Transcriptome Database Research Articles

Highly sensitive microfluidic sensor using integrated optical fiber and real-time single-cell Raman spectroscopy for diagnosis of pancreatic cancer

Pancreatic cancer is notoriously lethal due to its late diagnosis and poor patient response to treatments, posing a significant clinical challenge. This study introduced a novel approach that combines a single-cell capturing platform, tumor-targeted silver (Ag) nanoprobes, and precisely docking tapered fiber integrated with Raman spectroscopy. This approach focuses on early detection and progression monitoring of pancreatic cancer. Utilizing tumor-targeted Ag nanoparticles and tapered multimode fibers enhances Raman signals, minimizes light loss, and reduces background noise. This advanced Raman system allows for detailed molecular spectroscopic examination of individual cells, offering more practical information and enabling earlier detection and accurate staging of pancreatic cancer compared to conventional multicellular Raman spectroscopy. Transcriptomic analysis using high-throughput gene screening and transcriptomic databases confirmed the ability and accuracy of this method to identify molecular changes in normal, early, and metastatic pancreatic cancer cells. Key findings revealed that cell adhesion, migration, and the extracellular matrix are closely related to single-cell Raman spectroscopy (SCRS) results, highlighting components such as collagen, phospholipids, and carotene. Therefore, the SCRS approach provides a comprehensive view of the molecular composition, biological function, and material changes in cells, offering a novel, accurate, reliable, rapid, and efficient method for diagnosing and monitoring pancreatic cancer.

Establishment of Novel Simple Sequence Repeat (SSR) Markers from Chimonanthus praecox Transcriptome Data and Their Application in the Identification of Varieties.

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag-simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.

Septin 9 expression regulates 'don't eat me' signals and identifies an immune-epithelial class of intrahepatic cholangiocarcinoma.

Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and aggressive liver cancer with limited therapeutic options. Precise classification and immunotherapy are perspectives to improve the treatments. We reported the role of septin 9 in apico-basal polarity and epithelial-to-mesenchymal transition (EMT). Here, we aim to elucidate its role in iCCA. We analyzed single-cell transcriptomes from human iCCA tumor cells based on phenotype and cell state. Knockdown of the septin 9 gene (SEPT9) was done using small interfering RNA (siRNA); interferon-γ (IFN-γ) stimulation was performed using different CCA cells; gene expressions were analyzed by reverse transcription and real-time PCR analysis (RT-qPCR); and immunofluorescence, immunoblotting, and flow cytometry were performed to assess the expression of proteins. The differential distributions of SEPT9 and vimentin (VIM) gene expressions allowed us to define specific cellular trajectories of malignant cells and thus identified distinct clusters of iCCA cells. One cluster was enriched in VIM and extracellular-matrix (ECM) remodeling molecules, and another had high expression of SEPT9 and genes from the 'don't eat me' signal involved in immune escape. This antagonism between SEPT9 and VIM was confirmed by in vitro experiments. Notably, SEPT9 and 'don't eat me' gene expressions were inversely correlated to those of vimentin and the EMT markers. SEPT9 expression was upregulated by IFN-γ and SEPT9 knockdown decreased expression of 'don't eat me' signal genes and increased expression of mesenchymal markers. Cancer Cell Line Encyclopedia (CCLE) transcriptome database analyses confirmed that iCCA cells enriched in septin 9 exhibit epithelial-like features. This study revealed septin 9 as a cytoskeleton element of iCCA epithelial-like cells and a regulator of the immune system response. It also brings new insights into the enigmatic relationship between EMT and immune response. Notably, we decoded a potential mechanism that could sensitize patients to immunotherapies.

Insights into chlorantraniliprole exposure via activating cytochrome P450-mediated xenobiotic metabolism pathway in the Procambarus clarkii: Identification of P450 genes involved in detoxification

To investigate the impact of chlorantraniliprole on Procambarus clarkii, acute toxicity tests were performed. Results indicated that 96 h post-exposure to chlorantraniliprole (60 mg/L) led to the separation of the hepatopancreas basement membrane, causing cell swelling, rupture, and vacuolation. Moreover, acid phosphatase (ACP) and alkaline phosphatase (AKP) activities exhibited divergent trends across four concentrations of chlorantraniliprole (0, 30, 60, and 90 mg/L). Hydrogen peroxide (H2O2) and catalase (CAT) levels significantly increased, while total superoxide dismutase (T-SOD) and malonaldehyde (MDA) activities decreased, indicating oxidative stress in the hepatopancreas. A total of 276 differentially expressed genes (DEGs) were identified, with 204 up-regulated and 72 down-regulated. Out of these, 114 DEGs were successfully annotated and classified into 99 pathways, with a primary focus on the cytochrome P450-mediated xenobiotic metabolism pathway. The DEGs enriched in this pathway, along with transcriptome data, were validated using quantitative-polymerase chain reaction. This study enhances the transcriptome database of P. clarkii and provides fundamental insights into its immune defense and antioxidant mechanisms. Additionally, it lays a theoretical foundation for future research on disease prevention in P. clarkii within rice-shrimp culture systems.

RNA Helicase DDX5 Maintains Cardiac Function by Regulating CamkIIδ Alternative Splicing.

Heart failure (HF) is a leading cause of morbidity and mortality worldwide. RNA-binding proteins are identified as regulators of cardiac disease; DDX5 (dead-box helicase 5) is a master regulator of many RNA processes, although its function in heart physiology remains unclear. We assessed DDX5 expression in human failing hearts and a mouse HF model. To study the function of DDX5 in heart, we engineered cardiomyocyte-specific Ddx5 knockout mice. We overexpressed DDX5 in cardiomyocytes using adeno-associated virus serotype 9 and performed transverse aortic constriction to establish the murine HF model. The mechanisms underlined were subsequently investigated using immunoprecipitation-mass spectrometry, RNA-sequencing, alternative splicing analysis, and RNA immunoprecipitation sequencing. We screened transcriptome databases of murine HF and human dilated cardiomyopathy samples and found that DDX5 was significantly downregulated in both. Cardiomyocyte-specific deletion of Ddx5 resulted in HF with reduced cardiac function, an enlarged heart chamber, and increased fibrosis in mice. DDX5 overexpression improved cardiac function and protected against adverse cardiac remodeling in mice with transverse aortic constriction-induced HF. Furthermore, proteomics revealed that DDX5 is involved in RNA splicing in cardiomyocytes. We found that DDX5 regulated the aberrant splicing of Ca2+/calmodulin-dependent protein kinase IIδ (CamkIIδ), thus preventing the production of CaMKIIδA, which phosphorylates L-type calcium channel by serine residues of Cacna1c, leading to impaired Ca2+ homeostasis. In line with this, we found increased intracellular Ca2+ transients and increased sarcoplasmic reticulum Ca2+ content in DDX5-depleted cardiomyocytes. Using adeno-associated virus serotype 9 knockdown of CaMKIIδA partially rescued the cardiac dysfunction and HF in Ddx5 knockout mice. These findings reveal a role for DDX5 in maintaining calcium homeostasis and cardiac function by regulating alternative splicing in cardiomyocytes, identifying the DDX5 as a potential target for therapeutic intervention in HF.

Exploring transcriptomic databases: unraveling circadian gene disruptions in lower grade glioma

The study explored the role of circadian rhythm genes (CRGs) in lower grade glioma (LGG) development and found that certain genes, such as CRY1, NPAS2, and RORB, were associated with increased or decreased risk of LGG. The study also investigated the correlation between CRGs and immune cell infiltration, revealing a negative association with macrophage infiltration and a positive correlation with B cell and CD8 + T cell infiltration. Additionally, the study identified major mutated CRGs, including PER2, BMAL1, CLOCK, and BMAL2, and their potential interaction with other CNS-associated genes. The study suggests that CRGs play a crucial role in immune response and tumorigenesis in LGG patients and warrants further investigation.

First regional reference database of northern Adriatic diatom transcriptomes

Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.

Mining GATA Transcription Factor Encoding Genes in The Cocoa Tree (<i>Theobroma cacao</i> L.) Suggests Their Potential Roles in Embryo Development and Biotic Stress Response

GATA transcription factors (TFs) are widely recognized as significant regulators, characterized by a DNA-binding domain that consists of a type IV zinc finger motif. This TF family has been widely investigated in numerous higher plant species. The purpose of the present work was to comprehensively analyze the GATA TF in cocoa plant (Theobroma cacao L.) by using various bioinformatics tools. As a result, a total of 24 members of the GATA TFs have been identified and annotated in the assembly of the cocoa plant. According to phylogenetic analysis, these TcGATA proteins were classified into four distinct groups, including groups I (10 members), II (seven members), III (five members), and IV (two members). Next, our investigation indicated that the TcGATA proteins in different groups exhibited a high variation in their physic-chemical features due to their different protein lengths, gene structures, and conserved motif distributions, whereas the TcGATA proteins in the same clade might share the common conserved motifs. Additionally, the gene duplication of the TcGATA genes in the cocoa plant was also investigated. Of our interest, the relative expression levels of the TcGATA genes were investigated according to available transcriptome databases. The results exhibited differential expression patterns of all TcGATA genes in various developmental stages of zygotic and somatic embryogenesis, indicating that these TcGATA genes divergently function during various developmental stages of the zygotic and somatic embryos. Moreover, TcGATA genes were differently expressed under Phytophthora megakarya treatment across different points of treatment and cocoa varieties. To sum up, our findings could provide a basis for a further deep understanding of the GATAs in the cocoa plant.

Genome-Wide Analysis of the WOX Family and Its Expression Pattern in Root Development of Paeonia ostii.

Tree peony (Paeonia suffruticosa Andr.) is a woody plant with high ornamental, medicinal, and oil values. However, its low rooting rate and poor rooting quality are bottleneck issues in the micropropagation of P. ostii. The WUSCHEL-related homeobox (WOX) family plays a crucial role in root development. In this study, based on the screening of the genome and root transcriptome database, we identified ten WOX members in P. ostii. Phylogenetic analysis revealed that the ten PoWOX proteins clustered into three major clades, the WUS, intermediate, and ancient clade, respectively. The conserved motifs and tertiary structures of PoWOX proteins located in the same clade exhibited higher similarity. The analysis of cis-regulatory elements in the promoter indicated that PoWOX genes are involved in plant growth and development, phytohormones, and stress responses. The expression analysis revealed that PoWOX genes are expressed in distinct tissues. PoWOX4, PoWOX5, PoWOX11, and PoWOX13b are preferentially expressed in roots at the early stage of root primordium formation, suggesting their role in the initiation and development of roots. These results will provide a comprehensive reference for the evolution and potential function of the WOX family and offer guidance for further study on the root development of tree peony.

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations.

Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of transcriptomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Such platforms can help bridge the gap between computational and wet lab scientists through user-friendly web-based interfaces needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.

Glucose transporters and sodium glucose co-transporters cooperatively import glucose into energy-demanding organs in carcinogenic liver fluke Clonorchis sinensis.

The liver fluke Clonorchis sinensis imports large amounts of glucose to generate energy and metabolic intermediates through glycolysis. We hypothesized that C. sinensis absorbs glucose through glucose transporters and identified four subtypes of glucose transporter (CsGTP) and one sodium glucose co-transporter (CsSGLT) in C. sinensis. Expressed sequence tags encoding CsGTPs were retrieved from the C. sinensis transcriptome database, and their full-length cDNA sequences were obtained by rapid amplification of cDNA ends (RACE). The tissue distribution of glucose transporters in C. sinensis adults was determined using immunohistochemical staining. Developmental expression was measured using RT-qPCR. The transport and distribution of glucose into living C. sinensis were monitored using confocal microscopy. Membrane topology and key functional residues of CsGTPs were homologous to their counterparts in animals and humans. CsGTP1, 2, and 4 were transcribed 2.4-5.5 times higher in the adults than metacercariae, while CsGTP3 was transcribed 2.1 times higher in the metacercariae than adults. CsSGLT transcription was 163.6 times higher in adults than in metacercariae. In adults, CsSGLT was most abundant in the tegument; CsGTP3 and CsSGLT were localized in the vitelline gland, uterine wall, eggs, mesenchymal tissue, and testes; CsGTP4 was found in sperm and mesenchymal tissue; and CsGTP1 was mainly in the sperm and testes. In C. sinensis adults, exogenous glucose is imported in a short time and is present mainly in the middle and posterior body, in which the somatic and reproductive organs are located. Of the exogenous glucose, 53.6% was imported through CsSGLT and 46.4% through CsGTPs. Exogenous glucose import was effectively inhibited by cytochalasin B and phlorizin. We propose that CsSGLT cooperates with CsGTPs to import exogenous glucose from the environmental bile, transport glucose across mesenchymal tissue cells, and finally supply energy-demanding organs in C. sinensis adults. Studies on glucose transporters may pave the way for the development of new anthelmintic drugs.

Metabolic Profiling and Transcriptome Analysis Provide Insights into the Anthocyanin Types and Biosynthesis in Zingiber striolatum Diels Flower Buds in Three Planting Modes

The flower buds of Zingiber striolatum Diels are considered a special vegetable in China, and they are rich in anthocyanins. However, the detailed composition types and the molecular mechanism of anthocyanin biosynthesis in Z. striolatum flower buds are still unclear. In this study, targeted metabolites were used to analyze and identify the anthocyanin types of Z. striolatum in three planting modes: monoculture (CK), intercropping with maize (ZP), and intercropping with soybean (SP). A total of 48 anthocyanins were identified with significant differential accumulation in Z. striolatum flower buds. Among them, cyanidin-3-O-glucoside was the main composition type of anthocyanins. Furthermore, the composition types of blue anthocyanin were identified in flower buds. A total of 15 structure genes were obtained from the transcriptome database of Z. striolatum flower buds. The qRT-PCR results revealed that the expression levels of ZsC4H-1, ZsC4H-2, ZsCHS-2, ZsCHI, ZsF3H, ZsF3’H, ZsDFR, ZsF3’5’H-3, and ZsANS genes were the highest in the ZP model. This study showed that the ZP model contributes to anthocyanin synthesis and accumulation of Z. striolatum flower buds among the three planting modes of Z. striolatum. These findings provide valuable information for research on the planting model and anthocyanin biosynthesis in Z. striolatum flower buds.

Loss of NLRP6 increases the severity of kidney fibrosis.

While NLRP3 contributes to kidney fibrosis, the function of most NOD-like receptors (NLRs) in chronic kidney disease (CKD) remains unexplored. To identify further NLR members involved in the pathogenesis of CKD, we searched for NLR genes expressed by normal kidneys and differentially expressed in human CKD transcriptomics databases. For NLRP6, lower kidney expression correlated with decreasing glomerular filtration rate. The role and molecular mechanisms of Nlrp6 in kidney fibrosis were explored in wild-type and Nlrp6-deficient mice and cell cultures. Data mining of single-cell transcriptomics databases identified proximal tubular cells as the main site of Nlrp6 expression in normal human kidneys and tubular cell Nlrp6 was lost in CKD. We confirmed kidney Nlrp6 downregulation following murine unilateral ureteral obstruction. Nlrp6-deficient mice had higher kidney p38 MAPK activation and more severe kidney inflammation and fibrosis. Similar results were obtained in adenine-induced kidney fibrosis. Mechanistically, profibrotic cytokines transforming growth factor beta 1 (TGF-β1) and TWEAK decreased Nlrp6 expression in cultured tubular cells, and Nlrp6 downregulation resulted in increased TGF-β1 and CTGF expression through p38 MAPK activation, as well as in downregulation of the antifibrotic factor Klotho, suggesting that loss of Nlrp6 promotes maladaptive tubular cell responses. The pattern of gene expression following Nlrp6 targeting in cultured proximal tubular cells was consistent with maladaptive transitions for proximal tubular cells described in single-cell transcriptomics datasets. In conclusion, endogenous constitutive Nlrp6 dampens sterile kidney inflammation and fibrosis. Loss of Nlrp6 expression by tubular cells may contribute to CKD progression.

Sequencing and analysis of transcriptome to reveal regulation of gene expression for polysaccharide synthesis in Dendrobium officinale under different light quality

Light is a key factor affecting the growth and quality formation of Dendrobium officinale Kimura et Migo. In this study, we used D. officinale under different light conditions as experimental materials to explore the key genes that regulate its polysaccharide content. In addition, we cloned the UGPase gene and validated the gene by bioinformatics analysis and real-time quantitative PCR. Compared with the natural light control group, 494, 1630 and 599 differentially expressed genes were screened under different light quality conditions of red, blue and yellow, respectively. GO and KEGG enrichment analyses of these differentially expressed genes showed that the differentially expressed genes were enriched in the light signal transduction process under different light quality conditions. Bioinformatics analyses showed that the sequences of the genes were highly conserved with the sequences of the UGPase genes of other species, and had the highest sequence similarity with Phalaenopsis, which is also a member of the orchid family. Real-time quantitative PCR results showed that red light had the most significant promoting effect on the UGPase gene of D. officinale. In this study, we applied high-throughput sequencing technology to establish a transcriptome database of D. officinale under different light conditions and obtained a large amount of transcriptional information about D. officinale. The related genes affecting the quality of D. officinale were analysed at the transcriptional level, and the D. officinale UGPase gene was cloned, and its expression was analysed in different tissues and under different light conditions.

Unveiling phenylpropanoid regulation: the role of DzMYB activator and repressor in durian (Durio zibethinus) fruit.

DzMYB2 functions as an MYB activator, while DzMYB3 acts as an MYB repressor. They bind to promoters, interact with DzbHLH1, and influence phenolic contents, revealing their roles in phenylpropanoid regulation in durian pulps. Durian fruit has a high nutritional value attributed to its enriched bioactive compounds, including phenolics, carotenoids, and vitamins. While various transcription factors (TFs) regulate phenylpropanoid biosynthesis, MYB (v-myb avian myeloblastosis viral oncogene homolog) TFs have emerged as pivotal players in regulating key genes within this pathway. This study aimed to identify additional candidate MYB TFs from the transcriptome database of the Monthong cultivar at five developmental/postharvest ripening stages. Candidate transcriptional activators were discerned among MYBs upregulated during the ripe stage based on the positive correlation observed between flavonoid biosynthetic genes and flavonoid contents in ripe durian pulps. Conversely, MYBs downregulated during the ripe stage were considered candidate repressors. This study focused on a candidate MYB activator (DzMYB2) and a candidate MYB repressor (DzMYB3) for functional characterization. LC-MS/MS analysis using Nicotiana benthamiana leaves transiently expressing DzMYB2 revealed increased phenolic compound contents compared with those in leaves expressing green fluorescence protein controls, while those transiently expressing DzMYB3 showed decreased phenolic compound contents. Furthermore, it was demonstrated that DzMYB2 controls phenylpropanoid biosynthesis in durian by regulating the promoters of various biosynthetic genes, including phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), chalcone isomerase (CHI), and dihydroflavonol reductase (DFR). Meanwhile, DzMYB3 regulates the promoters of PAL, 4-coumaroyl-CoA ligase (4CL), CHS, and CHI, resulting in the activation and repression of gene expression. Moreover, it was discovered that DzMYB2 and DzMYB3 could bind to another TF, DzbHLH1, in the regulation of flavonoid biosynthesis. These findings enhance our understanding of the pivotal role of MYB proteins in regulating the phenylpropanoid pathway in durian pulps.

IMPLICATIONS OF YWHAH GENE EXPRESSION IN THE EARLY DETECTION OF SEPSIS.

Sepsis, a complex and multifaceted condition, is a common occurrence with serious implications for critically ill patients in the intensive care unit (ICU). The YWHAH gene encodes the 14-3-3n protein, a member of the 14-3-3 protein family. While existing research primarily focuses on the role of 14-3-3n in conditions such as schizophrenia and various cancers, our study revealed that the expression of the YWHAH gene remained relatively stable in both infected individuals and healthy controls. Through Venn plot analysis following weighted gene correlation network analysis, we observed a potential association between elevated YWHAH expression and the transition from infection to sepsis. In a comprehensive analysis of public single-cell transcriptome databases, the expression of YWHAH was found to be distinctive in cases of sepsis and infection. These findings were corroborated through an in vitro analysis utilizing real-time polymerase chain reaction. This study represents the initial identification of variations in YWHAH gene expression between patients with infection and sepsis, potentially offering insights for the development of early detection and treatment strategies for sepsis.

Identification of ethanol analgesia quantitative trait loci and candidate genes in BXD recombinant inbred mouse lines.

Alcohol consumption produces acute analgesic effects, and people experiencing pain conditions may drink alcohol to alleviate discomfort. However, tolerance to the analgesic properties of alcohol could prompt escalating consumption and dependence. Both nociception and alcohol-induced analgesia are under significant genetic control. Understanding the genetic architecture of these processes could inform better treatment options for people with pain conditions. This study aims to identify quantitative trait loci (QTL) driving variation in ethanol-induced analgesia across BXD recombinant inbred mouse lines. Male and female mice from 62 BXD strains received ethanol or saline oral gavage for five days and were tested for hot plate (HP) latency at baseline, Day 1, and Day 5. QTL mapping of HP phenotypes identified a significant provisional QTL on chromosome 17 for Day 1 HP latency in mice receiving ethanol. An additional highly suggestive QTL was present on chromosome 9 for the difference in pre- and post-ethanol thermal nociception. Candidate genes within QTL support intervals were provisionally identified using HP phenotypic correlations to transcriptomic database, expression QTL analysis, and other bioinformatics inquiries. The combined behavioral and bioinformatic analyses yielded strong ethanol analgesia candidate genes, specifically Myo6. Thus, the results of this genetic study of ethanol-induced analgesia in BXD mouse strains may contribute significantly to our understanding of the molecular basis for individual variation in the analgesic response to acute ethanol.

Ascorbate peroxidase catalyses synthesis of protocatechualdehyde from p-hydroxybenzaldehyde in Lycoris aurea

Protocatechualdehyde is a plant natural phenolic aldehyde and an active ingredient with important bioactivities in traditional Chinese medicine. Protocatechualdehyde is also a key intermediate in the synthesis of Amaryllidaceae alkaloids for supplying the C6-C1 skeleton. However, the biosynthesis of protocatechualdehyde in plants remains obscure. In this study, we measured the protocatechualdehyde contents in the root, bulb, scape and flower of the Amaryllidaceae plant Lycoris aurea (L’Hér.) Herb., and performed the correlation analysis between the protocatechualdehyde contents and the transcriptional levels of the phenolic oxidization candidate protein encoding genes. We found that a novel ascorbate peroxidase encoded by the contig_24999 in the L. aurea transcriptome database had potential role in the biosynthesis of protocatechualdehyde. The LauAPX_24999 gene was then cloned from the cDNA of the scape of L. aurea. The transient expression of LauAPX_24999 protein in Arabidopsis protoplasts demonstrated that LauAPX_24999 protein was localized in the cytoplasm, thus belonging to Class II L-ascorbate peroxidase. Subsequently, LauAPX_24999 protein was heterogenously expressed in Escherichia coli, and identified that LauAPX_24999 biosynthesized protocatechualdehyde from p-hydroxybenzaldehyde using L-ascorbic acid as the electron donor. The protein structure modelling and molecular docking indicated that p-hydroxybenzaldehyde could access to the active pocket of LauAPX_24999 protein, and reside at the δ-edge of the heme group while L-ascorbic acid binds at the γ-heme edge. To our knowledge, LauAPX_24999 is the first enzyme discovered in plants able to biosynthesize protocatechualdehyde from p-hydroxybenzaldehyde, and offers a competent enzyme resource for the biosynthesis of Amaryllidaceae alkaloids via synthetic biology.

Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships.

The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely. We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis. The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.

Genome-wide identification and integrated analysis of the FAR1/FHY3 gene family and genes expression analysis under methyl jasmonate treatment in Panax ginseng C. A. Mey.

Ginseng (Panax ginseng C. A. Mey.) is an important and valuable medicinal plant species used in traditional Chinese medicine, and its metabolite ginsenoside is the primary active ingredient. The FAR1/FHY3 gene family members play critical roles in plant growth and development as well as participate in a variety of physiological processes, including plant development and signaling of hormones. Studies have indicated that methyl jasmonate treatment of ginseng adventitious roots resulted in a significant increase in the content of protopanaxadiol ginsenosides. Therefore, it is highly significant to screen the FAR1/FHY3 gene family members in ginseng and preliminarily investigate their expression patterns in response to methyl jasmonic acid signaling. In this study, we screened and identified the FAR1/FHY3 family genes in the ginseng transcriptome databases. And then, we analyzed their gene structure and phylogeny, chromosomal localization and expression patterns, and promoter cis-acting elements, and made GO functional annotations on the members of this family. After that, we treated the ginseng adventitious roots with 200 mM methyl jasmonate and investigated the trend of the expression of four genes containing the largest number of methyl jasmonate cis-acting elements at different treatment times. All four genes were able to respond to methyl jasmonate, the most significant change was in the PgFAR40 gene. This study provides data support for subsequent studies of this family member in ginseng and provides experimental reference for subsequent validation of the function of this family member under methyl jasmonic acid signaling.