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Background: Grape is a plant that is sensitive to low temperature and vulnerable to low-temperature damage. However, little is known about the roles of lncRNAs, miRNAs and mRNAs in regulating the hypothermia response mechanism in Vitis amurensis Rupr. Methods: In this study, the expression and regulatory network of low-temperature response genes were studied in the phloem of grape under different low-temperature stress. Results: Here, we performed analyses related to RNA-seq and miRNA-seq on grape phloem tissues from five periods of cold resistance campaigns. Three RNAs (lncRNAs, miRNAs and mRNAs) obtained by KEGG and GO analyses were used to identify starch and sucrose metabolism associated with cold resistance, and specific changes in BP, CC, and MF were identified in four comparisons. Venn diagrams, thermograms and pathway maps were used to analyze the differentially expressed genes (DEGs), and their specific gene expression during the cold exercise were obtained. The six DEGs finally selected were used for qRT-PCR to verify the RNA-seq data. In addition, we found that the regulatory networks of miRNAs and lncRNAs correspond to the six DEGs. This study will contribute to further experimental studies to elucidate the cold resistance mechanism of Vitis amurensis Rupr. Conclusions: The low-temperature response genes of grape are mainly enriched in the starch and sucrose metabolism, and they are regulated by miRNAs and lncRNAs. The conclusions will provide basic information for further understanding of the cold resistance mechanism of grape in the future. [ABSTRACT FROM AUTHOR]

Hydrangea macrophylla is an ornamental plant with varied calyx colors. Interestingly, from red, to purple, to blue, the colors of all Hydrangea macrophylla are formed by unique delphinidin-3-O-glucoside and aluminum ions (Al3+) and 5-O-p-coumaroylquinic acid. The sepals of 'Blue Mama' changed from pink to blue, and the contents of delphinidin-3-O-glucoside and aluminum ions increased under 3 g/L aluminum sulfate treatment. However, the mechanism of the effect of aluminum ions on the synthesis and metabolism of anthocyanins in Hydrangea macrophylla is still unclear. In this project, transcriptome sequencing and anthocyanin metabolome analysis were performed on the sepals of 'Blue Mama' during flower development at the bud stage (S1), discoloration stage (S2) and full-bloom stage (S3) under aluminum treatment. It was found that delphinidin, delphinidin-3-O-glucoside and delphinidin-3-O-galactoside were the main differential metabolites. The structural genes CHS, F3H, ANS, DFR and BZI in the anthocyanin synthesis pathway were up-regulated with the deepening in sepal color. There was no significant difference between the aluminum treatment and the non-aluminum treatment groups. However, seven transcription factors were up-regulated and expressed to regulate anthocyanin synthesis genes CHS, F3H, BZI and 4CL, promoting the sepals to turn blue. The KEGG enrichment pathway analysis of differentially expressed genes showed that the glutathione metabolism and the ABC transporter pathway were closely related to anthocyanin synthesis and aluminum-ion transport. GST (Hma1.2p1_0158F.1_g069560.gene) may be involved in the vacuolar transport of anthocyanins. The expression of anthocyanin transporter genes ABCC1 (Hma1.2p1_0021F.1_g014400.gene), ABCC2 (Hma1.2p1_0491F.1_g164450.gene) and aluminum transporter gene ALS3 (Hma1.2p1_0111F.1_g053440.gene) were significantly up-regulated in the aluminum treatment group, which may be an important reason for promoting the transport of anthocyanin and aluminum ions to vacuoles and making the sepals blue. These results preliminarily clarified the mechanism of aluminum ion in the synthesis and transport of anthocyanin in Hydrangea macrophylla, laying a foundation for the further study of the formation mechanism of 'blue complex' in Hydrangea macrophylla. [ABSTRACT FROM AUTHOR]

Sucrose phosphate synthase (SPS) is an important link in the process of sugar metabolism. In addition, it is also involved in abiotic stresses in plants. In order to study the SPS gene family and its role in abiotic stress, we identified the MdSPS gene family members by bioinformatics methods such as correlation analysis, the HMM method, and the Clustering method, and analyzed the transient expression of MdSPS genes by quantitative real-time fluorescence analysis (qRT-PCR). The MdSPS gene family consists of a total of 19 members divided into three subfamilies distributed on 14 chromosomes in apples. The MdSPS gene family has 12 collinearity gene pairs, indicating significant duplication. Most members of this family contain a large number of plant hormone response elements, light-inducible elements, and abiotic stress response elements 2kb upstream of the promoter. Codon bias analysis shows that there are 28 high-frequency codons and no codons with strong preference in this family. Gene chip results showed that only MdSPS2, MdSPS3, MdSPS11, and MdSPS17 were up-regulated in roots, and they were all members of subfamily C. The qRT-PCR analysis showed that all members of this family responded significantly to drought stress, salt stress, and low temperature stress. Interestingly, the relative expression of MdSPS12 was significantly down-regulated under salt stress and low temperature stress. In addition, the expression of MdSPS3, MdSPS8, MdSPS11, and MdSPS17 was more than 20 fold higher than that of the control under drought stress, salt stress, and low temperature stress. These four genes could be candidates for molecular breeding in the MdSPS family. [ABSTRACT FROM AUTHOR]

To explore the impact of shade treatment on grape berries, 'Marselan' grape berries were bagged under different light transmission rates (100% (CK), 75% (A), 50% (B), 25% (C), 0% (D)). It was observed that this treatment delayed the ripening of the grape berries. The individual weight of the grape berries, as well as the content of fructose, glucose, soluble sugars, and organic acids in the berries, was measured at 90, 100, and 125 days after flowering (DAF90, DAF100, DAF125). The results revealed that shading treatment reduced the sugar content in grape berries; the levels of fructose and glucose were higher in the CK treatment compared to the other treatments, and they increased with the duration of the shading treatment. Conversely, the sucrose content exhibited the opposite trend. Additionally, as the weight of the grape berries increased, the content of soluble solids and soluble sugars in the berries also increased, while the titratable acidity decreased. Furthermore, 16 differentially expressed genes (DEGs) were identified in the photosynthesis-antenna protein pathway from the transcriptome sequencing data. Correlation analysis revealed that the expression levels of genes VIT_08s0007g02190 (Lhcb4) and VIT_15s0024g00040 (Lhca3) were positively correlated with sugar content in the berries at DAF100, but negatively correlated at DAF125. qRT-PCR results confirmed the correlation analysis. This indicates that shading grape clusters inhibits the expression of genes in the photosynthesis-antenna protein pathway in the grape berries, leading to a decrease in sugar content. This finding contributes to a deeper understanding of the impact mechanisms of grape cluster shading on berry quality, providing important scientific grounds for improving grape berry quality. [ABSTRACT FROM AUTHOR]

Background: Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4). Results: The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. Conclusions: Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport. [ABSTRACT FROM AUTHOR]

Background: Anthocyanin synthase (ANS) is the enzyme downstream of the anthocyanins synthesis pathway and the rate-limiting enzyme of the synthesis pathway. It catalyzes the conversion of colorless anthocyanins to anthocyanins and plays an important role in plant color presentation and stress resistance. However, ANS gene is rarely studied in grapes. Results: In this study, 121 VvANS genes were identified and distributed on 18 chromosomes, VvANS family members were divided into 8 subgroups. Secondary structure prediction showed mainly irregular coils and α-helices, and subcellular localization indicated that VvANS gene family is mainly located in chloroplast, cytoplasm and nucleus. The promoter region of the VvANS gene family contains multiple cis-acting elements that are associated with light, abiotic stress, and hormones. Intraspecific collinearity analysis showed that there were 13 pairs of collinearity between VvANS genes. Interspecific collinearity analysis showed that there was more collinearity between grape, apple and Arabidopsis, but less collinearity between grape and rice. Microarray data analysis showed that VvANS17, VvANS23 and VvANS75 had higher expression levels in flesh and peel, while VvANS25, VvANS64 and VvANS106 had higher expression levels in flower. The results of qRT-PCR analysis showed that VvANS genes were expressed throughout the whole process of fruit coloring, such as VvANS47 and VvANS55 in the green fruit stage, VvANS3, VvANS64 and VvANS90 in the initial fruit color turning stage. The expression levels of VvANS21, VvANS79 and VvANS108 were higher at 50% coloring stage, indicating that these genes play an important role in the fruit coloring process. VvANS4, VvANS66 and VvANS113 had the highest expression levels in the full maturity stage. Conclusions: These results indicated that different members of VvANS gene family played a role in different coloring stages, and this study laid a foundation for further research on the function of ANS gene family. [ABSTRACT FROM AUTHOR]

To elucidate the structural characteristics, phylogeny and biological function of anthocyanin synthase (ANS) and its role in anthocyanin synthesis, members of the strawberry ANS gene family were obtained by whole genome retrieval, and their bioinformatic analysis and expression analysis at different developmental stages of fruit were performed. The results showed that the strawberry ANS family consisted of 141 members distributed on 7 chromosomes and could be divided into 4 subfamilies. Secondary structure prediction showed that the members of this family were mainly composed of random curls and α-helices, and were mainly located in chloroplasts, cytoplasm, nuclei and cytoskeletons. The promoter region of the FvANS gene family contains light-responsive elements, abiotic stress responsive elements and hormone responsive elements, etc. Intraspecific collinearity analysis revealed 10 pairs of FvANS genes, and interspecific collinearity analysis revealed more relationships between strawberries and apples, grapes and Arabidopsis, but fewer between strawberries and rice. Chip data analysis showed that FvANS15, FvANS41, FvANS47, FvANS48, FvANS49, FvANS67, FvANS114 and FvANS132 were higher in seed coat tissues and endosperm. FvANS16, FvANS85, FvANS90 and FvANS102 were higher in internal and fleshy tissues. Quantitative real-time PCR (qRT-PCR) showed that the ANS gene was expressed throughout the fruit coloring process. The expression levels of most genes were highest in the 50% coloring stage (S3), such as FvANS16, FvANS19, FvANS31, FvANS43, FvANS73, FvANS78 and FvANS91. The expression levels of FvANS52 were the highest in the green fruit stage (S1), and FvANS39 and FvANS109 were the highest in the 20% coloring stage (S2). These results indicate that different members of the FvANS gene family play a role in different pigmentation stages, with most genes playing a role in the expression level of the rapid accumulation of fruit coloring. This study lays a foundation for further study on the function of ANS gene family. [ABSTRACT FROM AUTHOR]

Drought is one of the main abiotic factors affecting grape quality. However, the impacts of drought stress on sugar and related gene expression during grape berry ripening remain unclear. In this experiment, the grapes were subjected to different levels of continuous water stress from 45 to 120 days after flowering (DAA) to study the changes in berry sugar content and the expression of genes related to sugar metabolism under different water stresses. Data supported that glucose, fructose, sucrose, and soluble sugars increased from 45 DAA. Combined with previous research results, T1, T2, and Ct grape berries with 60 ~ 75 DAA and large differences in sucrose, fructose, glucose and soluble sugars compared with the Ct were selected for RNA sequencing (RNA‐seq). Through transcriptome analysis, 4471 differentially expressed genes (DEGs) were screened, and 65 genes in photosynthesis, ABA signaling pathway and photosynthetic carbon metabolism pathway were analyzed further by qRT‐PCR. At 60 DAA, the relative expression levels of CAB1R, PsbP, SNRK2, and PYL9 were significantly upregulated in response to water stress, while AHK1, At4g02290 were down‐regulated. At 75 DAA, the relative expression levels of ELIP1, GoLS2, At4g02290, Chi5, SAPK, MAPKKK17, NHL6, KINB2, and AHK1 were upregulated. And CAB1R, PsbA, GoLS1, SnRK2, PYL9, and KINGL were significantly downregulated under moderate water stress. In addition, PsbA expression was down‐regulated in response to water stress. These results will help us to fully understand the potential connections between glucose metabolism and gene expression in grapes under drought stress. [ABSTRACT FROM AUTHOR]

Simple Summary: MEG3 is a class of lncRNA, which is considered a tumor suppressor. It is lost or decreased in different biological processes of various human tumors and is closely related to various diseases. MEG3 can modulate the expression of target genes through transcription, translation, post-translational modification and epigenetic regulation. Studies have shown that MEG3 dysfunction has been linked to a poor prognosis and drug resistance. MEG3 mediates the hallmarks of cancer through a variety of mechanisms, acting as a tumor suppressor to limit tumor growth. Hence, MEG3 is a potential prognostic marker and antitumor therapeutic target. Long non-coding RNAs (lncRNAs) are critical regulators in various biological processes involved in the hallmarks of cancer. Maternally expressed gene 3 (MEG3) is lncRNA that regulates target genes through transcription, translation, post-translational modification, and epigenetic regulation. MEG3 has been known as a tumor suppressor, and its downregulation could be found in various cancers. Furthermore, clinical studies revealed that impaired MEG3 expression is associated with poor prognosis and drug resistance. MEG3 exerts its tumor suppressive effect by suppressing various cancer hallmarks and preventing cells from acquiring cancer-specific characteristics; as it could suppress tumor cells proliferation, invasion, metastasis, and angiogenesis; it also could promote tumor cell death and regulate tumor cell metabolic reprogramming. Hence, MEG3 is a potential prognostic marker, and overexpressing MEG3 might become a potential antitumor therapeutic strategy. Herein, we summarize recent knowledge regarding the role of MEG3 in regulating tumor hallmarks as well as the underlying molecular mechanisms. Furthermore, we also discuss the clinical importance of MEG3, as well as their potential in tumor prognosis and antitumor therapeutic strategies. [ABSTRACT FROM AUTHOR]

The APETALA2/ethylene responsive AP2/ERF element-binding factors (AP2/ERFs), as a class of transcription factors (TFs), play an important role in plant growth and development as well as various biotic and/or abiotic stresses responses. AP2/ERF gene families have been widely identified in a lot of plants, but there was little known about this gene family in strawberry. To investigate the characteristics and functions of strawberry FvAP2/ERF gene family in abiotic stresses, a total of 139 FvAP2/ERF genes were identified in this study. The sequence alignment and phylogenetic analysis clustered AP2/ERF gene family into four subfamilies (AP2, RAV, ERF, and DREB). Chromosome location analysis revealed that the tandem duplication and the whole-genome duplications (WGDs) may result in the expansion of FvAP2/ERF gene family. The qRT-PCR (quantitative real-time PCR) indicated 14 FvAP2/ERFs underwent up- or down-regulated expression in response to abiotic stresses. In summary, these results offered vital information for further evolutionary and functional characterization of FvAP2/ERF genes, and it also gave some guidance for improving the resistance of strawberry in the growth process. Ultimately, this study may contribute to the selection and breeding of high-yield, high-quality, and highly resistant strawberry varieties. [ABSTRACT FROM AUTHOR]

• Single-cell sequencing reveals that natural killer cells are most responsive to and damaged by the moxifloxacin environment. • Moxifloxacin environment promotes elevated cytokine and chemokine expression and activation of their signaling pathways in natural killer cells. • Moxifloxacin induces apoptosis by reducing mitochondrial DNA and inhibiting mitochondrial respiratory chain complex function in natural killer cells. • Moxifloxacin environment can activate immediate early response gene expression and mediate early activation response of natural killer cells. As antibiotics become more prevalent, accuracy and safety are critical. Moxifloxacin (MXF) have been reported to have immunomodulatory effects on a variety of immune cells and even anti-proliferative and pro-apoptotic effects, but the mechanism of action is not fully clear. Peripheral blood mononuclear cells (PBMC) from experimental groups of healthy adults (n = 3) were treated with MXF (10ug/ml) in vitro for 24 h. Single-cell sequencing was performed to investigate differences in the response of each immune cell to MXF. Flow cytometry determined differential gene expression in subsets of most damaged NK cells. Pseudo-time analysis identified drivers that influence MXF-stimulated cell differentiation. Detection of mitochondrial DNA and its involvement in the mitochondrial respiratory chain pathway clarifies the origin of MXF-induced stress injury. Moxifloxacin-environmental NK cells are markedly reduced: a new subset of NK cells emerges, and immediate-early-response genes in this subset indicate the presence of an early activation response. The inhibitory receptor-dominant subset shows enhanced activation, leading to increased expression of cytokines and chemokines. The near-mature subset showed greater cytotoxicity and the most pronounced cellular damage. CD56bright cells responded by antagonizing the regulation of activation and inhibitory signals, demonstrating a strong cleavage capacity. The severe depletion of mitochondrial genes was focused on apoptosis induced by the mitochondrial respiratory chain complex. NK cells exhibit heightened sensitivity to the MXF environment. Different NK subsets upregulate the expression of cytokines and chemokines through different activation pathways. Concurrently, MXF induces impairment of the mitochondrial oxidative phosphorylation system, culminating in apoptosis. [ABSTRACT FROM AUTHOR]