A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples.

RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.

The ZIP9-centered androgen pathway compensates for the 2605 MHz radiofrequency electromagnetic radiation-mediated reduction in resistance to H2O2 damage in Sertoli cells of adult rats.

The direct biological effects of radiofrequency electromagnetic radiation (RF-EMR) from wireless communication equipment on the testes are still unclear. Our previous study proved that long-term exposure to 2605 MHz RF-EMR gradually damage spermatogenesis and resulted in time-dependent reproductive toxicity by directly disrupting blood-testis barrier circulation. Although short-term exposure did not cause readily observable damage to fertility, whether it caused specific biological effects and how these effects contributed to the time-dependent reproductive toxicity of RF-EMR were currently unknown. Studies on this issue are important for elucidating the time-dependent reproductive toxicity of RF-EMR. The present study established a 2605 MHz RF-EMR (SAR=1.05 W/Kg) scrotal exposure model with rats and extracted primary Sertoli cells for exposure to investigate the direct biological effects of short-term RF-EMR exposure on the testis. The results showed that short-term RF-EMR exposure did not decrease sperm quality and spermatogenesis, but it increased the levels of testicular testosterone (T) and zinc transporter 9 (ZIP9) in Sertoli cells of rats. In vitro, 2605 MHz RF-EMR exposure did not increase the apoptosis rate of Sertoli cells, but it increased the apoptosis rate and MDA of Sertoli cells exposed to H2O2. T reversed these changes and increased ZIP9 level in Sertoli cells, whereas inhibiting ZIP9 expression significantly suppressed these T-mediated protective effects. Moreover, T increased the levels of phosphorylated inositol-requiring enzyme 1 (P-IRE1), phosphorylated protein kinase R (PKR)-like endoplasmic reticulum kinase (P-PERK), phosphorylated eukaryotic initiation factor 2a (P-eIF2a) and phosphorylated activating transcription factor 6 (P-ATF6) in Sertoli cells, and these effects were reversed by ZIP9 inhibition. With prolonged exposure time, testicular ZIP9 was gradually downregulated, and testicular MDA increased. ZIP9 level was negatively correlated with MDA level in the testes of exposed rats. Thus, although short-term exposure to 2605 MHz RF-EMR (SAR=1.05 W/kg) did not significantly disturb spermatogenesis, it suppressed the ability of Sertoli cells to resist external insults, which was rescued by enhancing the ZIP9-centered androgen pathway in the short term. Increasing the unfolded protein response might be an important downstream mechanism involved. These results promote a better understanding of the time-dependent reproductive toxicity of 2605 MHz RF-EMR.

Modulation of itch and pain signals processing in ventrobasal thalamus by thalamic reticular nucleus.

Thalamic reticular nucleus (TRN) is known to be crucial for dynamically modulating sensory processing. Recently, the functional role of TRN in itch and pain sensation processing has drawn much attention. We found that ventrobasal thalamus (VB) neurons exhibited scratching behavior-related and nociceptive behavior-related neuronal activity changes, and most of VB neurons responsive to pruritic stimulus were also activated by nociceptive stimulus. Inhibition of VB could relieve itch-induced scratching behaviors and pathological pain without affecting basal nociceptive thresholds, and activation of VB could facilitate scratching behaviors. Tracing and electrophysiology recording results showed that VB mainly received inhibitory inputs from ventral TRN. Furthermore, optogenetic activation of TRN-VB projections suppressed scratching behaviors, and ablation of TRN enhanced scratching behaviors. In addition, activation of TRN-VB projections relieved the pathological pain without affecting basal nociceptive thresholds. Thus, our study indicates that TRN modulates itch and pain signals processing via TRN-VB inhibitory projections.

PBN-PVT projections modulate negative affective states in mice.

Long-lasting negative affections dampen enthusiasm for life, and dealing with negative affective states is essential for individual survival. The parabrachial nucleus (PBN) and thalamic paraventricular nucleus (PVT) are critical for modulating affective states in mice. However, the functional roles of PBN-PVT projections in modulating affective states remain elusive. Here, we show that PBN neurons send dense projection fibers to the PVT and form direct excitatory synapses with PVT neurons. Activation of the PBN-PVT pathway induces robust behaviors associated with negative affective states without affecting nociceptive behaviors. Inhibition of the PBN-PVT pathway reduces aversion-like and fear-like behaviors. Furthermore, the PVT neurons innervated by the PBN are activated by aversive stimulation, and activation of PBN-PVT projections enhances the neuronal activity of PVT neurons in response to the aversive stimulus. Consistently, activation of PVT neurons that received PBN-PVT projections induces anxiety-like behaviors. Thus, our study indicates that PBN-PVT projections modulate negative affective states in mice.

Gypenosides Inhibit Inflammatory Response and Apoptosis of Endothelial and Epithelial Cells in LPS-Induced ALI: A Study Based on Bioinformatic Analysis and in vivo/vitro Experiments.

INTRODUCTION: Severe inflammatory response leads to poor prognosis of acute lung injury (ALI), the role of gypenosides (GPs) on ALI is not fully clear. The study aimed at investigating the effects of GPs on ALI. METHODS: We firstly established LPS-induced ALI mice model. Then, we tested whether GPs contributed to alleviate inflammatory response and lung injury of ALI in vivo. In order to identify specific mechanisms of the phenomenon, we conducted a bioinformatic analysis of LPS-induced ALI mice based on GEO database to identify hub differentially expressed genes (DEGs). PPI network of the DEGs was used to find hub-genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted based on the DAVID database to identify which pathways the genes enriched. Then, we tested whether GPs inhibited lung injury and inflammatory response via the enriched pathways. We also tested whether GPs inhibited the apoptosis of endothelial and epithelial cells secondary to severe inflammation. RESULTS: We found GPs significantly alleviated lung injury and improved the survival rate of LPS-induced ALI mice in vivo. Bioinformatic analysis identified 20 hub-genes from DEGs, they were mainly enriched in NF-κB and TNF-α pathways. GPs could reduce the lung injury and inflammatory response via inhibiting NF-κB and TNF-α pathways in vivo. Our results indicated that GPs also inhibited inflammatory response of epithelial and endothelial cells via NF-κB and TNF-α pathways in vitro. Severe inflammatory response could also lead to apoptosis of endothelial and epithelial cells. Our results indicated that GPs effectively inhibited the apoptosis of endothelial and epithelial cells. CONCLUSION: Our study suggested GPs contributed to alleviated lung injury in vivo and inhibited inflammation and apoptosis of endothelial and epithelial cells in vitro, providing novel strategies for the prevention and therapy for ALI.

Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae).

As a promising novel marine fish model for future research on marine ecotoxicology as well as an animal model of human disease, the genome information of yellowstripe goby (Mugilogobius chulae) remains unknown. Here we report the first annotated chromosome-level reference genome assembly for yellowstripe goby. A 20.67-cM sex determination region was discovered on chromosome 5 and seven potential sex-determining genes were identified. Based on combined genome and transcriptome data, we identified three key lipid metabolic pathways for high-fat accumulation in the liver of yellowstripe goby. The changes in the expression patterns of MGLL and CPT1 at different development stage of the liver, and the expansion of the ABCA1 gene, innate immune gene TLR23, and TRIM family genes may help in balancing high-fat storage in hepatocytes and steatohepatitis. These results may provide insights into understanding the molecular mechanisms of sex determination and high-fat storage in the liver of marine fishes.

Posterior Thalamic Nucleus Mediates Facial Histaminergic Itch.

Itch induces a desire to scratch and leads to skin damage in some severe conditions. Much progress has been made in the peripheral and spinal level, and recent findings suggested that we need to focus on the central circuitry mechanism. However, the functional role of the thalamus in itch signal processing remains largely unknown. We showed that the posterior thalamic nucleus (Po) played a vital role in modulating facial histaminergic itch signal processing. We found that the calcium signal of Po neurons was increased during the histaminergic itch-induced scratching behavior in the cheek model, and pharmacogenetic suppression of Po neurons reduced the scratching behaviors. Retrograde mapping results suggested that the Po receives information from the somatosensory cortex, motor cortex, parabrachial nucleus (PBN), the principal sensory trigeminal nucleus (PrV) and the spinal trigeminal nucleus (SpV), which participate in itch signal transmission from head and body. Thus, our study indicates that the Po is critical in modulating facial histaminergic itch signal processing.

ZEAMAP, a Comprehensive Database Adapted to the Maize Multi-Omics Era.

As one of the most extensively cultivated crops, maize (Zea mays L.) has been extensively studied by researchers and breeders for over a century. With advances in high-throughput detection of various omics data, a wealth of multi-dimensional and multi-omics information has been accumulated for maize and its wild relative, teosinte. Integration of this information has the potential to accelerate genetic research and generate improvements in maize agronomic traits. To this end, we constructed ZEAMAP, a comprehensive database incorporating multiple reference genomes, annotations, comparative genomics, transcriptomes, open chromatin regions, chromatin interactions, high-quality genetic variants, phenotypes, metabolomics, genetic maps, genetic mapping loci, population structures, and populational DNA methylation signals within maize inbred lines. ZEAMAP is user friendly, with the ability to interactively integrate, visualize, and cross-reference multiple different omics datasets.

Activation of CaMKII and GluR1 by the PSD-95-GluN2B Coupling-Dependent Phosphorylation of GluN2B in the Spinal Cord in a Rat Model of Type-2 Diabetic Neuropathic Pain.

The mechanisms underlying type-2 diabetic neuropathic pain (DNP) are unclear. This study investigates the coupling of postsynaptic density-95 (PSD-95) to N-methyl-D-aspartate receptor subunit 2B (GluN2B), and the subsequent phosphorylation of GluN2B (Tyr1472-GluN2B) in the spinal cord in a rat model of type-2 DNP. Expression levels of PSD-95, Tyr1472-GluN2B, Ca2+/calmodulin-dependent protein kinase II (CaMKII) and its phosphorylated counterpart (Thr286-CaMKII), and α-amino-3-hydroxy-5-methyl-4-soxazole propionic acid receptor subtype 1 (GluR1) and its phosphorylated counterpart (Ser831-GluR1) were significantly increased versus controls in the spinal cord of type-2 DNP rats whereas the expression of total spinal GluN2B did not change. The intrathecal injection of Ro25-6981 (a specific antagonist of GluN2B) or Tat-NR2B9c (a mimetic peptide disrupting the interaction between PSD-95 and GluN2B) induced an antihyperalgesic effect and blocked the increased expression of Tyr1472-GluN2B, CaMKII, GluR1, Thr286-CaMKII, and Ser831-GluR1 in the spinal cords; the increase in spinal cord PSD-95 was not affected. These findings indicate that the PSD-95-GluN2B interaction may increase phosphorylation of GluN2B, and subsequently induce the expression of phosphorylation of CaMKII and GluR1 in the spinal cord of type-2 DNP rats. Targeting the interaction of PSD-95 with GluN2B may provide a new therapeutic strategy for type-2 DNP.

Long-term exposure to 4G smartphone radiofrequency electromagnetic radiation diminished male reproductive potential by directly disrupting Spock3-MMP2-BTB axis in the testes of adult rats.

The correlation between long-term exposure to SRF-EMR and the decline in male fertility is gradually receiving increasing attention from the medical society. While male reproductive organs are often exposed to SRF-EMR, little is currently known about the direct effects of long-term SRF-EMR exposure on the testes and its involvement in the suppression of male reproductive potential. The present study was designed to investigate this issue by using 4G SRF-EMR in rats. A unique exposure model using a 4G smartphone achieved localized exposure to the scrotum of the rats for 6 h each day (the smartphone was kept on active talk mode and received an external call for 1 min over 10 min intervals). Results showed that SRF-EMR exposure for 150 days decreased sperm quality and pup weight, accompanied by testicular injury. However, these adverse effects were not evident in rats exposed to SRF-EMR for 50 days or 100 days. Sequencing analysis and western blotting suggested Spock3 overexpression in the testes of rats exposed to SRF-EMR for 150 days. Inhibition of Spock3 overexpression improved sperm quality decline and alleviated testicular injury and BTB disorder in the exposed rats. Additionally, SRF-EMR exposure suppressed MMP2 activity, while increasing the activity of the MMP14-Spock3 complexes and decreasing MMP14-MMP2 complexes; these results were reversed by Spock3 inhibition. Thus, long-term exposure to 4G SRF-EMR diminished male fertility by directly disrupting the Spock3-MMP2-BTB axis in the testes of adult rats. To our knowledge, this is the first study to show direct toxicity of SRF-EMR on the testes emerging after long-term exposure.

High-Throughput Identification and Analysis of Novel Conotoxins from Three Vermivorous Cone Snails by Transcriptome Sequencing.

The venom of each Conus species consists of a diverse array of neurophysiologically active peptides, which are mostly unique to the examined species. In this study, we performed high-throughput transcriptome sequencing to extract and analyze putative conotoxin transcripts from the venom ducts of 3 vermivorous cone snails (C. caracteristicus, C. generalis, and C. quercinus), which are resident in offshore waters of the South China Sea. In total, 118, 61, and 48 putative conotoxins (across 22 superfamilies) were identified from the 3 Conus species, respectively; most of them are novel, and some possess new cysteine patterns. Interestingly, a series of 45 unassigned conotoxins presented with a new framework of C-C-C-C-C-C, and their mature regions were sufficiently distinct from any other known conotoxins, most likely representing a new superfamily. O- and M-superfamily conotoxins were the most abundant in transcript number and transcription level, suggesting their critical roles in the venom functions of these vermivorous cone snails. In addition, we identified numerous functional proteins with potential involvement in the biosynthesis, modification, and delivery process of conotoxins, which may shed light on the fundamental mechanisms for the generation of these important conotoxins within the venom duct of cone snails.

High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail (Conus quercinus) by Transcriptome Sequencing.

The primary objective of this study was to realize the large-scale discovery of conotoxin sequences from different organs (including the venom duct, venom bulb and salivary gland) of the vermivorous Oak cone snail, Conus quercinus. Using high-throughput transcriptome sequencing, we identified 133 putative conotoxins that belong to 34 known superfamilies, of which nine were previously reported while the remaining 124 were novel conotoxins, with 17 in new and unassigned conotoxin groups. A-, O1-, M-, and I2- superfamilies were the most abundant, and the cysteine frameworks XIII and VIII were observed for the first time in the A- and I2-superfamilies. The transcriptome data from the venom duct, venom bulb and salivary gland showed considerable inter-organizational variations. Each organ had many exclusive conotoxins, and only seven of all the inferred mature peptides were common in the three organs. As expected, most of the identified conotoxins were synthesized in the venom duct at relatively high levels; however, a number of conotoxins were also identified in the venom bulb and the salivary gland with very low transcription levels. Therefore, various organs have different conotoxins with high diversity, suggesting greater contributions from several organs to the high-throughput discovery of new conotoxins for future drug development.

[The relationship between autophagy activation in spinal cord and type 2 diabetic neuropathic pain in rats].

OBJECTIVE: To investigate the relationship between autophagy function in spinal cord and type 2 diabetic neuropathic pain in rats. METHODS: Forty-two male Sprague-Dawley rats were fed with a high-sugar, high-fat diet for 8 weeks to induce the insulin resistance, and then received a single intraperitoneal streptozocin (STZ) injection to establish type 2 diabetes rat model. Two weeks after STZ injection, mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL) of rats were detected, the rats with MWT and TWL decreasing to below 80% compared to baseline were chosen as type 2 diabetic neuropathic pain rats (group DNP, n=24), the rest of the rats were chosen as type 2 diabetic non-neuropathic pain rats (group DA, n=18). And another 18 normal rats randomly selected from the total were classified as control group (group C) and fed with common forage for 8 weeks. The MWT and TWL were measured again on the 3rd, 7th and 14th day after determining the grouping of DA and DNP, and then, the lumbar segments 4~6 of the spinal cord were removed from the executed rats for determination of the expressions of microtubule-associated protein light chain 3 (LC3)、Beclin-1and P62 by Western blot. The co-expressions of P62 with GFAP or OX-42 or NeuN in spinal dorsal horn were detected in another 6 lumbar segments of diabetic neuropathic pain (DNP) rats on the 7th day by immunofluorescence double dye method. RESULTS: Compared with group C, the insulin level was increased and ISI decreased in SD rats fed with high-sugar, high-fat diet, that meant the rats in insulin-resistance. After STZ injection, blood glucose rose to the standard of type 2 diabetes mellitus, i.e. ≥ 16.7 mmol/L. Compared with group C and group DA, MWT was significantly decreased, TWL shortened and the expression of LC3-Ⅱ and Beclin-1 in the spinal dorsal horn up-regulated, P62 expression down-regulated on the 3rd, 7th and 14th day in group DNP (P<0.05). P62 was mainly localized in spinal dorsal horn and coexisted with neurons, and spots of P62 immunoreactivity could be detected in a few microglia but not observed in astrocyte. CONCLUSIONS: The changes in expression of LC3-Ⅱ、Beclin-1 and P62 in spinal cord of type 2 diabetes neuropathic pain rats means autophagy activation of spinal, up-regulated autophagy of neurons in spinal dorsal horn mainly involves in the formation and development of type 2 diabetic neuropathic pain in rats.

Cortex Mori Radicis extract attenuates myocardial damages in diabetic rats by regulating ERS.

Diabetic cardiomyopathy (DCM) is diagnosed when patients with diabetes develop ventricular dysfunction but do not exhibit coronary atherosclerosis or hypertension. Cortex Mori (CM) Radicis,he epidermis of the root of Morus alba L, has been traditionally used for cough treatment in oriental medicine. In this study, we investigated the protection of myocardium by CM in streptozotocin (STZ)-induced diabetic rats and the underlying mechanisms. Diabetes was induced in rats by an injection of STZ at 25mg/kg. The animals were randomly divided into 4 groups: control, diabetes, diabetes with CM treatment, diabetes with CM preventative treatment. Pathological changes were examined by hematoxylin-eosin staining. Extracellular matrix content was assessed by Masson's trichrome staining and Western blot. Endoplasmic reticulum (ER) stress-associated molecules and main components of the mitogen-activated protein kinase (MAPK) pathway were also measured by Western blot. Myocardial damages were induced by the injection of STZ as evidenced by abnormal blood glucose and pathological cardiac changes. Administration of CM markedly ameliorated myocardial damages such as cardiac hypertrophy and fibrosis. ER stress was down-regulated, and p38 and ERK were suppressed by CM. Thus, CM may have therapeutic potential in the treatment of DCM by attenuating ER stress and ERK and p38 MAPK activation.

[The mechanism of RvD1 alleviates type 2 diabetic neuropathic pain by influencing microglia polarization in rats].

OBJECTIVE: To study the relationship between microglia polarization in the spinal dorsal horn and type 2 diabetic neuropathic pain (DNP). And explore the mechanism of RvD1 alleviating type 2 diabetic neuropathic pain. METHODS: Type 2 diabetes mellitus (T2DM) rats came from the male SD rats which were fed by high-fat and high-sucrose diet and given intraperitoneal streptozotocin(STZ), then detected fa sting blood glucose level, the mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL), which was to prepare the type 2 DNP model rats. And they were randomly divided into 3 groups:type 2 DNP group (group D), type 2 DNP and RvD1 group (group R), type 2 DNP and solvent control group (group S), 36 rats in each group. After being given STZ 14 days, the rats of group D, R, S were placed a catheter in subarachnoid cavity. Three days later, the RvD1 10µl (10 ng/µl) and 100% ethanol 10µl were injected into subarach-noid cavity through the catheter once a day for 14 consecutive days. Another 36 normal rats were served as normal control group (group N) and were fed with common forage. MWT and TWL were measured at 1, 3, 7, 14 days after Subarachnoid injection, then the nine rats'spinal cord of the lumbar segment 4~6 were removed to detect the expression of inducible nitric oxide synthase(iNOS) and arginase 1(Arg1) by Western blot, the marker of microglia M1 and M2 polarization. RESULTS: Compared with group N, MWT was decreased significantly and TWL was shortened, the expression of Arg1 was down-regulated and the expression of iNOS was up-regulated in spinal dorsal horn at the 1, 3, 7, 14 days in groups D and S (P < 0.05). Compared with group D, MWT was significantly increased and TWL was prolonged, the expression of Arg1 was up-regulated and the expression of iNOS was down-regulated in spinal dorsal horn at the 7, 14 days in group R (P < 0.05). There was no significant difference in the MWT, TWL and expression of Arg1 and iNOS between D and S groups. CONCLUSIONS: RvD1 promotes mi-croglia toward M2 polarization and alleviates type 2 diabetic neuropathic pain in rats.

High-throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcriptome sequencing.

BACKGROUND: The venom of predatory marine cone snails mainly contains a diverse array of unique bioactive peptides commonly referred to as conopeptides or conotoxins. These peptides have proven to be valuable pharmacological probes and potential drugs because of their high specificity and affinity to important ion channels, receptors and transporters of the nervous system. Most previous studies have focused specifically on the conopeptides from piscivorous and molluscivorous cone snails, but little attention has been devoted to the dominant vermivorous species. RESULTS: The vermivorous Chinese tubular cone snail, Conus betulinus, is the dominant Conus species inhabiting the South China Sea. The transcriptomes of venom ducts and venom bulbs from a variety of specimens of this species were sequenced using both next-generation sequencing and traditional Sanger sequencing technologies, resulting in the identification of a total of 215 distinct conopeptides. Among these, 183 were novel conopeptides, including nine new superfamilies. It appeared that most of the identified conopeptides were synthesized in the venom duct, while a handful of conopeptides were identified only in the venom bulb and at very low levels. CONCLUSIONS: We identified 215 unique putative conopeptide transcripts from the combination of five transcriptomes and one EST sequencing dataset. Variation in conopeptides from different specimens of C. betulinus was observed, which suggested the presence of intraspecific variability in toxin production at the genetic level. These novel conopeptides provide a potentially fertile resource for the development of new pharmaceuticals, and a pathway for the discovery of new conotoxins.

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies.

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system.

Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation.

The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea.