factor-E2-related factor-2 (Nrf2) phase II detoxification enzymes. Collectively, this study demonstrates that SFN prevents K₂Cr₂O₇-induced lung toxicity in rats through enhancing Nrf2-mediated exogenous antioxidant defenses via activation of the Akt/GSK-3β/Fyn signaling pathway. SFN may be a novel natural substance to cure Cr-induced lung toxicity.

Transcriptomic analysis to elucidate the response of honeybees (Hymenoptera: Apidae) to amitraz treatment

Amitraz is an acaricide that is widely used in apiculture. Several studies have reported that in honeybees (Apis mellifera Linnaeus; Hymenoptera: Apidae), amitraz affects learning, memory, behavior, immunity, and various other physiological processes. Despite this, few studies have explored the molecular mechanisms underlying the action of amitraz on honeybees. Here, we investigated the transcriptome of honeybees after exposure to 9.4 mg/L amitraz for 10 d, a subchronic dose. Overall, 279 differentially expressed genes (DEGs) were identified (237 upregulated, 42 downregulated). Several, including Pla2, LOC725381, LOC413324, LOC724386, LOC100577456, LOC551785, and P4504c3, were validated by quantitative PCR. According to gene ontology, DEGs were mainly involved in metabolism, biosynthesis, and translation. Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that amitraz treatment affected the relaxin signaling pathway, platelet activation, and protein digestion and absorption.

Transcriptome Analysis Reveals the Tolerance Mechanism of Mantis Shrimp (Oratosquilla oratoria) under a Lipopolysaccharide Challenge

Lipopolysaccharide (LPS), a major cell wall component of Gram-negative bacteria, is considered to lead to some disease development in commercial crustaceans. However, mantis shrimps Oratosquilla oratoria (Crustacea: Stomatopoda) have a strong vitality and ability to resist disease. To study the tolerance mechanism of mantis shrimp, transcriptome analyses were conducted in hepatopancreas of O. oratoria under LPS challenge investigation. Totally, 84 547 044 clean reads were obtained from transcriptomes (43 159 230 in OP (control), 41 387 814 in OL (treatment), respectively). Unigenes, the longest transcript of each gene, with a total length of 68 318 880 bp and the total number of 100 978 were obtained. 8369 (8.28%) of unigenes were successfully annotated in all databases and 54 888 (54.35%) were annotated in at least one database. Finally, 1012 differentially expressed genes (DEGs) including 439 and 573 showed significantly upregulated and downregulated were determined between OL and OP, respectively. Moreover, those DEGs only expressed in OL or OP accounted for 8.99%. The functional classification based on GO and KEGG indicated that the common enrichment categories for the DEGs are "amino sugar metabolic" and "cellular homeostasis" and that the progress of nutrient metabolic and homeostasis in cells is important in facing variable environmental conditions. Protein-protein interaction analysis elucidated proteins, β-actin (ACTB_G1), T-complex protein subunits (TCPs), heat shock proteins (HSPs), hydroxysteroid dehydrogenase-like protein 2 (HSDL2), kinesin family member 5 (KIF5), methylglutaconyl-CoA hydratase (AUH), and myosin heavy chain (MYH) may play key roles in response to an LPS challenge. This study laid a foundation to further investigate the possible adaptation way that O. oratoria survives in a bacterial challenge.

Transcriptome analysis of hemocytes from the white shrimp Litopenaeus vannamei with the injection of dopamine

As a crucial neuroendocrine-immune factor, dopamine (DA) could regulate the immune system of Litopenaeus vannamei. To understand the immune mechanisms and regulatory pathways of DA in L. vannamei, the transcriptome analysis of hemocytes of L. vannamei with injection of DA (10^-6 mol/shrimp) at 3 and 12 h were performed in this study. Moreover, quantitative real-time PCR (qPCR) method was applied to validate the accuracy of transcriptome sequencing and analyze the expression pattern of candidate differentially expressed genes (DEGs) at different time points (0, 3, 6, 12, and 24 h) after DA injection. The results showed that a total of 51382 unigenes with a N50 length of 2341 bp were generated. And 1397 and 457 DEGs were obtained by comparative transcriptome at 3 and 12h respectively. Moreover, the results of functional annotation and enriched pathway showed that the DEGs were involved in phagosome (ko04145), lysosome (ko04142), Endocytosis (ko04144), and NOD-like receptor signaling pathway (ko04621). Besides, the Pearson's correlation coefficient (R) between transcriptome sequencing and qPCR was 0.845, which confirmed the reliability of the transcriptome sequencing results and the accuracy of assembly. Furthermore, the expression pattern of 15 candidate DEGs, containing 9 up-regulated and 6 down-regulated DEGs at 3 h, indicated the regulation of DA in physiological functions especially in the immune system. Therefore, these results revealed that DA induced the expressions of membrane receptors or proteins, activated intracellular signaling pathways, regulated cellular and humoral immune systems, controlled antioxidation and apoptosis, and was involved in the regulation of neuroendocrine system. These findings are helpful to promote the understanding on the effects of biogenic amines on physiological functions and regulatory networks of crustacean, and offer a substantial material and foundation for researching the immune response of crustacean.

The Single-molecule long-read sequencing of Scylla paramamosain

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.

Transcriptomic analysis of immune-related genes in the lipopolysaccharide-stimulated hepatopancreas of the mudflat crab Helice tientsinensis

The mudflat crab Helice tientsinensis is one of the most economically important aquaculture species in China. Nevertheless, it is susceptible to various diseases caused by viruses, bacteria and rickettsia-like organisms. A better understanding of the immune system and genes related to the responses to bacterial and viral infection is required. Herein, the hepatopancreas transcriptome of H. tientsinensis was analyzed by comparing control and lipopolysaccharide (LPS)-stimulated RNA-Seq data, yielding 91,885,038 bp and 13.78 Gb of clean reads. Following assembly and annotation, 93,207 unigenes with an average length of 883 bp were identified, of which 31,674 and 13,700 were annotated in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Following LPS, 4845 differentially expressed genes (DEGs) were identified, of which 2491 and 2354 were up- and down-regulated, respectively. To further investigate immune-related DEGs, KEGG enrichment analysis identified immune response pathways, most notably the peroxisome and Toll-like receptor signaling pathways. Quantitative real time-PCR (qRT-PCR) confirmed the up-regulation of a random selection of DEGs. This systematic transcriptomic analysis of the innate immune pathway in H. tientsinensis expands our understanding of the immune system in crabs.

Comparative transcriptome analysis of Eriocheir japonica sinensis response to environmental salinity

Chinese mitten crabs (Eriocheir japonica sinensis) are catadromous, spending most of their lives in fresh water, but moving to a mixed salt-fresh water environment for reproduction. The characteristics of this life history might imply a rapidly evolutionary transition model for adaptation to marine from freshwater habitats. In this study, transcriptome-wide identification and differential expression on Chinese mitten crab groups were analysed. Results showed: clean reads that were obtained totalled 93,833,096 (47,440,998 in Group EF, the reference, and 46,392,098 in Group ES, the experimental) and 14.08G (7.12G in Group EF 6.96G in Group ES); there were 11,667 unigenes (15.29%) annotated, and they were located to 230 known KEGG pathways in five major categories; in differential expression analysis, most of the top 20 up-regulated pathways were connected to the immune system, disease, and signal transduction, while most of the top 20 down-regulated pathways were related to the metabolism system; meanwhile, 8 representative osmoregulation-related genes (14-3-3 epsilon, Cu2+ transport ATPase, Na+/K+ ATPase, Ca2+ transporting ATPase, V-ATPase subunit A, Putative arsenite-translocating ATPase, and Cation transport ATPase, Na+/K+ symporter) showed up-regulation, and 1 osmoregulation-related gene (V-ATPase subunit H) showed down-regulation. V-ATPase subunit H was very sensitive to the transition of habitats. These results were consistent with the tests of qRT-PCR. The present study has provided a foundation to further understand the molecular mechanism in response to salinity changing in water.

Adaptively differential expression analysis in gill of Chinese mitten crabs (Eriocheir japonica sinensis) associated with salinity changes

Desalination of marine species has become an important development direction for aquaculture in China and other countries. However, that how to regulate the salt balance to adapt to new freshwater habitats is a serious challenge for marine species in desalination of aquaculture. In the study, Chinese mitten crabs (Eriocheir japonica sinensis) was selected to analyse the adaptively differential expression in salinity changes for their novel characteristics of life history. The results showed that gill was the most relevant tissue in osmoregulation that was validated by biomarkers (Na⁺/K⁺-ATP, V-type H⁺-ATPase) with qPCR. Na⁺/K⁺-ATPase is a primary transporter and maintains the body fluid osmolality by actively pumping Na⁺ to the hemolymph, and V-type H⁺-ATPase is responsible for acid-base balance and nitrogen excretion. So both transcriptome data and qPCR results showed the significantly differential expression of Na⁺/K⁺-ATPase and V-type H⁺-ATPase in gills. Moreover, NAK-α had the most significantly differential expression level in salinity change, and other genes such as GST, HSP90, S27, UBE, VATB also revealed significantly up-regulation. They are considered the key enzymes during the transition from a marine environment to land. Present results have provided a foundation to further understand the molecular adaptive mechanism in desalination of marine species.

Transcriptome Analysis Reveals Potential Antioxidant Defense Mechanisms in Antheraea pernyi in Response to Zinc Stress

The growth and development of the Chinese oak silkworm, Antheraea pernyi, are strongly influenced by environmental conditions, including heavy metal pollution. An excess of heavy metals causes cellular damage through the production of free radical reactive oxygen species. In this study, transcriptome analysis was performed to investigate global gene expression when A. pernyi was exposed to zinc infection. With RNA sequencing (RNA-Seq), a total of 25 795 510 and 38 158 855 clean reads were obtained from zinc-treated and control fat body libraries, respectively. We identified 2399 differential expression genes (DEGs) (1845 upregulated and 544 downregulated genes) in the zinc-treated library. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were related to the peroxisome pathway that was associated with antioxidant defense. Our results suggest that fat bodies of A. pernyi constitute a strong antioxidant defense against heavy metal contamination.