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Bract coloration is one of the key ornamental traits in Bougainvillea, yet research has predominantly focused on phenotypic color traits and pigment composition, with limited understanding of the molecular mechanisms underlying color formation. This gap hinders the improvement and innovation in bract coloration. To elucidate the regulatory mechanisms of bract coloration in Bougainvillea and to enhance the utilization of its germplasm resources, this study employed the Illumina Novaseq 6000 sequencing platform to conduct transcriptomic sequencing on 21 samples of bracts exhibiting seven distinct phenotypes. Comparative analysis against Nr, Pfam, EggNOG, GO, and KEGG databases annotated 90,279 unigenes. The highest annotation rates were achieved with the Nr (40.13%), GO (30.44%), and EggNOG (25.64%) databases. Among the species annotated, Beta vulgaris (20.08%) and Chenopodium quinoa (14.58%) shared the highest homology with Bougainvillea bract transcriptomes. WGCNA analysis identified 12 positively correlated tissue-specific modules, of which 2 are related to bract color formation. By comparing transcriptome data and genes within these specific modules against the KEGG database, a total of 321 unigenes associated with bract color formation in Bougainvillea were discovered. Among these, 220 unigenes are involved in anthocyanin synthesis, 43 unigenes are involved in betalain synthesis, 23 unigenes are annotated as Chlorophyll a-b binding protein genes, and 35 unigenes participate in carotenoid synthesis. Quantitative real-time PCR (qRT-PCR) validation of 16 differentially expressed genes (DEGs) including PAL2, CHS1, ANS, BZ1, 6GT, CDOPA5GT, ANR, CHS2, and DOPA, revealed significant expression differences among magenta, yellow, white, and cherry-colored bracts, suggesting their potential as candidate genes for bract color development. This study not only enriches the transcriptomic data of Bougainvillea but also identifies genes associated with bract coloration, providing a valuable theoretical basis for future gene cloning, genetic engineering, and breeding efforts in Bougainvillea. [ABSTRACT FROM AUTHOR]

Hemsleyazhejiangensis C.Z. Zhang (Cucurbitaceae) is a rare and endangered plant species endemic to eastern China and is listed as a key protected species in Zhejiang Province. However, owing to the lack of genomic information and efficient molecular markers, the genetic diversity and population structure of this species remain unknown. In this study, we conducted transcriptome sequencing and de novo assembly of two H. zhejiangensis individuals to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers. Using CandiSSR software, 345 candidate polymorphic EST-SSRs were identified. Twenty EST-SSRs were developed for illustrating the genetic diversity and structure of the four populations of H. zhejiangensis. The populations of ZX (Taishun, Zhejiang) and WYL (Taishun, Zhejiang) have the closest kinship, whereas the populations from WYS (Mount Wuyi, Fujian) showed the farthest kinship with all populations from Zhejiang, suggesting that geographic isolation may significantly impede gene exchange and reduce the genetic diversity of this species. The availability of genomic resource will facilitate subsequent population genetic analyses and molecular breeding, which will be of great significance in formulating strategies for the conservation and utilization of H. zhejiangensis. [ABSTRACT FROM AUTHOR]

Saussurea laniceps is renowned for its extraordinary medicinal ingredients diversity, which is an important Tibetan medicinal plant in China. Flavonoids play an important role in the medicinal efficacy of S. laniceps. The species, however, has become increasingly scarce and endangered. Therefore, the use of callus to propagate medicinal resources is of great significance. We found that cold acclimation increased flavonoids content in S. laniceps callus. RNA-seq revealed a total of 18,414 and 21,215 differentially expressed genes at 6 d and 9 d cold (4 °C) periods, respectively. Besides, 456 differential expressed transcriptional factor genes were identified, among which AP2-EREBP, WRKY, NAC, MYB, bHLH and WD40 had the ability to induce the transcription of genes associated with flavonoid synthesis. A total of 34 unigenes were identified and linked to the flavonoids and related derivative biosynthesis pathway. The high expression levels of genes in regulating flavonoids biosynthesis (e.g., PAL, 4CL, CHS, CHI and F3’H) were identified. Besides, 66 up-regulated transporter genes were also detected, including the ATP-binding cassette (ABC) family (23), GST (13), MATE (12), vacuolar-associated proteins (8) and H+-ATPase (10). Consequently, these findings suggest that cold-acclimated callus could be an effective alternative resource for flavonoids in S. laniceps, which is valuable for the conservation and usage of this wild and endangered plant.Key message: The cold acclimation of Saussurea laniceps callus resulted in an increase in flavonoid content, with the initiation of both the anthocyanins and isoflavones sub-pathways within the flavonoid pathway. [ABSTRACT FROM AUTHOR]

Main conclusion: Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time–quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101 kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics. [ABSTRACT FROM AUTHOR]

Rheum pumilum stands as both a quintessential alpine plant and a significant traditional Chinese and Tibetan medicinal herb. Unraveling the molecular intricacies of seed germination in Rh. pumilum not only unveils the genetic foundations of plant seed germination strategies in high-altitude environments but also offers insights for cultivating Rh. pumilum medicinal materials. Employing transcriptome sequencing and the Weighted Gene Co-expression Network Analysis, this study delved into the shifts in gene expression levels across various stages of seed germination in Rh. pumilum. The process of seed germination in Rh. pumilum entails a cascade of complex physiological events. Six hormones (ABA, IAA, ETH, GA, BR, CK) emerged as pivotal players in seeds breaking in shells and the facilitation of rapid seed germination in Rh. pumilum. Fourteen transcription factor families (LOB, GRAS, B3, bHLH, bZIP, EIL, MYB, MYB related, NAC, TCP, WRKY, HSF, PLATZ, and SBP) along with four key genes (E2.4.1.13, EIN3, BZR, and BIN2) were identified that may be associated with both biotic and abiotic environmental stress. The ETR, ACACA and ATPeV0C genes were linked with energy accumulation during the initial stages of seed germination, CYP707A may play an important role in breaking seed dormancy, while the BRI1 gene may be correlated with swift seed germination. Additionally, several unidentified genes were recognized to play key roles in seed germination of Rh. pumilum, warranting further investigation. Moreover, Rh. pumilum demonstrates full activation of crucial physiological functions such as energy metabolism, signal transduction, and responses to biological and abiotic stresses during the seed breaking in shells. This study provides molecular evidence elucidating the swift seed germination strategies adopted by alpine plants to thrive in high-altitude environments. Furthermore, it serves as a foundational reference for enhancing seed germination rates and breeding practices to promote the sustainable development of Rh. pumilum medicinal materials. [ABSTRACT FROM AUTHOR]

Understanding the molecular mechanisms involved in the effects of oxidative stress in humans and animals is important to minimize the damage it causes, leading to various intestinal diseases. Our aim is to study the genes and pathways involved in oxidative stress in the gut using mouse small intestinal epithelial cells (MODE-K) as a model. The MODE-K cell line was divided into two different groups: one group was treated with hydrogen peroxide (H2O2) and the other group was not. To analyze the effects of H2O2 exposure, cell viability, apoptosis rate and reactive oxygen species (ROS) levels were determined. Next, transcriptome sequencing was performed, differentially expressed genes (DEGs) were identified and function annotation was performed, followed by a series of bioinformatics analyses. Real-time PCR was used to confirm the transcriptome data. Our results showed that H2O2-induced oxidative stress significantly increased ROS synthesis and promoted cell apoptosis in mouse small intestinal epithelial cells. During oxidative stress, 1207 DEGs (859 up-regulated, 348 down-regulated) were identified. According to GO analysis, DEGs are annotated into 51 different GO classifications including 22 biological processes, 15 cellular components and 14 molecular functions. In addition, using KEGG, PPI and correlation analysis, the two most significant subnetworks were identified. Ten correlated nodal DEGs of the first subnetwork correspond to MAPK, NF-kappa B and PI3K-AKT signaling pathways, and six correlated DEGs of the second subnetwork are associated with mitochondria. KDM6B was found to link these two subnetworks. The results suggest that oxidative stress affects epithelial growth, metabolism and apoptosis in a mouse model of intestinal cells through signaling pathways such as MAPK and PI3K/AKT/NF-kappa B, and mitochondria-related genes that are interconnected through the PTGS2-KDM6B-MT-ATP6 pathway. [ABSTRACT FROM AUTHOR]

Schizophrenia (SCZ) symptoms can be classified as positive and negative ones, each of which has distinct traits and possibly differences in gene expression and regulation. The co-expression networks linked to PANSS (Positive and Negative Syndrome Scale) scores were identified by weighted gene co-expression network analysis (WGCNA) using the expression profiles of miRNA and mRNA in the peripheral blood of first-episode SCZ patients. The heterogeneity between positive and negative symptoms was demonstrated using gene functional enrichment, gene-medication interaction, and immune cell composition analysis. Then, target gene prediction and correlation analysis of miRNA and mRNA constructed a symptom-related miRNA-mRNA regulatory network, screened regulatory pairs, and predicted binding sites. A total of six mRNA co-expression modules, two miRNA co-expression modules, and ten hub genes were screened to be significantly associated with positive symptoms; five mRNA co-expression modules and eight hub genes were correlated with negative symptoms. Positive symptom-related modules were significantly enriched in axon guidance, actin skeleton regulation, and sphingolipid signaling pathway, while negative symptom-related modules were significantly enriched in adaptive immune response, leukocyte migration, dopaminergic synapses, etc. The development of positive symptoms may have been influenced by potential regulatory pairings such as miR-98-5p-EIF3J, miR-98-5p-SOCS4, let-7b-5p-CLUH, miR-454-3p-GTF2H1, and let-7b-5p-SNX17. Additionally, immune cells were substantially connected with several hub genes for symptoms. Positive and negative symptoms in SCZ individuals were heterogeneous to some extent. miRNAs such as let-7b-5p and miR-98-5p might contribute to the incidence of positive symptoms by targeting mRNAs, while the immune system's role in developing negative symptoms may be more nuanced. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is an age-related progressive neurodegenerative disease, and approximately 10% of AD cases are early-onset familial AD (EOFAD), which is mainly linked to point mutations in genes encoding presenilins (PS1 and PS2). Mutations in PS2 are extremely rare and have not received enough attention. Recently, studies have found that Rho GTPase activity is closely related to the pathogenesis of AD. In this study, we used transcriptome sequencing in PS2 siRNA-transfected SH-SY5Y cells and found a group of differentially expressed genes (DEGs) related to the regulation of GTPase activity. Among those DEGs, the most significantly downregulated was Rho guanine nucleotide exchange factor 5 (ARHGEF5). GTPase activity in PS2 siRNA-transfected cells was significantly decreased. Then, we found that the expression of ARHGEF5 and the GTPase activity of Mitochondrial Rho GTPase 2 (Miro2) in PS2 D439A mutant SH-SY5Y cells were significantly decreased. We found for the first time that PS2 can bind to Miro2, and the PS2 D439A mutation reduced the binding between PS2 and Miro2, reduced the expression of Miro2, and resulted in an imbalance in mitochondrial fusion/fission dynamics. In conclusion, PS2 gene knockdown may participate in the pathogenesis of AD through the regulation of GTPase activity. The imbalance in mitochondrial dynamics mediated by the PS2 D439A mutation through regulation of the expression and GTPase activity of Miro2 may be a potential pathogenic mechanism of AD. [ABSTRACT FROM AUTHOR]

Triadimefon, a type of triazole systemic fungicide, has been extensively used to control various fungal diseases. However, triadimefon could lead to severe environmental pollution, and even threatens human health. To eliminate triadimefon residues, a triadimefon-degrading bacterial strain TY18 was isolated from a long-term polluted site and was identified as Enterobacter hormaechei. Strain TY18 could grow well in a carbon salt medium with triadimefon as the sole nitrogen source, and could efficiently degrade triadimefon. Under triadimefon stress, a total of 430 differentially expressed genes (DEGs), including 197 up-regulated and 233 down-regulated DEGs, were identified in strain TY18 using transcriptome sequencing (RNA-Seq). Functional classification and enrichment analysis revealed that these DEGs were mainly related to amino acid transport and metabolism, carbohydrate transport and metabolism, small molecule and pyrimidine metabolism. Interestingly, the DEGs encoding monooxygenase and hydrolase activity acting on carbon–nitrogen were highly up-regulated, might be mainly responsible for the metabolism in triadimefon. Our findings in this work suggest that strain E. hormaechei TY18 could efficiently degrade triadimefon for the first time. They provide a great potential to manage triadimefon biodegradation in the environment successfully. [ABSTRACT FROM AUTHOR]

The OVATE gene family plays an important role in regulating the development of plant organs and resisting stress, but its expression characteristics and functions in sorghum have not been revealed. In this study, we identified 26 OVATE genes in the sorghum BTx623 genome, which were divided into four groups and distributed unevenly across 9 chromosomes. Evolutionary analysis showed that after differentiation between sorghum and Arabidopsis, the OVATE gene family may have experienced unique expansion events, and all OVATE family members were negatively selected. Transcriptome sequencing and RT-qPCR results showed that OVATE genes in sorghum showed diverse expression characteristics, such as gene SORBl_3001G468900 and SORBl_3009G173400 were significantly expressed in seeds, while SORBI_3005G042700 and SORBI_3002G417700 were only highly expressed in L1. Meantime, in the promoter region, a large number of hormone-associated cis-acting elements were identified, and these results suggest that members of the OVATE gene family may be involved in regulating specific development of sorghum leaves and seeds. This study improves the understanding of the OVATE gene family of sorghum and provides important clues for further exploration of the function of the OVATE gene family. [ABSTRACT FROM AUTHOR]

The brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive pest of rice (Oryza sativa L.). Utilizing resistant rice cultivars that harbor resistance gene/s is an effective strategy for integrated pest management. Due to the co-evolution of BPH and rice, a single resistance gene may fail because of changes in the virulent BPH population. Thus, it is urgent to explore and map novel BPH resistance genes in rice germplasm. Previously, an indica landrace from India, Paedai kalibungga (PK), demonstrated high resistance to BPH in both in Wuhan and Fuzhou, China. To map BPH resistance genes from PK, a BC1F2:3 population derived from crosses of PK and a susceptible parent, Zhenshan 97 (ZS97), was developed and evaluated for BPH resistance. A novel BPH resistance locus, BPH39, was mapped on the short arm of rice chromosome 6 using next-generation sequencing-based bulked segregant analysis (BSA-seq). BPH39 was validated using flanking markers within the locus. Furthermore, near-isogenic lines carrying BPH39 (NIL-BPH39) were developed in the ZS97 background. NIL-BPH39 exhibited the physiological mechanisms of antibiosis and preference toward BPH. BPH39 was finally delimited to an interval of 84 Kb ranging from 1.07 to 1.15 Mb. Six candidate genes were identified in this region. Two of them (LOC_Os06g02930 and LOC_Os06g03030) encode proteins with a similar short consensus repeat (SCR) domain, which displayed many variations leading to amino acid substitutions and showed higher expression levels in NIL-BPH39. Thus, these two genes are considered reliable candidate genes for BPH39. Additionally, transcriptome sequencing, DEGs analysis, and gene RT-qPCR verification preliminary revealed that BPH39 may be involved in the jasmonic acid (JA) signaling pathway, thus mediating the molecular mechanism of BPH resistance. This work will facilitate map-based cloning and marker-assisted selection for the locus in breeding programs targeting BPH resistance. [ABSTRACT FROM AUTHOR]

Lonicera japonica Flos is a valuable herb in the Lonicerae family. While transcriptomic studies on L. japonica have focused on different tissues (stems, leaves, flowers) or flowering stages, few have investigated the molecular mechanisms underlying chemical composition synthesis influenced by exogenous factors, such as foliar fertilization. Moreover, most transcriptomic studies on L. Japonica have been conducted on chlorogenic acid and luteoloside, and the molecular synthesis mechanism of the overall chemical composition has not been analyzed. Methods: We conducted a single-factor, four-level foliar fertilization experiment using yeast polysaccharides. Different yeast polysaccharides concentrations were sprayed on L. japonica for six consecutive days with dynamic sampling. High-performance liquid chromatography determined the active ingredients in each group. The two groups exhibiting the most significant differences were selected for transcriptomic analysis to identify key synthetic genes responsible for L. japonica's active ingredients. Key results: Principal component analysis conducted on samples collected on September 8 revealed significant differences in the active ingredient amounts between the 0.1 g/L yeast polysaccharides treatment group and the control group. Transcriptome sequencing analysis identified 218 significantly differentially expressed genes, including 60 upregulated and 158 downregulated genes. Twelve differential genes involved in the chemical components synthesis pathway of L. japonica under yeast polysaccharides treatment were identified: PAL1, PAL2, PAL3, 4CL1, 4CL, CHS1, CHS2, CHS, CHI1, CHI2, F3H, and SOH. Conclusions: This study contributes to the theoretical understanding of essential synthetic genes associated with L. japonica's active ingredients. It offers data support for further gene exploration and sheds light on the molecular mechanisms underlying L. japonica quality formation. These findings hold significant implications for enhancing the content of secondary metabolites of L. japonica. [ABSTRACT FROM AUTHOR]

Hypertension is a pathological state of the metabolic syndrome that increases the risk of cardiovascular disease. Managing hypertension is challenging, and we aimed to identify the pathogenic factors and discern therapeutic targets for metabolic hypertension (MHR). An MHR rat model was established with the combined treatment of a high-sugar, high-fat diet and ethanol. Histopathological observations were performed using hematoxylin–eosin and Sirius Red staining. Transcriptome sequencing was performed to screen differentially expressed genes. The role of ubiquitin-specific protease 18 (USP18) in the proliferation, apoptosis, and oxidative stress of HUVECs was explored using Cell Counting Kit-8, flow cytometry, and enzyme-linked immunosorbent assays. Moreover, USP18 downstream signaling pathways in MHR were screened, and the effects of USP18 on these signaling pathways were investigated by western blotting. In the MHR model, total cholesterol and low-density lipoprotein levels increased, while high-density lipoprotein levels decreased. Moreover, high vessel thickness and percentage of collagen were noted along with increased malondialdehyde, decreased superoxide dismutase and catalase levels. The staining results showed that the MHR model exhibited an irregular aortic intima and disordered smooth muscle cells. There were 78 differentially expressed genes in the MHR model, and seven hub genes, including USP18, were identified. USP18 overexpression facilitated proliferation and reduced apoptosis and oxidative stress in HUVECs treated with Ang in vitro. In addition, the JAK/STAT pathway was identified as a USP18 downstream signaling pathway, and USP18 overexpression inhibited the expression of JAK/STAT pathway-related proteins. Conclusively, USP18 restrained MHR progression by promoting cell proliferation, reversing apoptosis and oxidative stress, and suppressing the JAK/STAT pathway. [ABSTRACT FROM AUTHOR]

Mesenchymal stem cell (MSC)-derived exosomes are considered as alternative to cell therapy in various diseases. This study aimed to understand the effect of bone marrow MSC-derived exosomes (BMMSC-exos) on spinal cord injury (SCI) and to unveil its regulatory mechanism on ferroptosis. Exosomes were isolated from BMMSCs and the uptake of BMMSCs-exos by PC12 cells was determined using PKH67 staining. The effect of BMMSC-exos on SCI in rats was studied by evaluating pathological changes of spinal cord tissues, inflammatory cytokines, and ferroptosis-related proteins. Transcriptome sequencing was used to discover the differential expressed genes (DEGs) between SCI rats and BMMSC-exos-treated rats followed by functional enrichment analyses. The effect of BMMSC-exos on ferroptosis and interleukin 17 (IL-17) pathway was evaluated in SCI rats and oxygen–glucose deprivation (OGD)-treated PC12 cells. The results showed that particles extracted from BMMSCs were exosomes that could be taken up by PC12 cells. BMMSC-exos treatment ameliorated injuries of spinal cord, suppressed the accumulation of Fe2+, malondialdehyde (MDA), and reactive oxygen species (ROS), with the elevated glutathione (GSH). Also, BMMSC-exos downregulated the expression of acyl-CoA synthetase long chain family member 4 (ACSL4) and upregulated glutathione peroxidase 4 (GPX4) and cysteine/glutamate antiporter xCT. A total of 110 DEGs were discovered and they were mainly enriched in IL-17 signaling pathway. Further in vitro and in vivo experiments showed that BMMSC-exos inactivated IL-17 pathway. BMMSC-exos promote the recovery of SCI and inhibit ferroptosis by inhibiting the IL-17 pathway, which provides BMMSC-exos as an alternative to the management of SCI. [ABSTRACT FROM AUTHOR]

Single-cell joint analysis of methylome and transcriptome reveals how the methylation regulates the transcriptional activity. However, traditional bench-top protocols for single-cell DNA methylation and RNA transcription co-detection are labor-intensive, cost-ineffective and contaminant-prone. Herein, we establish the DMF-scMT-seq, a highly-efficient and cost-effective method to simultaneously analyze single-cell DNA methylation and transcriptional activity based on digital microfluidics. DMF-scMT-seq automates the workflow of single-cell isolation, cellular hypotonic lysis, nucleic acid separation and methylome/transcriptome library construction in a contactless and addressable way. The system ensures high accuracy (R>0.85), high gene detection ability (14,697 genes per cell at 4 million sequencing depth), and high CpG coverage (677,198 CpG sites per cell at 1 million sequencing depth). By using DMF-scMT-seq, the relationship of DNA methylation and RNA transcription under different genomic contexts is resolved. We further apply DMF-scMT-seq to study the dynamics of transcription regulation with methylation-inhibiting anti-tumor Decitabine, and identify the methylated promoter/gene body driven genes in response to Decitabine treatment. DMF-scMT-seq facilitates the construction of the correlation of DNA methylation and transcriptional activity at the single-cell level in a flexible, sensitive and accurate way, which is anticipated to be a powerful tool in studying single-cell biological systems. [ABSTRACT FROM AUTHOR]

Sepsis has a systemic inflammatory response syndrome caused by infection. While neutrophils play contradictory roles in different stages of sepsis. Neutrophils have been proven to play an antibacterial role by producing neutrophil extracellular traps (NETs). Although the NET is beneficial to bacteria resistance, abnormal NET increases tissue damage. The complement C5a receptor 1 (C5ar1) is a gene related to strong inflammatory reactions and is found to be associated with inflammatory factors. This study found that there were 45 down-regulated genes and 704 up-regulated genes in sepsis rats by transcriptome sequencing. And those genes were significantly related to inflammation and immunity by GO and KEGG enrichment analysis involving the chemokine signaling pathway, the Toll-like receptor (TLR) signaling pathway, and the Fc gamma R-mediated phagocytosis. Additionally, the C5ar1 gene was significantly upregulated with interesting potential in sepsis and used for further study. This study used cecum ligation and puncture (CLP) rats that were respectively injected intravenously with PBS or the lentivirus vector to explore the effect of C5ar1 on CLP rats. It demonstrated that silenced- C5ar1 inhibited the ALT, AST, BUN, and CREA levels, improved the lung and spleen injury, and reduced the TNF-α, IL-6, IL-1β, IL-10, cf-DNA, and cfDNA/MPO levels. Additionally, silenced C5ar1 inhibited the TLR2, TLR4, and peptidylarginine deiminase 4 expression levels, which suggested the improvement of silenced C5ar1 on sepsis via inhibiting NETs and the TLR signaling pathway. This study provides a basis and new direction for the study of treatment on sepsis. [ABSTRACT FROM AUTHOR]

Background: With the development of sequencing technologies, there is increasing evidence that long noncoding RNAs (lncRNAs) are involved in systemic lupus erythematosus (SLE). The level of NR_103776.1 expression in SLE and its clinical associations are still not well defined. Objective: To identify differentially expressed lncRNAs and explore their functional roles in SLE. Methods: Transcriptome sequencing was used to screen differentially expressed lncRNAs and mRNAs. Expression validation of clinical samples was performed by QRT-PCR. Bioinformatics was used to analyze its prognostic value and potential function. Results: Of the 231 significantly differentially expressed lncRNAs, NR_103776.1 could be used to distinguish not only SLE patients and rheumatoid arthritis patients but also active SLE patients, stable SLE patients, and healthy controls. NR_103776.1 was significantly and negatively correlated with inflammatory indexes (CRP and ESR). NR_103776.1 dysregulation might contribute to the metabolism of RNA and proteins in SLE patients. Conclusions: This study not only provided a transcriptome profile of lncRNAs aberrantly expressed in individual nucleated cells of SLE patients but also suggested NR_103776.1 as a novel potential diagnostic biomarker. [ABSTRACT FROM AUTHOR]

Laser therapy has shown promising outcomes in treating infantile hemangiomas. However, the molecular mechanisms underlying laser treatment for IH remain incompletely elucidated. This study aimed to unravel the molecular mechanisms of laser therapy in IH treatment. We evaluated the inhibitory effects of laser treatment on the proliferation and promotion of apoptosis in human hemangioma endothelial cells (HemECs) through cell counting kit-8 (CCK-8) assay, Hoechst 33342 staining, and flow cytometric analysis. Transcriptome sequencing analysis of HemECs following laser treatment revealed a significant decrease in the expression level of the GSTM5 gene. The qRT-PCR and western blot analysis also showed that GSTM5 expression in HemECs was downregulated compared to human umbilical vein endothelial cells (HUVECs), and concomitantly, the p62-Nrf2 pathway was suppressed. Using siRNA to downregulate GSTM5 expression, we observed that inhibiting GSTM5 expression could restrain cell proliferation, elevate intracellular ROS levels, and induce apoptosis in HemECs. Furthermore, upon inhibition of the p62-Nrf2 pathway using p62-specific siRNA, a significant decrease in GSTM5 expression and an elevation in intracellular ROS levels were noted in laser-treated HemECs. These findings suggested that laser treatment may operate by inhibiting the p62-Nrf2 pathway, thereby downregulating GSTM5 expression, elevating ROS levels, and consequently inducing apoptosis in HemECs. [ABSTRACT FROM AUTHOR]

Background: Complex pathophysiological changes accompany denervation-induced skeletal muscle atrophy, but no effective treatment strategies exist. Our previous study indicated that extracellular vesicles derived from skin-derived precursors-derived Schwann cells (SKP-SC-EVs) can effectively mitigate denervation-induced muscle atrophy. However, the specific molecular mechanism remains unclear. Methods and results: In this study, we used bioinformatics methods to scrutinize the impact of SKP-SC-EVs on gene expression in denervation-induced skeletal muscle atrophy. We found that SKP-SC-EVs altered the expression of 358 genes in denervated skeletal muscles. The differentially expressed genes were predominantly participated in biological processes, including cell cycle, inflammation, immunity, and adhesion, and signaling pathways, such as FoxO and PI3K.Using the Molecular Complex Detection (MCODE) plugin, we identified the two clusters with the highest score: cluster 1 comprised 37 genes, and Cluster 2 consisted of 24 genes. Then, fifty hub genes were identified using CytoHubba. The intersection of Hub genes and genes obtained by MCODE showed that all 23 genes related to the cell cycle in Cluster 1 were hub genes, and 5 genes in Cluster 2 were hub genes and associated with inflammation. Conclusions: Overall, the differentially expressed genes in denervated skeletal muscle following SKP-SC-EVs treatment are primarily linked to the cell cycle and inflammation. Consequently, promoting proliferation and inhibiting inflammation may be the critical process in which SKP-SC-EVs delay denervation-induced muscle atrophy. Our findings contribute to a better understanding of the molecular mechanism of SKP-SC-EVs delaying denervation-induced muscle atrophy, offering a promising new avenue for muscle atrophy treatment. [ABSTRACT FROM AUTHOR]

In the process of tooth development, the interaction between genetic information, epigenetic inheritance, and environment jointly affects the teeth formation. At present, the mechanism of dental fluorosis is rarely studied from transcriptomics, and there is no report on epigenetic perspective. In the study, SD rats were randomly divided into dental fluorosis group and control group fed with NaF (150 mg/L) or distilled water for 8 weeks. After 3.5 days of birth, the RNAs or DNA of rat mandibular molars were detected by RNA-seq or MethylTarget, respectively. The results demonstrated that a total of 1723 differentially expressed genes (DEGs) and 2511 differential expression lncRNAs (DE-lncRNAs) were mainly involved in the ion channels, calcium ion transport, and immunomodulatory signaling pathways. ATP2C1 and Nr1d1, which were related to Ca2+ transport, cellular calcium homeostasis, endoplasmic reticulum stress and immunity, may be the key genes in the formation of dental fluorosis. Notably, we also found that the immune response plays an important role in the formation of dental fluorosis, and a large amount of DEGs was enriched in immune regulation and NF-κB signaling pathways. Furthermore, the methylation levels of 13 sites were increased in Ago4, Atf3, Atp2c1, Dusp1, Habp4, and Mycl, while methylation levels of 5 CpG sites decreased in Ago4, Atp2c1, Habp4, and Traf6, and conformably, the expression of these genes have been significantly changed. This study comprehensively analyzed the occurrence mechanism of dental fluorosis from transcriptomics and epigenetics, so as to provide theoretical reference for further research. [ABSTRACT FROM AUTHOR]

Background: Complex pathophysiological changes accompany denervation-induced skeletal muscle atrophy, but no effective treatment strategies exist. Our previous study indicated that extracellular vesicles derived from skin-derived precursors-derived Schwann cells (SKP-SC-EVs) can effectively mitigate denervation-induced muscle atrophy. However, the specific molecular mechanism remains unclear. Methods and results: In this study, we used bioinformatics methods to scrutinize the impact of SKP-SC-EVs on gene expression in denervation-induced skeletal muscle atrophy. We found that SKP-SC-EVs altered the expression of 358 genes in denervated skeletal muscles. The differentially expressed genes were predominantly participated in biological processes, including cell cycle, inflammation, immunity, and adhesion, and signaling pathways, such as FoxO and PI3K.Using the Molecular Complex Detection (MCODE) plugin, we identified the two clusters with the highest score: cluster 1 comprised 37 genes, and Cluster 2 consisted of 24 genes. Then, fifty hub genes were identified using CytoHubba. The intersection of Hub genes and genes obtained by MCODE showed that all 23 genes related to the cell cycle in Cluster 1 were hub genes, and 5 genes in Cluster 2 were hub genes and associated with inflammation. Conclusions: Overall, the differentially expressed genes in denervated skeletal muscle following SKP-SC-EVs treatment are primarily linked to the cell cycle and inflammation. Consequently, promoting proliferation and inhibiting inflammation may be the critical process in which SKP-SC-EVs delay denervation-induced muscle atrophy. Our findings contribute to a better understanding of the molecular mechanism of SKP-SC-EVs delaying denervation-induced muscle atrophy, offering a promising new avenue for muscle atrophy treatment. [ABSTRACT FROM AUTHOR]

We aim to elucidate how miRNAs regulate the mRNA signature of atrial fibrillation (AF), to gain mechanistic insight and identify candidate targets for future therapies. We present combined miRNA–mRNA sequencing using atrial tissues of patient without AF (n = 22), with paroxysmal AF (n = 22) and with persistent AF (n = 20). mRNA sequencing previously uncovered upregulated epithelial to mesenchymal transition, endothelial cell proliferation and extracellular matrix remodelling involving glycoproteins and proteoglycans in AF. MiRNA co-sequencing discovered miRNAs regulating the mRNA expression changes. Key downregulated miRNAs included miR-135b-5p, miR-138-5p, miR-200a-3p, miR-200b-3p and miR-31-5p and key upregulated miRNAs were miR-144-3p, miR-15b-3p, miR-182-5p miR-18b-5p, miR-4306 and miR-206. MiRNA expression levels were negatively correlated with the expression levels of a multitude of predicted target genes. Downregulated miRNAs associated with increased gene expression are involved in upregulated epithelial and endothelial cell migration and glycosaminoglycan biosynthesis. In vitro inhibition of miR-135b-5p and miR-138-5p validated an effect of miRNAs on multiple predicted targets. Altogether, the discovered miRNAs may be explored in further functional studies as potential targets for anti-fibrotic therapies in AF. [ABSTRACT FROM AUTHOR]

Gastric adenocarcinoma (GAC) is one of the world's most lethal malignant tumors. It has been established that the occurrence and progression of GAC are linked to molecular changes. However, the pathogenesis mechanism of GAC remains unclear. In this study, we sequenced 6 pairs of GAC tumor tissues and adjacent normal tissues and collected GAC gene expression profile data from the TCGA database. Analysis of this data revealed 465 differentially expressed genes (DEGs), of which 246 were upregulated and 219 were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were observably enriched in ECM-receptor interaction, protein digestion and absorption, and gastric acid secretion pathways. Six key genes (MATN3, COL1A1, COL5A2, P4HA3, SERPINE1 and VCAN) associated with poor GAC prognosis were screened from the protein‒protein interaction (PPI) network by survival analysis, and P4HA3 and MATN3 have rarely been reported to be associated with GAC. We further analyzed the function of P4HA3 in the GAC cell line SGC-7901 by RT‒qPCR, MTT, flow cytometry, colony formation, wound healing, Transwell and western blot assays. We found that P4HA3 was upregulated in the SGC-7901 cell line versus normal control cells. The outcomes of the loss-of-function assay illustrated that P4HA3 significantly enhanced the ability of GAC cells to proliferate and migrate. This study provides a new basis for the selection of prognostic markers and therapeutic targets for GAC. [ABSTRACT FROM AUTHOR]

Driver genomic alterations in pediatric immature T-cell acute lymphoblastic leukemia are not fully known. We report two cases of novel EVX fusions involved in the transcriptional activation of HOX family genes, ETV6::EVX2 and MSI2::EVX1/HOXA13, which activate HOXD and HOXA cluster genes transcription through enhancer hijacking. HOXA and HOXD were the only key transcription factors activated in these cases, which indicates their important roles in leukemogenesis. Our findings elucidate potential drivers for development of T-cell lymphoblastic leukemia, and are valuable for diagnosis and risk stratification of pediatric T-ALL in the era of precision medicine. [ABSTRACT FROM AUTHOR]

Global warming and ocean acidification represent major threats to coral reefs, the combination of these stressors may have concomitant impacts on coral holobionts. However, the molecular mechanisms of the impacts and synergistic effects of acidification and warming on coral holobionts are rarely known, particularly from the point of coral-Symbiodiniaceae symbioses. In this study, using branching Acropora valida and massive Galaxea fascicularis as representatives in a laboratory system simulating acidification (pH 7.7) and/or warming (32 °C), the response of coral host, Symbiodiniaceae and their symbiotic association were investigated by high-throughput transcriptome sequencing (RNA-Seq) with pH 8.1 and 26 °C as controls. Based on differentially expressed genes (DEGs) analysis, acidification and/or warming show greater impacts on the gene expression of coral host than its symbiotic Symbiodiniaceae. Synergistic effects of combined acidification and warming are suggested by comparison with single stress, especially the synergistic negative effects on coral-Symbiodiniaceae symbioses are suggested, because the expression of most of the genes related to photosynthesis, nutrient metabolism and transfer, and the symbionts recognition are downregulated indicating the instability of the coral-Symbiodiniaceae symbioses. This study provides molecular evidence for the synergy of acidification and warming on coral holobionts. In particular, the synergistic negative effects on the nutrients and symbionts recognition-based coral-Symbiodiniaceae symbioses are highlighted, which is helpful for predicting the response of coral holobionts to future global climate changes. [ABSTRACT FROM AUTHOR]

Aeonium arboreum 'Halloween' is an indoor foliage succulent plant with coloured photosensitive leaves found mostly in China. However, the current understanding regarding the mechanism of coloured leaf formation in succulents is elusive. Qualitative and quantitative analysis of flavonoids and transcriptome sequencing was carried out on dark and light-treated 'Halloween' leaves to investigate how light affects the leaf colour of the succulents. The findings supported the evidence that the red color of 'Halloween' leaves is mainly attributed to the high accumulation of cyanidin 3-O-galactoside. A total of 89 513 unigenes from the transcriptome were identified, and 65.24% of these have annotations in the NR, NT, KEGG, SwissProt, PFAM, GO and KOG databases. A total of 20 898 DEGs were obtained following the light treatment compared to the dark treatment, including 11804 up-regulated genes and 9094 downregulated genes. The KEGG enrichment analysis identified 20 metabolic pathways with the most significant enrichment of DEGs, including the flavonoid and phenylpropanoid synthesis pathways, which are closely associated with anthocyanin metabolism. Almost all structural genes and transcription factors related to flavonoid metabolism were up-regulated as verified by qRT-PCR, and five transcription factors, AaMYB113, AaMYB114, AaMYB4, AaHY5 and AaCOP1, were initially screened for their possible involvement in regulating light-induced anthocyanin synthesis. This study contributes to a deeper understanding of the effects of light on leaf colouration in Aeonium arboreum 'Halloween' and in succulents. [ABSTRACT FROM AUTHOR]

Key message: This study enriched the understanding of the mechanism of nitrogen tolerance and starvation of yellowhorn and provided a reference for the breeding of low-nitrogen tolerance germplasm in the future. Yellowhorn is a rare woody oil crop in China, which can survive in barren, drought, cold, and even saline-alkali environments. However, its growth and development can be seriously affected by low-nitrogen stress. A comprehensive understanding of its transcriptional regulation activities under low-nitrogen stress is expected to indicate the key molecular mechanisms of its tolerance to low nitrogen levels. In this study, yellowhorn was divided into control, low-nitrogen, and nitrogen-free groups for treatment. Samples were treated for 15 days before assessing physiological characteristics and transcriptome analysis. Under low-nitrogen and no-nitrogen condition, a total of 10,733 differentially expressed genes were identified, among which 3870 genes were up-regulated and 6,863 genes were down-regulated. Under low-nitrogen stress, the most up-regulated genes were enriched in the phenylpropane synthesis pathway, flavonoid synthesis pathway, and plant hormone signal transduction pathway. Our determination of total flavonoids and proanthocyanidins also verified the upregulation of these three pathways. Brassinosteroid, salicylic, and jasmonic acid (BR, SA and JA, respectively) pathway-related genes were significantly up-regulated in the signal transduction pathway of plant hormones. This study provided a comprehensive review of the transcriptomics changes of yellowhorn under low nitrogen stress and detailed its insights into the relevant mechanism of BR, SA, and JA signaling pathway in resisting low-nitrogen stress, laying a solid foundation to further identify the corresponding molecular mechanism of yellowhorn and other woody oil plants. [ABSTRACT FROM AUTHOR]

Objectives: Limited information is available about the biological characterization of peri-implant soft tissue at the transcriptional level. The aim of this study was to investigate the effect of dental implant on the soft tissue in vivo by using paired samples and compare the differences between peri-implant soft tissue and periodontal gingiva at the transcriptional level. Methods: Paired peri-implant soft tissue and periodontal gingiva tissue from 6 patients were obtained, and the pooled RNAs were analyzed by deep sequencing. Venn diagram was used to further screen out differentially expressed genes in every pair of samples. Annotation and enrichment analysis was performed. Further verification was done by quantitative real-time PCR. Results: Totally 3549 differentially expressed genes (DEGs) were found between peri-implant and periodontal groups. The Venn diagram further identified 185 DEGs in every pair of samples, of which the enrichment analysis identified significant enrichment for cellular component was associated with external side of plasma membrane, for molecular function was protein binding, for biological process was immune system process, and for KEGG pathway was cytokine-cytokine receptor interaction. Among the DEGs, CST1, SPP1, AQP9, and SFRP2 were verified to be upregulated in peri-implant soft tissue. Conclusions: Peri-implant soft tissue showed altered expressions of several genes related to the cell-ECM interaction compared to periodontal gingiva. Clinical relevance: Compared to periodontal gingiva, altered cell-ECM interactions in peri-implant may contribute to the susceptibility of peri-implant diseases. At the transcriptional level, periodontal gingiva is generally considered the appropriate control for peri-implantitis, except regarding the cell-ECM interactions. [ABSTRACT FROM AUTHOR]

Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality Illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve upregulated genes including a protease-like secreted in CO(2) response (LOC101500970), amino acid permease 4-like (LOC101506539), and downregulated genes MYB-related protein 305-like (LOC101493897), receptor like protein 29 (LOC101491695). WGCNA analysis and pairwise comparison of datasets, successfully constructed four co-expression modules. Transcription factor families including bHLH, MYB, MYB-related, C2H2 zinc finger, ERF, WRKY and NAC transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds after fertilization. [ABSTRACT FROM AUTHOR]

Perilla as herb, ornamental, oil and edible plant is widely used in East Asia. Until now, the mechanism of regulated leaf coloration is still unclear. In this study, four different kinds of leaf colors were used to measure pigment contents and do transcriptome sequence to postulate the mechanism of leaf coloration. The measurements of chlorophyll, carotenoid, flavonoid, and anthocyanin showed that higher contents of all the aforementioned four pigments were in full purple leaf 'M357', and they may be determined front and back leaf color formation with purple. Meanwhile, the content of anthocyanin was controlled back leaf coloration. The chromatic aberration analysis and correlative analysis between different pigments and L*a*b* values analysis also suggested front and back leaf color change was correlated with the above four pigments. The genes involved in leaf coloration were identified through transcriptome sequence. The expression levels of chlorophyll synthesis and degradation related genes, carotenoid synthesis related genes and anthocyanin synthesis genes showed up-/down-regulated expression in different color leaves and were consistent of accumulation of these pigments. It was suggested that they were the candidate genes regulated perilla leaf color formation, and genes including F3'H, F3H, F3',5'H, DFR, and ANS are probably important for regulating both front and back leaf purple formation. Transcription factors involved in anthocyanin accumulation, and regulating leaf coloration were also identified. Finally, the probable scheme of regulated both full green and full purple leaf coloration and back leaf coloration was postulated. Key message: The contents of pigments determined front and back leaf coloration, and the key regulated gene were identified, and the probable scheme of regulated front and back leaf coloration was postulated. [ABSTRACT FROM AUTHOR]

Background: Under natural conditions, ginger (Zingiber officinale Rosc.) rarely blossom and has seed, which limits new variety breeding of ginger and industry development. In this study, the effects of different photoperiods and light quality on flowering induction in ginger were performed, followed by gene expression analysis of flower buds differentiation under induced treatment using RNA-seq technology. Results: First, both red light and long light condition (18 h light/6 h dark) could effectively induce differentiation of flower buds in ginger. Second, a total of 3395 differentially expressed genes were identified from several different comparisons, among which nine genes, including CDF1, COP1, GHD7, RAV2-like, CO, FT, SOC1, AP1 and LFY, were identified to be associated with flowering in induced flower buds and natural leaf buds. Aside from four down-regulated genes (CDF1, COP1, GHD7 and RAV2-like), other five genes were all up-regulated expression. These differentially expressed genes were mainly classified into 2604 GO categories, which were further enriched into 120 KEGG metabolic pathways. Third, expression change of flowering-related genes in ginger indicated that the induction may negatively regulated expression of CDF1, COP1, GHD7 and RAV2-like, and subsequently positively regulated expression of CO, FT, SOC1, LFY and AP1, which finally led to ginger flowering. In addition, the RNA-seq results were verified by qRT-PCR analysis of 18 randomly selected genes, which further demonstrated the reliability of transcriptome analysis. Conclusion: This study revealed the ginger flowering mechanism induced by light treatment and provided abundant gene information, which contribute to the development of hybrid breeding of ginger. [ABSTRACT FROM AUTHOR]

Key message: Transcriptomic, physiological, and qRT-PCR analysis revealed the potential mechanism by which SlPRE2 regulates plant growth and stomatal size via multiple phytohormone pathways in tomato. Paclobutrazol resistance proteins (PREs) are atypical members of the basic/helix-loop-helix (bHLH) transcription factor family that regulate plant morphology, cell size, pigment metabolism and abiotic stress in response to different phytohormones. However, little is known about the network regulatory mechanisms of PREs in plant growth and development in tomato. In this study, the function and mechanism of SlPRE2 in tomato plant growth and development were investigated. The quantitative RT-PCR results showed that the expression of SlPRE2 was regulated by multiple phytohormones and abiotic stresses. It showed light-repressed expression during the photoperiod. The RNA-seq results revealed that SlPRE2 regulated many genes involved in photosynthesis, chlorophyll metabolism, phytohormone metabolism and signaling, and carbohydrate metabolism, suggesting the role of SlPRE2 in gibberellin, brassinosteroid, auxin, cytokinin, abscisic acid and salicylic acid regulated plant development processes. Moreover, SlPRE2 overexpression plants showed widely opened stomata in young leaves, and four genes involved in stomatal development showed altered expression. Overall, the results demonstrated the mechanism by which SlPRE2 regulates phytohormone and stress responses and revealed the function of SlPRE2 in stomatal development in tomato. These findings provide useful clues for understanding the molecular mechanisms of SlPRE2-regulated plant growth and development in tomato. [ABSTRACT FROM AUTHOR]

Background: Ovarian metastasis (OM) poses a major threat to the outcome of gastric cancer (GC) patients. Recently, immunotherapy emerged as a novel promising therapeutic strategy to treat late-stage GC, whereas its efficacy is influenced by tumor immune microenvironment (TIME). M2 macrophage, a key subset within TIME, plays dual immunosuppressive and pro-tumorigenic roles in cancer progression and is recognized as a potential therapeutic target. However, molecular mechanisms underlying OM remain elusive and the TIME-related prognostic and immunotherapeutic index for these patients is yet to establish. Methods: Differential expressed genes (DEGs) between paired normal mucosa, primary GC and OM of patients from Fudan University Shanghai Cancer Center (FUSCC) cohort (n = 6) were identified by transcriptome sequencing, followed by the functional annotation of enriched hallmark pathways of DEGs between them. CIBERSORT was used to profile the relative expression level of 22 immune cell subsets in normal tissues, primary and metastatic tumors, followed by weighted gene coexpression network analysis (WGCNA) uncovering immune cell-correlated gene sets. The intersected genes between DEGs and M2 macrophage-related genes were processed by least absolute shrinkage and selection operator (LASSO) regression analysis to construct a predictive signature, M2GO, which was further validated by training set and test set of The Cancer Genome Atlas-Stomach Adenocarcinoma (TCGA-STAD), GSE62254 and GSE84437 cohorts. GC patients were divided into M2GO-high and -low subgroup according to the optimal cutoff value of the M2GO score. Furthermore, the clinical, molecular and immune features between M2GO-high and -low subgroups were analyzed. Clinical cohorts of immunotherapy were used to validate the predictive value of M2GO in regard to immunotherapy effectiveness. Results: Transcriptomic sequencing and follow-up analyses of triple-matched normal tissues, primary and ovarian metastatic tumors identified distinctive sets of DEGs and enriched immune-, cancer- and metastasis-related pathways between them. Of note, M2 macrophage, a major immunosuppressive and pro-tumorigenic component within TIME, was significantly up-regulated in OMs. WGCNA and LASSO regression were applied to establish a novel OM- and M2 macrophage-related predictive signature, M2GO, based on M2 macrophage-related prognostic genes including GJA1, MAGED1 and SERPINE1. M2GO served as an independent prognostic factor of GC patients. Comprehensive molecular and immune characterization of M2GO-based subgroups uncovered their distinctive features in terms of enriched functional pathways, tumor mutation burden, key immune checkpoints, major regulators of natural immune cGAS-STING pathway, infiltrated subsets of immune cells and tumor immune exclusion/dysfunction (TIDE) score. Notably, the M2GO score was significantly lower in responsive group than non-responsive group (P < 0.05) in clinical cohort of metastatic GC patients undergoing immunotherapy. Conclusion: Transcriptomic characterization of paired normal mucosae, primary and ovarian metastatic tumors revealed their unique molecular and immune features. Follow-up analyses established a novel OM- and M2 macrophage-related signature, M2GO, which served as a promising prognostic and immunotherapeutic biomarker to distinguish the clinical outcome, molecular and immune features of GC patients and predict their differential responses to immunotherapy. [ABSTRACT FROM AUTHOR]

It is shown that great progress was recently made in the treatment of repetitive transcranial magnetic stimulation (rTMS) for neurological and psychiatric diseases. This study aimed to address how rTMS exerted it therapeutic effects by regulating competitive endogenous RNAs (ceRNAs) of lncRNA-miRNA-mRNA. The distinction of lncRNA, miRNA and mRNA expression in male status epilepticus (SE) mice treated by two different ways, low-frequency rTMS (LF-rTMS) vs. sham rTMS, was analyzed by high-throughput sequencing. The Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Gene–Gene Cross Linkage Network was established; pivotal genes were screened out. qRT-PCR was used to verify gene–gene interactions. Our results showed that there were 1615 lncRNAs, 510 mRNAs, and 17 miRNAs differentially which were expressed between the LF-rTMS group and the sham rTMS group. The expression difference of these lncRNAs, mRNAs, and miRNAs by microarray detection were consistent with the results by qPCR. GO functional enrichment showed that immune-associated molecular mechanisms, biological processes, and GABA-A receptor activity played a role in SE mice treated with LF-rTMS. KEGG pathway enrichment analysis revealed that differentially expressed genes were correlated to T cell receptor signaling pathway, primary immune deficiency and Th17 cell differentiation signaling pathway. Gene–gene cross linkage network was established on the basis of Pearson's correlation coefficient and miRNA. In conclusion, LF-rTMS alleviates SE through regulating the GABA-A receptor activity transmission, improving immune functions, and biological processes, suggesting the underlying ceRNA molecular mechanisms of LF-rTMS treatment for epilepsy. [ABSTRACT FROM AUTHOR]

Alternative splicing (AS) is the direct cause of different transcripts in eukaryotes and plays a vital role in biological processes such as plant growth and signal transduction. Reproductive development is the key process for rice production. Although numerous studies on AS in plants have been identified, AS of reproductive development stage between japonica and indica rice has not been conducted. In this research, we identified 6994 genes (19.2% of the total number of genes) corresponding to 14,517 AS events from the rice genome using the transcriptome data of 58 representative panicles of japonica rice and indica rice. Among the different types of AS, the frequency of exon skipping (SE) is the highest, accounting for more than 87%; the frequency of the alternative 3′ splice site (A3SS) type is about twice that of the alternative 5′ splice site (A5SS) type. GO enrichment analysis results showed that AS genes were mainly enriched in cellular and metabolic processes in the biological process classification. Moreover, 68 differentially AS events involved 56 genes. The expression of these five genes (OscTPI, OsLOL1, RBS1, PTB1 and OsPDIL1;1) was significantly different between the two subspecies. The analysis of AS events in panicles of japonica and indica rice provide new information regarding AS occurrence and function during these two subspecies differentiation in rice domestication and provide a theoretical basis for subsequent variety improvement. [ABSTRACT FROM AUTHOR]

Background: Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. Materials and methods: In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. Results: A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. Conclusion: The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm. [ABSTRACT FROM AUTHOR]

In previous study, we reported the identification, tissue distribution, and the roles of Spdsx played in the testis, androgenic gland, and ovary in Scylla paramamosain. Here, we primally identify its potential target genes in the ovary with RNAi and RNA-Seq technology. By comparing the transcriptome data of two groups (ovaries that injected with dsRNA for EGFP and Dsx), we found that 6520 Unigenes were differentially expressed, including a plenty of conserved crucial genes involved in ovarian development, such as vitellogenin (vtg), vtg receptor (vtgR), apolipoprotein D, adenylate cyclase 3, adenylate cyclase 5, cyclin A, cyclin B, and cell division cycle 2 (cdc2). In addition, these DEGs were also enriched in pathways related to ovary development, including PI3K-Akt signaling pathway, MAPK signaling pathway, insulin signaling pathway, Wnt signaling pathway, relaxin signaling pathway, estrogen signaling pathway, progesterone-mediated oocyte maturation, ovarian steroidogenesis, and oocyte meiosis. Moreover, several genes were selected for qRT-PCR to validate the accuracy of the bioinformatic result. According to current transcriptome result, we speculate that the Spdsx is a crucial regulator of ovary development in S. paramamosain. To the best of our knowledge, the current study was the first report about dsx function through comparative transcriptome analysis in crustacean species, which not only identified relevant genes and pathways involved in ovarian development of S. paramamosain, but also shed light on the regulatory mechanisms of dsx at the molecular level in crustacean. [ABSTRACT FROM AUTHOR]

MicroRNA (miRNA) was verified to display an important molecular regulatory role in the development of skeletal muscle. In this study, we identified the differentially expressed miRNAs from longissimus dorsi muscle of Dazu black goat at different stages (75 days embryonic stage [ET]) and 1 day after birth [DC]) to understand the regulatory role of miRNAs in the development of skeletal muscle. This work is expected to provide a theoretical basis for goat breeding in meat production. Results revealed a total of 218,161,800 clean tags from all the libraries; 546 significant differentially (p < 0.05) expressed miRNAs (DE_miRNAs) were identified, including 321 up-regulated and 225 down-regulated DE_miRNAs. Moreover, GO and KEGG analyses of the genes targeted by the DE_miRNAs revealed 59 and 345 significantly enriched GO terms and pathways associated with muscle development, respectively, such as the PI3K/Akt, Wnt. A total of 21 miRNAs from 546 DE_miRNAs were selected to estimate the agreement rate between miRNA-seq by RT-qPCR, and the results showed that the expressed pattern was completely unified from both. In brief, a series of miRNAs related to muscle development was identified in this study. This work provides valuable information to further understand the molecular regulatory mechanism of muscle development in goats. [ABSTRACT FROM AUTHOR]

The long-followed practice of using garlic cloves for garlic asexual reproduction has resulted in virus accumulation and genetic depression. Aerial bulbs, the preferred material for virus-free garlic seedling cultivation in vitro, undergo dormancy, but gibberellin can quickly break this state. In this study, exogenous GA3 was applied to dormant aerial bulbs and transcriptome sequencing was then performed using control and gibberellin-treated aerial bulbs. Genes differentially expressed in response to the gibberellin treatment were analyzed and screened and their relationship to GA3-induced dormancy break of aerial bulbs was explored. According to our results, exogenous GA3 was able to effectively break aerial bulb dormancy. Transcriptome sequencing uncovered 4931 and 74,636 genes that were respectively up- and down-regulated in response to gibberellin treatment. 37,957 differentially expressed genes were successfully assigned to KEGG pathways, among which the most DEGs were annotated in metabolism pathway (23,245 genes, accounting for 61.24%), followed by the genetic information processing pathway (9235 genes, accounting for 24.33%). More DEGs were enriched in spliceosome, ribosome, ribosome biogenesis in eukaryotes, and ubiquitin-mediated proteolysis pathways and the enrichment results were significant. In addition, carbohydrate and amino acid metabolism pathways are active. The significant DEGs related to calcium signaling, hormonal signaling, and transcription factors were screened out. Among them, the expression of DEGs related to hormonal signaling was consistent with the change of endogenous hormone content in aerial bulbs. Finally, the outcome of a qRT-PCR analysis was consistent with our transcriptome sequencing results, thus indicating that the latter was reliable. [ABSTRACT FROM AUTHOR]

Key message: Stamen degeneration and meiosis failure during the second flowering of 'Changchun' were mainly attributed to the coordinated regulation of hormone metabolism, environmental temperature, and genetic factors. Magnolia × soulangeana 'Changchun', a woody ornamental plant, blossoms twice a year after once flower bud differentiation, with fertile flower buds in spring and sterile flower buds in summer. The phenotype of stamens of 'Changchun' in summer displays a decrease in length and width, and no pollen, thus aborting. Cytological evidence exhibited that the microspore mother cells in anthers failed to complete meiosis during summer flowering. Compared with spring flowering period, the contents of endogenous substances and hormones decreased in summer, such as IAA/GA, ABA/GA, IAA/ABA hormone ratios also changed, indicating that energy and substances needed for stamen development in summer were insufficient, and hormone balance was broken. Transcriptome data showed that there were 46,230 differentially expressed genes (DEGs) between spring and summer flower buds, including 19,816 up-regulated genes and 26,414 down-regulated genes. Further analysis identified that most of the significantly enriched DEGs were involved in DNA, nucleus, microtubules and other GO items related to meiosis process, which was mutually confirmed with cytological results, suggesting that abnormal meiosis may be the core problem of fertility decline of stamen in summer flower buds of 'Changchun'. Besides, genes related to hormone signaling and heat stress that may affect stamen development were also differentially expressed. This study provided a basis for further understanding the stamen abortion mechanism of 'Changchun', and also provided a reference for exploring the fertility regulation of woody ornamental plants. [ABSTRACT FROM AUTHOR]

High amylopectin starch is an important modified starch for food processing industries. Despite a thorough understanding of starch biosynthesis pathway, the regulatory mechanism responsible for amylopectin biosynthesis is not well explored. The present study utilized transcriptome sequencing approach to understand the molecular basis of high amylopectin content in three high amylopectin mutant wheat lines ('TAC 6', 'TAC 358', and 'TAC 846') along with parent variety 'C 306'. Differential scanning calorimetry (DSC) of high amylopectin starch identified a high thermal transition temperature and scanning electron microscopy (SEM) revealed more spherical starch granules in mutant lines compared to parent variety. A set of 4455 differentially expressed genes (DEGs) were identified at two-fold compared to the parent variety in high amylopectin wheat mutants. At ten-fold, 279 genes, including two starch branching genes (SBEIIa and SBEIIb), were up-regulated and only 30 genes, including the starch debranching enzyme (DBE), were down-regulated. Among the genes, different isoforms of sucrose non-fermenting-1-related protein kinase-1 (TaSnRK1α2-3B and TaSnRK1α2-3D) and its regulatory subunit, sucrose non-fermenting-4 (SNF-4-2A, SNF-4-2B, and SNF-4-5D), were found to be highly up-regulated. Further, expression of the DEGs related to starch biosynthesis pathway and TaSnRK1α2 and SNF-4 was performed using qRT-PCR. High expression of TaSnRK1α2, SNF-4, and SBEII isoforms suggests their probable role in high amylopectin starch biosynthesis in grain endosperm. [ABSTRACT FROM AUTHOR]

The objective of this study was to identify different transcriptome expression profiles involved in the pathogenesis of diabetic nephropathy (DN) and to illustrate the diagnostic and therapeutic potential of mRNAs, long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) in DN progression. The participants were divided into four groups: normoalbuminuria (group DM), microalbuminuria (group A2), macroalbuminuria (group A3) and healthy controls (group N). There were three individuals in each group for sequencing. Transcriptome sequencing analysis was performed on the peripheral blood of all the participants to identify the differential expression of mRNAs, lncRNAs, and circRNAs between intervention groups and controls. The functional enrichment analysis, the short time-series expression miner (STEM) program, and the miRNA–circRNA–mRNA network were further conducted. To verify the reproducibility of transcriptome sequencing, 10 and 30 blood samples were collected from the control and diseased groups, respectively. Four candidate biomarkers were selected from differentially expressed circRNAs (circ_0005379, circ_0002024, and circ_0000567, and circ_0001017) and their concentrations in the blood were measured using quantitative PCR (qPCR). In the comparison of A2 with N, 549 mRNAs, 1259 lncRNAs, and 12 circRNAs were screened. In the comparison of A3 with N, 1217 mRNAs, 1613 lncRNAs, and 24 circRNAs were screened. Moreover, in the comparison of diabetes mellitus (DM) with N, 948 mRNAs, 1495 lncRNAs, and 25 circRNAs were screened. Functional enrichment analysis showed that differentially expressed mRNAs were related to insulin secretion, insulin resistance, and inflammation, while differentially expressed lncRNAs were mainly associated with crossover junction endodeoxyribonuclease activity. In STEM analysis, a total of 481 mRNAs and 152 differential expression circRNAs showed a significant tendency. The key relationships in the miRNA–circRNA–mRNA network were identified, such as hsa-miR-103a-3p-circ_0005379-PTEN, hsa-miR-497-5p-circ_0002024-IGF1R and hsa-miR-1269a-circ_0000567-SOX6. In addition, qPCR showed consistent results with RNA sequencing. We found that differentially expressed mRNAs, lncRNAs, and circRNAs participated in DN development. Circ_0005379, circ_0002024, and circ_0000567 could be adopted as potential biomarkers for DN. [ABSTRACT FROM AUTHOR]

Demodex canis is an important parasitic mite causing skin lesions in dogs. However, molecular studies on this species are limited because of the lack of transcriptomic data. To obtain functional genes of D. canis, mites were collected and RNA was extracted for transcriptome sequencing and functional annotation. Coding sequences (CDSs) of important functional genes were screened and identified using bioinformatics strategies. Six complete CDSs were amplified by specific primers, cloned and sequenced. Results demonstrated that the quantity of the RNA extracted from 100 mites was 12.8 ng and the RNA integrity number was 5.4, indicating that it could be used to construct a cDNA library. Transcriptome sequencing yielded 263,619 unigenes, of which 151,048 (57.3%) were functionally annotated. Using bioinformatics strategies, 58 total CDSs were identified as homologous to those of closely related mite species, including 16 types of allergen genes, 13 types of protease genes, and nine types of motion-related genes. The verified CDSs were almost identical to the CDSs of unigenes. Phylogenetic analyses of tropomyosin further revealed that the verified CDSs clustered successively with those of Demodex species and Tetranychus species in Raphignathae, which agreed with the morphological classification, demonstrating the reliability of the transcriptomic data. In conclusion, this study is the first to successfully sequence transcriptome of D. canis, perform functional annotation, and verify CDSs, which will provide ample data for further studies on the functional genes and molecular pathogenic mechanism of D. canis. [ABSTRACT FROM AUTHOR]

Safflower (Carthamus tinctorius L.) is known for its oil quality and ability to grow in drought conditions. The threat to global food security posed by challenges of climate change has stressed the use of functional genomics in current plant breeding approaches. Plant steroid hormones called brassinosteroids (BRs) are at the nexus of regulating plant growth and development, and plant stress responses. Enhanced BR levels or signalling have increased crop yields by up to 40% while also conferring broad range stress tolerance. Currently there is no information on the BR biosynthesis and signalling pathways in safflower. A de novo transcriptomic analysis of untreated and 24-epibrassinolide (EBR)-treated safflower leaves was conducted using the Illumina sequencing platform. Approximately 5 GB clean data were generated from untreated and EBR-treated samples that assembled into 34,456 and 36,997 transcripts (combined 50,630), and 30,180 and 32,333 CoDing sequences (CDS) (combined 43,637), respectively. More than 71% of the CDS were annotated with majority of hits against Cynara cardunculus var. scolymus, a thistle in the safflower family. A total of 74 KEGG pathways were identified in safflower. Six genes, including DWF4 that codes for a rate-limiting enzyme in BR biosynthesis, were mapped to the BR biosynthesis pathway using the KEGG mapper. [ABSTRACT FROM AUTHOR]

Microbial weathering processes can significantly promote soil properties and reduce rock-to-soil ratio. Some soil-inhabiting bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, our understanding of the molecular mechanisms involved during bacterial rock-dissolution is still limited. In this study, we performed silicate rock-dissolution experiments on a Pseudomonas sp. NLX-4 strain isolated from an over-exploited mining site. The results revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids. Through employing genome and transcriptome sequencing (RNA-seq), we identified the major regulatory genes. Specifically, 15 differentially expressed genes (DEGs) encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated in silicate rock cultures of NLX-4 strain. Our study reports a potential bacterial based approach for improving the ecological restoration of over-exploited rock mining sites. [ABSTRACT FROM AUTHOR]

As an important economic shellfish, the pearl oyster, Pinctada fucata, and its larvae are an ideal model for studying molecular mechanisms of larval development in invertebrates. Larval development directly affects the quantity and quality of pearl oysters. MicroRNAs (miRNAs) may play important roles in development, but the effects of miRNA expression on P. fucata early development remain unknown. In this study, miRNA and mRNA transcriptomics of seven different P. fucata developmental stages were analyzed using Illumina RNA sequencing. A total of 329 miRNAs, including 87 known miRNAs and 242 novel miRNAs, and 33,550 unigenes, including 26,333 known genes and 7217 predicted new genes, were identified in these stages. A cluster analysis showed that the difference in the numbers of miRNAs was greatest between fertilized eggs and trochophores. In addition, the integrated mRNA transcriptome was used to predict target genes for differentially expressed miRNAs between adjacent developmental stages, and the target genes were subjected to a gene ontology enrichment analysis. Using the gene ontology annotation, 100 different expressed genes and 95 differentially expressed miRNAs were identified as part of larval development regulation. Real-time PCR was used to identify eight mRNAs and three miRNAs related to larval development. The present findings will be helpful for further clarifying the regulatory mechanisms of miRNA in invertebrate larval development. [ABSTRACT FROM AUTHOR]

Previously, we reported the identification, tissue distribution and confirmed the roles of Spfoxl-2 in regulating vitellogenin (vtg) expression in Scylla paramamosain. Here, we primally analyzed its potential target genes in the ovary with RNAi and RNA-Seq technology. By comparing the transcriptome data of two groups (ovaries that injected with EGFP and Foxl-2 siRNA, respectively), we found 645 DEGs (differentially expressed genes), including several conserved crucial genes involved in ovarian development, such as vtg, vitellogenin receptor (vtgR), adenylate cyclase (AC), cyclinB, and cell division cycle 2 (cdc2). In addition, these DEGs were also enriched in pathways related to ovary development, including relaxin signaling pathway, ovarian steroidogenesis, and progesterone-mediated oocyte maturation. Moreover, several genes were selected for qRT-PCR to validate the accuracy of the bioinformatic result. To the best of our knowledge, the current study was the first report about foxl-2 function through comparative transcriptome analysis in crustacean species, which identified not only relevant genes and pathways involved in ovarian development of S. paramamosain, but also provided new insights into the regulatory mechanisms of foxl-2 at the molecular level in crustacean. [ABSTRACT FROM AUTHOR]

Long-term acclimation to monochromatic lights emerges in seaweeds. In this study, analysis based on physiological characteristics and transcriptome sequencing were employed to investigate the long-term acclimation of thalli of rhodophyte Pyropia haitanensis grown under white light (WL) and monochromatic blue light (BL), green light (GL), and red light (RL). The net photosynthesis of synchronically cultured thalli was highest under WL, while the net photosynthesis was significantly higher under GL and RL compared with BL, indicating the low utilization efficiency of BL and relatively high ones of GL and RL. Compared with WL, the PE/Chl. a ratio was significantly higher in BL-acclimated thalli and lower in both GL- and RL-acclimated thalli. The C/N ratio was decreased in BL-acclimated thalli and drastically increased in GL- and RL-acclimated thalli. Only a small amount of starch grains were observed in WL-acclimated thallus cells, and no starch grain was found in BL-acclimated thallus cells, whereas numerous starch grains were found in GL- and RL-acclimated thallus cells. These findings implied roles of pigments and allocation of carbon between carbohydrates and phycobiliproteins during monochromatic light acclimation. Transcriptome analysis showed that DEGs involving protein synthesis were mainly upregulated by BL, whereas DEGs involving energy-yielding carbohydrate catabolism were mainly downregulated by GL and RL. Besides, genes encoding light-harvesting complex, ferredoxin-NADP reductase, and key enzymes of carbon and nitrogen assimilation were upregulated by BL, yet downregulated by GL and RL. Those results indicated that P. haitanensis thalli could compensate for the low utilization efficiency of BL via the increase in phycoerythrin accumulation through upregulating enzymes acting on carbon and nitrogen assimilation, consequently activating downstream of protein synthesis. Mechanisms of photoacclimation under GL and RL might include the reduction in light energy absorption and photosynthetic electron transfer chain activity via downregulating genes encoding nitrogen assimilating enzymes, light-harvesting complexes and ferredoxin-NADP reductases, and the attenuation in accumulation and catabolism of photosynthates to avoid excessive energy-yielding that might cause a burden on metabolism. [ABSTRACT FROM AUTHOR]

To understand the defense mechanisms of spinach against insect attack at the molecular level, RNA-seq was used to compare the transcriptome of spinach leaves exposed to beet armyworm (Spodoptera exigua Hübner) larvae with that of unexposed control leaves. In total, 37,256 unigenes with an average length of 1134 bp were produced after de novo assembly of clean reads from two libraries. Based on mapping of the reads generated from each library to the unigenes, 1412 differentially expressed genes (DEGs) were identified in the insect-fed spinach leaves, including 1252 and 160 genes that were upregulated and downregulated, respectively. A MapMan analysis of the DEGs revealed that 206 genes were associated with abiotic (14 genes) and biotic (192 genes) stress responses. Based on these results, 107 and 7 DEGs with log2 fold changes ≥ 5 and 10, respectively, were identified. Notably, six of the seven highly over-expressed DEGs (WAK2-1, CAM3, CAM5-1, CAM6-1, CAM6-2 and CPK17-1) were associated with calcium ion (Ca2+) signaling. Moreover, these genes were highly co-over-expressed with several ECA (endoplasmic reticulum-type calcium-transporting-ATPase) genes known to be involved in Ca2+ transport, indicating that the Ca2+ signaling cascade plays an important role in the defense of spinach against insect attack. [ABSTRACT FROM AUTHOR]

Fruit firmness is an important trait of melons due to its effect on fresh fruit consumption, storage, and transport. However, information on the expression of genes influencing the fruit firmness of 'Baogua' (BG) melon (Cucumis melo ssp. agrestis Jeffrey) remains rare. This study aimed to identify the key genes associated with the firmness of BG fruit sampled at 14 and 28 days after pollination (dap) via transcriptome sequencing. A total of 1113 up-regulated and 2224 down-regulated differentially expressed genes (DEGs) were identified. The main Gene Ontology terms assigned to the DEGs were phosphotransferase activity, alcohol group as acceptor, protein phosphorylation, and protein kinase activity. The enriched KEGG pathways involving the DEGs were starch and sucrose metabolism, diterpenoid biosynthesis, plant hormone signal transduction, and MAPK signaling pathway–plant. In addition, qRT-PCR verified that four GAL genes, namely, CmGAL1–4, were differentially expressed at 0, 7, 14, 21, and 28 dap. Our data revealed that CmGAL1 expression was highest at 21 dap. However, the expression levels of CmGAL2–4 were highest at 14 dap. The sequence of CmGAL1 was similar to the sequences of homologs from melon and cucumber. Subcellular localization analysis revealed CmGAL1 was located in the cell membrane and cytoplasm. Our findings implied that fruit development at 14 dap, which is a key time-point, varies considerably from fruit development at 28 dap. Our present study provides new information on the genes associated with BG fruit firmness and help improve the storage and transport of BG fruit prior to processing. [ABSTRACT FROM AUTHOR]