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Multiple displacement amplification (MDA) has become one of the most commonly used method of whole genome amplification (WGA) due to the high processivity, strand displacement capacity and high fidelity of the phi29 DNA polymerase, MDA generate vast amount of DNA with higher molecules weight (up to 100kb) and greater genome coverage. Along with the development of the sequencing platform, it is possible to sequence the MDA-amplified DNA molecules with over 20kb by long-read sequencing. However, one of the challenges is the formation of chimeras, which exist in all MDA products, and seriously interfere with the downstream analysis of the long-read sequencing data of MDA-amplified DNA. In this study, we constructed 3rd-ChimeraMiner, a chimera detection pipeline for analyzing the long-read sequencing of MDA products, recognizing chimeras, and integrating chimeras into the downstream analysis. Five sequencing data of MDA with different magnification fold were analyzed in here, the proportions of chimeras are much higher than that of next-generation sequencing reads and increase with the increase of magnification folds, ranging from 42% to over 76%. After comparing, 99.92% of recognized chimeras have been demonstrated not to exist in original genomes. After detecting chimeras by 3rd-ChimeraMiner, the full-length mapping ratio increased, means more PacBio data could be used in downstream analysis, and mean 97.77% inversions were removed after transferred chimeras into normal reads. 3rd-ChimeraMiner revealed efficiency and accuracy in discovering chimeras from long-read sequencing data of MDA, and is promising to be widely used in single-cell sequencing.

This study aimed to investigate the prevalence and diversity of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli isolates from healthy individuals in a community and to elucidate their dissemination mechanism. Cefotaxime-resistant E. coli were isolated from 95 samples of healthy persons from one community in Yangzhou, China, and were tested for minimal inhibitory concentrations of 14 antimicrobial agents. The isolates were subjected to whole genome sequencing by Illumina Hiseq or PacBio single-molecule real-time sequencing. A total of 30 cefotaxime-resistant E. coli isolates were obtained, carrying blaCTX-M (n=29) or blaDHA (n=1), of which the blaCTX-M-55 (n=19) was the most predominant genotype. One novel blaCTX-M variant blaCTX-M-252 was identified. Thirteen CTX-M-55-producing E. coli isolates belonged to ST8369 from nasal (n=12) or faecal (n=1) samples shared the identical cgMLST type, resistance profiles, resistance genes, plasmid replicons, and a 5,053-bp blaCTX-M-55 structure ΔIS26-ΔISEcp1-blaCTX-M-55-Δorf477-ΔTn2. The blaCTX-M-55 gene was located on IncHI2/ST3 plasmid in E. coli ST8369. The lengths of blaCTX-M/blaDHA-carrying contigs in the remaining 17 E. coli strains ranged from 1,663 to 382,836 bp, located on chromosome (n=4) or plasmids (n=5); the location of the other eight contigs could not be determined due to incomplete assembly. The blaCTX-M was associated with ISEcp1 as previously reported. Nasal colonization of CTX-M-55-producing ST8369 E. coli strains has occurred among healthy individuals in one community. There is a potential risk of antimicrobial resistance dissemination between humans within one community through close contact or environment via aerosols or dust. Therefore, surveillance of nasal carriage of blaCTX-M in communities is warranted to further monitor the spread of the antimicrobial resistance genes in China.

To better understand geodynamic implications for the transition from adakitic to non-adakitic magmatism in a continental collision setting, an integrated study including zircon U–Pb ages and whole-rock geochemistry was performed for the Gahai and Erhai granitoid intrusions within the Qilian Block. The ca. 450–428 Ma Gahai biotite granite and Erhai muscovite-bearing granite are peraluminous S-type granites with adakitic geochemical characteristics, and have low Mg# (41.2–31.7) and εNd(t) (−10.8 to −6.5) values with two–stage Nd model ages of 2.05–1.72 Ga, implying their derivation almost entirely from an ancient crustal source under a thickened lower crust condition. The geochemical characteristics of the granites indicate that the Gahai and Erhai S-type granites were derived from partial melting of meta-greywacke and meta-pelite sources, respectively. In comparison, the ca. 415 Ma Gahai granodiorite belongs to metaluminous I-type granitoid and has low Sr/Y ratios as well as high Y and heavy rare Earth element (REE) concentrations, with nearly flat heavy REE patterns, implying a shallow source region. The granodiorites were most likely generated by partial melting of a K-rich basaltic magma source, with some contributions from mantle-derived melts. Synthesized data from this and previous studies suggest that the ca. 450–415 Ma Gahai and Erhai granitoids within the Qilian Block were generated in a post-collisional extensional regime triggered by the break-off of the northward subducting South Qilian Ocean slab beneath the Qilian Block. The geochemical transition from adakitic to non-adakitic intermediate-acidic magmas indicated that the thickened continental crust of the Qilian Block had experienced significant extension and thinning after ca. 420 Ma.

Multiple displacement amplification (MDA) is a popular single-cell whole-genome amplification (WGA) technique that can greatly improve the amplification efficiency of single-cell genomes. However, there is an inherent problem that cannot be completely solved, that is, the amplification bias. We here propose an improved MDA method based on low melting agarose gel, named gelMDA. Firstly, the agarose gel and solution were characterized with SEM and fluorescent reagent. Then, we used gelMDA for cDNA amplification in library preparation of RNA-seq, and conventional MDA was used as a comparison. The sensitivity, efficiency of gelMDA, and amplification bias were evaluated with fluorescence curve, product yield, and the sequencing results. Finally, gelMDA was used for single-cell transcriptome sequencing. The results showed that the sensitivity and product yield of gelMDA were significantly higher than those of conventional MDA. A lower coefficient of variation (CV) and a higher reproducibility were obtained from gelMDA sequencing results. A region of 30 μm in diameter was amplified from the tissue sections and successfully sequenced. In conclusion, gelMDA obtained higher amplification efficiency and lower amplification bias in the present study. It suggested the great potential in single-cell RNA amplification and sequencing.

Acute hepatopancreatic necrosis disease (AHPND) is a significant deadly infectious disease in the shrimp farming industry, causing serious economic losses globally every year. Because of the rapid progress speed, lack of effective treatment and high mortality rate of AHPND, monitoring with frequent diagnostic tests is vital for a successful prevention. The conventional histopathological diagnosis fell far short of the requirement for efficient monitoring, and the polymerase chain reaction (PCR)-based molecular diagnostic methods that rely on sophisticated thermocycler and trained personnel are hardly applicable in the field. Combining the recombinase polymerase amplification (RPA) and the lateral flow strips (LFSs), a diagnostic method suitable for on-site everyday monitoring of AHPND has been established in this study. This RPA-LFS method targeted the binary toxic photorhabdus insect-related genes PirA and PirB on a virulence plasmid of the AHPND-causative Vibrio parahaemolyticus strains. The diagnostic test was completed within 30 min at 37°C and showed good specificity and good sensitivity of 20 fg DNA of the AHPND shrimp or one colony-forming unit of the causative bacterium per reaction, which was better than the administration-approved standard AP4 assay. Crude templates from sample boiling could be directly used. Tests of clinical samples showed 100% consistency of this method with the standard AP4 assay. This RPA-LFS method can be a good choice for on-site diagnosis of AHPND with quick response time, easy procedure and low demand for resources, and should have significant value for the control of spreading of this dangerous disease in farmed shrimp.

Hypoxia is a common stressor in shrimp, but the molecular mechanisms underlying the adaptation of the ridgetail white prawn, Exopalaemon carinicauda, to hypoxia and reoxygenation remain poorly understood. In the present study, ridgetail white prawns were exposed to gradual changes in hypoxia for 6 h via oxygen consumption in a static respiration chamber and then rapidly aerated to allow reoxygenation for 8 h. The dissolved oxygen concentration after 6 h of hypoxia was 1.04 mg/L, and the survival rate of the shrimp was 47%. A transcriptomic analysis of hepatopancreas tissues after 0 (control), 3 (hypoxic starting point), and 6 (hypoxic lethal half point) h of exposure to hypoxia and after 1 and 8 h of reoxygenation was conducted using the Illumina HiSeqTM 4000 high-throughput sequencing platform. A total of 93,227 genes were obtained, and 4315 of these genes were identified as differentially expressed genes (DEGs) that respond to hypoxia and reoxygenation. A KEGG pathway enrichment analysis suggested that all identified DEGs were mostly enriched in ribosome biogenesis in eukaryotes, apoptosis, the longevity regulating pathway, the MAPK signaling pathway, and protein processing in the endoplasmic reticulum. In addition, 20,203 genes with RPKM values ≥1 were parsed into 20 modules through a weighted gene coexpression network (WGCNA), and three of these modules were related to hypoxia and reoxygenation. GO and KEGG enrichment analyses of these three modules were then performed, and three hub genes were identified based on their connectivity: RREB1 (Ras-responsive element-binding protein 1-like), UBE1 (ubiquitin-activating enzyme E1), and an unknown gene. This study might help further elucidate the hypoxia tolerance mechanism of E. carinicauda.

The gut-microbiota-brain axis is the most important complex and bidirectional pathway between the gastrointestinal tract and the central nervous system. This study investigated the potential of microbe-induced gut-to-brain signaling to modulate the effect of stress on depressive-like behavior, intestinal barrier, and neuroinflammation. Result showed that fecal microbiota transplantation increased the consumption of sucrose solutions and decreased the immobility time in forced swimming test. This treatment also increased Firmicutes and decreased Bacteroidetes and Desulfobacterota at phylum levels; reduced the loss of villi and epithelial cells; suppressed the inflammatory cell infiltration in the ileum; increased the expression of ZO-1, occludin; protected the mucosal layer function; and suppressed the high levels of inflammasomes (NLRP3, ASC, caspase-1, and IL-1β) in rat brain. In summary, fecal microbiota transplantation improves the depressive-like behavior, alters the gut microbiota imbalance, and alleviates the intestinal tract inflammation, intestinal mucosa disruption, and neuroinflammation in rats induced by chronic unpredictable mild stress.

AIM: To investigate effects of different corneal protective agents on ocular surface in vitrectomy in patients with diabetes.METHODS: Totally 90 patients(90 eyes)with diabetes who received vitrectomy were randomly divided into HPMC group(30 eyes), SHSCS group(30 eyes)and BSS group(30 eyes). Hydroxypropyl methyl cellulose(HPMC)and sodium hyaluronate sodium chondroitin sulfate(SHSCS)were used to cover the corneal surface to avoid the cornea drying in HPMC group and SHSCS group, respectively. Balanced salt solution(BSS)was continuously dripped on the cornea to keep the cornea moist in BSS group. Schirmer Ⅰ test(SⅠt), breaking up time(BUT)and central corneal thickness were performed before and after operation. Their changes were observed and compared.RESULTS: At 1wk and 1mo after operation, compared with HPMC group and SHSCS group, SⅠt was significantly increased and BUT was significantly shortened in BSS group(P0.05). At 1d after operation, the corneal thickness of BSS group was significantly increased compared with HPMC group and SHSCS group(P0.05).CONCLUSION:The patients with diabetes use HPMC and SHSCS can protect the cornea and maintain the stability of tear film in vitrectomy. Different corneal protectors can be selected according to the clinical practice.

Laser-supported laparoscopic partial nephrectomy is a promising new technique, but remains under experiment. We presented our single institutional experience of laparoscopic partial nephrectomy using the 980/1470-nm dual-diode laser system to investigate its feasibility, and oncological and functional outcomes. The study retrospectively evaluated 25 patients with small exophytic renal tumors, who underwent laparoscopic partial nephrectomy using a 980/1470-nm dual-diode laser. The demographics, surgical data, complications, pathological variables, oncological, and functional outcomes were reviewed. The changes in hemoglobin and estimated glomerular filtration rate (eGFR) before and after surgery were statistically analyzed. The investigators operated on a total of 25 patients. The off-clamping technique was performed for 23 cases, while the other two cases required renal artery clamping due to unsatisfactory hemostasis. The tumor diameter was 24.6± 6.2 mm, and the mean operative time was 104.4± 23.4 min. The median estimated intraoperative blood loss (EBL) was 100 ml (range 50-600 ml). No major complications (Clavien-Dindo >II) occurred perioperatively. The mean change in hemoglobin before and after the operation was 9 g/l, with a P value of

Background: Emerging evidence shows that circular RNAs (circRNAs) participate in the pathogenesis of multiple immune diseases. However, few studies have focused on the mechanisms of circRNAs involved in allergic rhinitis (AR). Methods: This study performed an RNA sequence (RNA-seq) profiling to identify the expression of circRNAs in nasal mucosa from ovalbumin-induced AR murine models and normal controls. Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) was then conducted to validate the differential expression of circRNAs. Bioinformatics analysis was applied to demonstrate the biological functions of the dysregulated circRNAs. Results: A total of 86 distinct circRNA candidates were sequenced, of which 51 were upregulated and 35 were downregulated. The T cell receptor, B cell receptor, and calcium signaling pathways may be involved in the pathology of AR. Furthermore, a circRNA-miRNA interaction network was constructed via miRNA response elements analysis. Some circRNAs were cor-related with miRNAs that are involved in T cell polarization and activation, thereby highlighting their potential role in the pathogenesis of AR. Conclusions: This study demonstrates a number of aberrantly expressed circRNAs related to AR, and offers a novel perspective into AR pathogenesis and future therapeutic strategies.

In many cancer types, the evolution of subclonal malignant cells leads to a diverse tumor population that can affect treatment efficacy. In addition, evolution throughout treatment can lead to resistant subclonal populations and eventual relapse. To effectively treat these cancers, it is essential to understand the subclonal architecture of the tumor, including the somatic mutations that differentiate each population. Many tools have been developed to attempt to cluster mutations or reconstruct the clonal architecture of a given tumor sample. However, few can accommodate multiple samples, which is common in longitudinal or metastasis studies. In addition, these tools typically focus on just one of the steps necessary for a full analysis (e.g., variant clustering, subclone hierarchical tree reconstruction, and tree visualization). Many require non-standard data formats, necessitating data format conversion between each step. These requirements make it very challenging for investigators without a deep understanding of each tool to perform a full subclonal analysis. To make the identification of temporal and spatial heterogeneity more streamlined and accessible to analysts with basic programming knowledge, we have developed a pipeline that takes somatic mutations in standard VCF file format as input and produces meaningful results that are easy to interpret. Variant data is extracted and formatted for the input to PyClone-VI (Gillis and Roth, 2020), which is used to cluster somatic variants based on their allele frequencies at each time point. SuperSeeker, an improvement on the SubcloneSeeker method developed within our lab (Qiao et al., 2014), implements advanced tumor subclone reconstruction algorithms to jointly analyze multiple samples and construct hierarchical trees that account for all subclones observed in a patient. A sample trace, or the cellular fraction of each subclone found in each sample, is also provided. The output of SuperSeeker is an updated VCF file with the tree and sample trace information added to the header. Finally, a GraphViz rendering of the hierarchical tree is made for easy visualization. In addition to this rendering, the final VCF file can also be used for interactive analysis and visualization of the results using our Oncogene.iobio web tool. This pipeline makes identifying temporal and spatial heterogeneity more efficient, requiring only standard file types as input, and basic command line knowledge. In a recently published study, we investigated subclonal evolution in 38 patients with CLL being treated with a BTKi. The initial subclonal architecture analysis for each patient in this study was laborious and time intensive. Using this pipeline, we can now identify subclonal evolution in these patients and create an interactive visualization more efficiently. This approach can streamline analyses, increase efficiency, and lead to a deeper understanding of a tumor’s subclonal evolution. Citation Format: Gage Black, Yi Qiao, Xiaomeng Huang, Gabor Marth. Streamlining the reconstruction of subclonal evolution in DNA sequencing data. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4295.

We examine a sample of 340 cataclysmic variables (CVs) from the latest data release of the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey, along with 18 objects that are newly classified as CVs. In this paper, we focus on investigating the photometric behaviors of these CVs using data from time-domain surveys. The orbital periods of three new and five previously known objects are determined from the long-term light curves displaying eclipses or ellipsoidal variations, and/or time-resolved spectra from LAMOST. For another 16 CVs with measured periods, it is more reliable to obtain consistent periods using light curves from different surveys, as the periods derived from single-site data are still questionable. Follow-up observations are needed to confirm whether the periods have physical meanings or are orbital-related. In our sample, we find that most of the objects have longer periods above the 2 ∼ 3 hr gap. Besides period estimates, we also carry out a separate detailed analysis of some valuable CVs, in terms of spectral characteristics and subtype determination. Finally, we discuss the observational properties of this sample, including the distributions of orbital periods, absolute magnitudes, and the statistical properties of each subclass of CVs. In addition, we pick out six non-CV systems, including five illumination-effect binaries, as well as one hot subdwarf, that we came across when searching for CVs, and we investigate their properties based on the spectra and photometric data.

Fast radio bursts (FRBs) are short pulses observed in radio band from cosmological distances. One class of models invoke soft gamma-ray repeaters (SGRs), or magnetars, as the sources of FRBs. Some radio pulses have been observed from some magnetars, however, no FRB-like events had been detected in association any magnetar burst, including one giant flare. Recently, a pair of FRB-like bursts (FRB 200428 hereafter) separated by milliseconds (ms) were detected from the general direction of the Galactic magnetar SGR J1935+2154. Here we report the detection of a non-thermal X-ray burst in the 1-250 keV energy band with the Insight-HXMT satellite, which we identify as emitted from SGR J1935+2154. The burst showed two hard peaks with a separation of 34 ms, broadly consistent with that of the two bursts in FRB 200428. The delay time between the double radio and X-ray peaks is about 8.57 s, fully consistent with the dispersion delay of FRB 200428. We thus identify the non-thermal X-ray burst is associated with FRB 200428 whose high energy counterpart is the two hard peaks in X-ray. Our results suggest that the non-thermal X-ray burst and FRB 200428 share the same physical origin in an explosive event from SGR J1935+2154., 24 pages, 9 figures, 6 tables; initial submission to a journal on May 9th, 2020. Significant changes include updated localization and detailed spectral evolution of the X-ray burst, and better determination of the two narrow X-ray peaks corresponding to the two radio pulses. Conclusions are strengthened. Nature Astronomy online on Feb. 18, 2021

Objective: Psychotic symptoms are prevalent in both clinical settings and the general population. The distribution of psychotic symptoms across patients with different types of psychotic and non-ps...

Precartilaginous stem cells (PCSCs) are able to initiate chondrocyte and bone development. The present study aimed to investigate the role of miR-143 and the underlying mechanisms involved in PCSC proliferation. In a rat growth plate injury model, tissue from the injury site was collected and the expression of miR-143 and its potential targets was determined. PCSCs were isolated from the rabbits' distal epiphyseal growth plate. Cell viability, DNA synthesis, and apoptosis were determined with MTT, BrdU, and flow cytometric analysis, respectively. Real time PCR and western blot were performed to detect the mRNA and protein expression of the indicated genes. Indian hedgehog (IHH) was identified as a target gene for miR-143 with luciferase reporter assay. Decreased expression of miR-143 and increased expression of IHH gene were observed in the growth plate after injury. miR-143 mimics decreased cell viability and DNA synthesis and promoted apoptosis of PCSCs. Conversely, siRNA-mediated inhibition of miR-143 led to increased growth and suppressed apoptosis of PCSCs. Transfection of miR-143 decreased luciferase activity of wild-type IHH but had no effect when the 3'-UTR of IHH was mutated. Furthermore, the effect of miR-143 overexpression was neutralized by overexpression of IHH. Our study showed that miR-143 is involved in growth plate behavior and regulates PCSC growth by targeting IHH, suggesting that miR-143 may serve as a novel target for PCSC-related diseases.

DNA quantification is important in the research of life sciences. In an independent quantification process, the extracted part of a DNA sample is usually difficult to be recycled for further use while the widely used real-time PCR is used to count the copies with certain sequences. Based on the popular multiple displacement amplification (MDA), we proposed and performed quantitative real-time MDA to obtain the information of template amount based on fluorescence signals while amplifying whole-genome DNA. The detection limit of real-time MDA was as low as 0.5 pg μl−1 (5 pg DNA input), offering the whole-genome research a promising tool to quantify the entire DNA during amplification without sacrificing sample completeness or introducing redundant steps.

Transfer hydrogenation of nitroarenes to the corresponding anilines using hydrazine hydrate and non-noble metal catalysts has already been widely studied. However, the toxicity resulting from excess hydrazine hydrate and the high reaction temperature limit its industrial application. Herein, a novel N-doped molybdenum oxide compound (Mo4O4N3) was in situ prepared from g-C3N4 and (NH4)6Mo7O24·4H2O (AHM). The as-prepared Mo4O4N3 can achieve a 99% yield of aniline using a stoichiometric molar ratio of hydrazine hydrate (–NO2 : N2H4·H2O = 1 : 1.5) at room temperature for 50 minutes. Mechanistic experiments and characterization techniques indicate that the acidic sites of unsaturated Mo in Mo4O4N3 can efficiently activate N2H4 molecules to form active hydrogen species for catalytic transfer hydrogenation of nitroarenes without the generation of hazardous NH3. Besides, Mo4O4N3 still exhibited excellent catalytic performance for the large-scale reaction without solvent. This work may offer a feasible and efficient strategy for arylamine production.

The extremely small amount of DNA in a cell makes it difficult to study the whole genome of single cells, so whole-genome amplification (WGA) is necessary to increase the DNA amount and enable downstream analyses. Multiple displacement amplification (MDA) is the most widely used WGA technique. Compared with amplification methods based on PCR and other methods, MDA renders high-quality DNA products and better genome coverage by using phi29 DNA polymerase. Moreover, recently developed advanced MDA technologies such as microreactor MDA, emulsion MDA, and micro-channel MDA have improved amplification uniformity. Additionally, the development of other novel methods such as TruePrime WGA allows for amplification without primers. Here, we reviewed a selection of recently developed MDA methods, their advantages over other WGA methods, and improved MDA-based technologies, followed by a discussion of future perspectives. With the continuous development of MDA and the successive update of detection technologies, MDA will be applied in increasingly more fields and provide a solid foundation for scientific research.

The linear 2-arboricity la2(G) of a graph G is the least integer k such that G can be partitioned into k edge-disjoint forests, whose component trees are paths of length at most 2. In this paper, we prove that if G is a 1-planar graph with maximum degree Δ, then $${\rm{l}}{{\rm{a}}_2}\left( G \right) \le \left\lceil {{{{\rm{\Delta + 1}}} \over 2}} \right\rceil + 7$$ . This improves a known result of Liu et al. (2019) that every 1-planar graph G has $${\rm{l}}{{\rm{a}}_2}\left( G \right) \le \left\lceil {{{{\rm{\Delta + 1}}} \over 2}} \right\rceil + 14$$ . We also observe that there exists a 7-regular 1-planar graph G such that $${\rm{l}}{{\rm{a}}_2}\left( G \right) = 6 = \left\lceil {{{{\rm{\Delta + 1}}} \over 2}} \right\rceil + 2$$ , which implies that our solution is within 6 from optimal.

We investigate the formation and properties of crude oil/water interfacial films. The time evolution of interfacial tension suggests the presence of short and long timescale processes reflecting the competition between different populations of surface-active molecules. We measure both the time-dependent shear and extensional interfacial rheology moduli. Late-time interface rheology is dominated by elasticity, which results in visible wrinkles on the crude oil drop surface upon interface disturbance. We also find that the chemical composition of the interfacial films is affected by the composition of the aqueous phase that it has contacted. For example, sulfate ions promote films enriched with carboxylic groups and condensed aromatics. Finally, we perform solution exchange experiments and monitor the late-time film composition upon the exchange. We detect the film composition change upon replacing chloride solutions with sulfate-enriched ones. To the best of our knowledge, we are the first to report the composition alteration of aged crude oil films. This finding might foreshadow an essential crude oil recovery mechanism.

Salinity is an important factor in the aquatic environment, and its fluctuations always result in osmotic stress, which affects the survival, distribution, and physiological activities of crustaceans. Crustaceans counter them through osmoregulation, which consists of many mechanisms. Palaemon gravieri is an important economic species in Palaemonidae, widely distributed in the southern East China Sea and the China Yellow Sea, and has a good adaptability to salinity stress. Currently, there are only a few studies on the effects of salinity on P. graviera. Therefore, it is particularly important to study the molecular responses of P. gravieri to salinity fluctuations. In this study, P. gravieri was treated with salinities of 10, 25, and 40, and the hepatopancreas and gills of shrimp in the different salinity groups were sampled after 24 h. The samples were used for RNA extraction and transcriptome analysis. In total, 80,994 unigenes were obtained, of which 19,114 were annotated. The differences in gene expression between different tissues at the same salinity were more significant. Many metabolism-related genes were downregulated in the gills, such as beta-hexosaminidase subunit alpha (HEXA), 10-formyltetrahydrofolate dehydrogenase (ALDH1L1), and Alcohol dehydrogenase class-3 (ADH5). Scanning transmission electron microscope analysis showed that the expression levels of some stress-(but not salinity stress) related genes changed after stress (mostly upregulated), suggesting the existence of secondary stress. Gene set enrichment analysis (GSEA) focused on the expression of transporters in osmoregulation, and the results showed that they mainly played a role in the gills, but ATP-binding cassette (ABC) transporters were more active in the hepatopancreas. This study showed that the response of P. gravieri to salinity change was different not only between the hepatopancreas and gills, but also between low salinity and higher salinity, and the ion transport-related genes were mainly expressed in the gills. Overall, these results improve our understanding of salt tolerance mechanism in P. gravieri.