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Major zygotic genome activation (ZGA) occurs at the late 2‐cell stage and involves the activation of thousands of genes, supporting early embryonic development. The reasons underlying the regulation of ZGA are not clear. Acetylation modifications of histone tails promote transcriptional activation, and the maternal deletion of H4K16ac leads to failure in ZGA. GATAD2B is one of the core subunits of the nucleosome remodelling and histone deacetylation (NuRD) complex. Our research has shown that GATAD2B exhibits specific nucleus localization and high protein expression from the late 2‐cell stage to the 8‐cell stage. This intriguing phenomenon prompted us to investigate the relationship between GATAD2B and the ZGA. We discovered a distinctive pattern of GATAD2B, starting from the late 2‐cell stage with nuclear localization. GATAD2B depletion resulted in defective embryonic development, including increased DNA damage at morula, decreased blastocyst formation rate, and abnormal differentiation of ICM/TE lineages. Consistent with the delay during the cleavage stage, the transcriptome analysis of the 2‐cell embryo revealed inhibition of the cell cycle G2/M phase transition pathway. Furthermore, the GATAD2B proteomic data provided clear evidence of a certain association between GATAD2B and molecules involved in the cell cycle pathway. As hypothesized, GATAD2B‐deficient 2‐cell embryos exhibited abnormalities in ZGA during the maternal‐to‐embryonic transition, with lower expression of the major ZGA marker MERVL. Overall, our results demonstrate that GATAD2B is essential for early embryonic development, in part through facilitating ZGA. [ABSTRACT FROM AUTHOR]

Delayed antimicrobial susceptibility testing (AST) results lead to empiric broad-spectrum antibiotic use, exerting selective pressure that promotes further antimicrobial resistance (AMR). Compared to genotypic AST approaches, phenotypic AST provides clinicians with a more comprehensive antibiotic susceptibility profile. Hence, there is a pressing need to develop phenotypic methods suitable for clinical settings with quick turnaround times. Herein, we developed a comprehensive phenotypic AST platform that harnessed catalase as a marker and the Fenton reaction as a vehicle. Signal outputs were generated through the formation of methylene blue (MB)/G-quadruplex complexes and doxorubicin (DOX)/double-stranded DNA (dsDNA) complexes. The dual signal mode enhanced the signal-to-noise ratio. Five prominent pathogens associated with AMR-related deaths were selected to validate the method's feasibility. Sixty clinical isolates were tested to assess the clinical practicality, and the results yielded susceptibility profiles that closely agreed with standard AST for 55 out of 60 isolates (91.7% concordance) but were obtained in only 111–126 min instead of requiring over 24 h. Furthermore, the receiver operating characteristic curve was employed to evaluate the diagnostic value, yielding an area under the curve (AUC) of 0.958. If integrated and advocated in clinical laboratories, this technique holds promise in effectively addressing AMR. • The biosensor is broadly applicable to most aerobic bacteria, with catalase as the marker. • We employ the I--facilitated Fenton reaction as intermediary, connecting target recognition to signal outputs. • The dual signal output capability provides mutual correction and signal-to-noise ratio enhancement. • The platform is validated by testing 60 clinical isolates from five prominent pathogenic bacteria. [ABSTRACT FROM AUTHOR]

Culture-free, rapid, and ultrasensitive quantification of Escherichia coli (E. coli) is urgently needed to diagnose clinical urinary tract infections (UTIs), especially point-of-care testing (POCT). Herein, a homogeneous sensitive multi-modal (fluorometer, smartphone, and self-developed handheld fluorometer) assay was developed to detect E. coli within 30 min, and nanoscale luminescent cadmium telluride quantum dots (CdTe QDs) were employed as signal reporters. E. coli outer membrane protease T (OmpT) is a biomarker for the specific proteolytic cleavage of peptides. p -Aminophenol (PAP), generated by leucine aminopeptidase (LAP) via secondary cleavage, was used to reduce Ag+. Cascade amplifications included Ag+ and copper sulfide nanoparticles (CuS NPs) to release Cu2+, CdTe QDs, and Cu2+/CuS NPs, which can ensure detection sensitivity. The method achieved single bacterium detection with great stability and selectivity. The fluorometer, handheld fluorometer and smartphone red-green-blue (RGB) value-based modes were determined to be 50, 15, and 15 clinical urine samples, respectively. The findings were consistent with clinical culture counting, and an area under the curve (AUC) of 0.95 with 90% sensitivity and 100% specificity was achieved. Overall, this OmpT-based catalytic biosensor can provide a solution for the POCT diagnosis of UTIs based on E. coli detection. • A homogeneous rapid fluorescence one-pot assay for Escherichia coli was developed. • The non-culture, rapid, multi-modal sensor had high sensitivity and selectivity. • This system was successfully applied to the analysis of E. coli in 50 urine clinical samples. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy is one of the major complications of diabetes and the main cause to lead to blindness for diabetic patients. However, the exact mechanisms involved in the progression of diabetic retinopathy are not completely known. Herein, we demonstrated a novel role of miR-221-3p in the microvascular dysfunction in diabetic retinopathy. MiR-221-3p expression was found to be substantially upregulated in the retina samples of diabetic rats. Besides, ganglion cell layer, inner nuclear layer, outer nuclear layer, and retinal pigment epithelium layer of diabetic rats expressed higher miR-221-3p than the matched areas of normal rats. High glucose-treated retinal microvascular endothelial cells RF/6A and HRECs exhibited higher miR-221-3p than that in normal condition. MiR-221-3p inhibition could alleviate the retinal vascular leakage induced by diabetes in vivo as evaluated by Evans blue leakage assay, and reduce the proliferation, accelerate the apoptosis development, and inhibit the migration capacity of high glucose-treated RF/6A cells in vitro, while miR-221-3p overexpression partially enhanced the detrimental effects. By bioinformatics analysis and luciferase reporter assay, we identified that TIMP3 is the direct target of miR-221-3p. TIMP3 overexpression counteracted the effect of miR-221-3p on the vessel leakage and endothelial cell function. In conclusion, this study highlights the negative role of miR-221-3p in the microvascular dysfunction in diabetic retinopathy by targeting TIMP3, representing a potential therapeutic target for human diabetic retinopathy. [ABSTRACT FROM AUTHOR]

• No single laboratory method could independently diagnose tuberculous meningitis. • Polymerase-chain-reaction is highly sensitive and specific for the diagnosis of tuberculous meningitis. • Metagenomic next-generation sequencing does not offer much strength in diagnosing tuberculous meningitis. The aim of this study was to comprehensively evaluate metagenomic next-generation sequencing (mNGS), Acid-fast bacillus stain (AFB), MGIT960 culture, polymerase-chain-reaction (PCR), and Xpert MTB/RIF in the diagnosis of tuberculous meningitis (TBM). A cohort of 280 patients who presented with suspected TBM (ie, headache or altered mental status with clinical signs of meningism) were analyzed. The sensitivities of the 5 assays for the diagnosis of TBM ranged from 10.0% to 70.0%. The AFB had the lowest sensitivity of 10.0% (0.5-45.9), while mNGS and PCR had the highest sensitivity, both at 70.0% (35.4-91.9). mNGS demonstrated a distinct advantage in identifying a wider array of pathogens, including viruses, in CSF samples. PCR was a cost-effective option with excellent sensitivity and specificity. However, no single method was statistically significantly better than any other in the diagnosis of TBM. New diagnostic techniques are urgently needed for the independent, rapid and accurate detection of Mycobacterium tuberculosis to guide the diagnosis of TBM. [ABSTRACT FROM AUTHOR]

While flavonoid metabolism’s regulation under light conditions by structural genes and transcription factors is understood, the roles of microRNAs (miRNAs) in this pathway have been rarely reported. In this paper, the accurate control of light was firstly enabled through the specially designed plant growth chamber which ensures consistency and accuracy of the cultivation of longan ECs and the repeatability of the experiments. Then, longan ECs were cultured in this chamber for 25 days. The change of growth rate of longan ECs was compared under different light qualities (dark, blue, green, white, green), intensities (16, 32, 64, 128, 256 μmol ·m-2 ·s-1), and durations (8 h, 12 h, 16 h, 20h, 24h). Results indicated that longan ECs had a high growth rate in the condition of blue or green light, at intensity ranged from 16 μmol·m-2·s-1 to 64 μmol·m-2·s-1, and duration from 8 h to 16 h. In addition, the contents of total flavonoids, rutin, and epicatechin were determined. Results indicated that flavonoid contents of longan ECs reached the highest value under blue light, at 32 μmol·m-2·s-1 and 12h/d. Blue light promoted the accumulation of epicatechin, but inhibited the synthesis of rutin. Finally, the expressions of flavonoid pathway genes, miRNAs and target genes were analyzed by qPCR. These results indicated that miR393 and its target gene DlTIR1-3, miR394 and its target gene DlAlMT12, and miR395 and its target gene DlAPS1 had a negative regulating relationship under blue light in longan ECs. Furthermore, miR393, miR394, and miR395 acted on target genes, which negatively regulated flavonoid key genes DlFLS and positively regulated key genes DlCHS, DlCHI, DlF3′H, DlDFR, DlLAR, and finally affected the accumulation of flavonoids. The treatment of longan ECs under the blue light at the intensity of 32 μmol·m-2·s-1 for 12 h/d inhibited the expression of miR393, miR394 and miR395, which promoted the expression of target genes and the accumulation of flavonoids and epicatechin, but inhibited the synthesis of rutin. [ABSTRACT FROM AUTHOR]

microRNA167 regulates vegetative and reproductive growth by controlling expression patterns of auxin response factors 6 and 8 (ARF6/8) in plants. However, their mutual regulatory roles during plant embryo development are still unknown. Here, we first identified miR167 family members, isolated the primary miR167 and its promoter, predicted endogenous target mimics (eTMs), identified miR167 targets, and analyzed their accumulation in Dimocarpus longan (longan). Four variants of dlo-miR167a and one dlo-miR167f were identified; their accumulation at the cotyledonary embryo stage suggests they may be required for cotyledon-shaped embryo morphogenesis in longan. We then isolated the miR167 precursor, primary transcript, and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, fungal elicitors, heat, low temperature, drought, methyl jasmonate, salicylic acid, gibberellic acid, and circadian control. Two eTM homologs of a phosphatidylinositol 3- and 4-kinase family protein containing a FAT domain and an unknown protein were predicted for miR167. miR167 mediates transcript degradation in longan somatic embryos for DlARF8 but not cleaves for DlARF6. Moreover, both the eTMs were barely detectable in incomplete compact pro-embryogenic cultures and torpedo-shaped embryos, but reached peaks at globular embryos, which was largely reciprocal to that of their corresponding miR167, indicating a potential role in the negative control of miR167 expression; increased DlARF6 is required for somatic embryo development; miR167a/DlARF8 pair is essential to globular embryo formation and subsequent conversion to cotyledonary embryos. In addition, eTM-miR167-ARF6-8 signal transduction was found to play a conserved role in root development of the longan cultivar ‘Sijimi.’ We conclude that eTM down-regulates miR167 via cleavage of DlARF8 mRNAs in longan somatic embryo development, especially during late developmental stages. [ABSTRACT FROM AUTHOR]

Ras-related nuclear protein (Ran) GTPase plays an important role in nucleo-cytoplasmic transportation of proteins and RNA, mitotic spindle assembly, microtubule assembly and nuclear envelope (NE) assembly. We previously identified the full-length cDNAs and a DNA of DlRan3A from longan ( Dimocarpus longan Lour.) somatic embryos and demonstrated its possible roles in cell activities during longan somatic embryogenesis (SE). However, thus far little is known of how Ran functions in the signaling pathways in plant embryos in response to changing environmental stimuli. To discover more biological roles of DlRan3A , we observed DlRan3A located in the nucleus and detected abundant accumulation of DlRan3A s in globular and cotyledon embryos during longan SE, which suggested its involvement in auxin signal pathways in longan early SE. The transcript level of the DlRan3A gene were also determined in longan embryogenic callus (EC) in response to different levels of exogenous phytohormones (indoleacetic acid (IAA), gibberellin A3 (GA 3 ), salicylic acid (SA), methyl jasmonate (MeJA), and ethephon (Eth)), salt, sucrose, prolonged culturing period and light quality treatments. IAA (1 mg/L), GA 3 (12 mg/L), SA (75 μm), MeJA (50 and 100 μm), and Eth (50 mg/L) modulate expression of DlRan3A to 1.3–1.4 folds, and the expression of DlRan3A was significantly affected by light quality, significantly induced to 2-fold by salt (10 g/L), 2.7-fold by sucrose (90 g/L) and was completely suppressed by prolonged cultivation (> 40 days). Deletion analysis suggested that both activation and repression regulatory elements co-exist in the DlRan3A promoter sequence and that the key cis-acting elements included ones in response to auxin, SA, MeJA, and stress. Promoter activities were induced to the highest level by IAA followed by SA, GA 3 and MeJA, while suppressed by ABA and Eth. Together, these results showed DlRan3A close involvement in phytohormones, light, and abiotic stress responsiveness during longan SE. [ABSTRACT FROM AUTHOR]

Somatic embryogenesis (SE), which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs) are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (Dimocarpus longan) SE. A total of 643 conserved and 29 novel miRNAs (including star strands) from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were dlo-miR156 family members and dlo-miR166c* associated with early embryonic culture developmental stages; dlo-miR26, dlo-miR160a, and families dlo-miR159, dlo-miR390, and dlo-miR398b related to heart-shaped and torpedo- shaped embryo formation; dlo-miR4a, dlo-miR24, dlo-miR167a, dlo-miR168a*, dlo-miR397a, dlo-miR398b.1, dlo-miR398b.2, dlo-miR808 and dlo-miR5077 involved in cotyledonary embryonic development; and dlo-miR17 and dlo-miR2089*-1 that have regulatory roles during longan SE. In addition, dlo-miR167a, dlo-miR808, and dlo-miR5077 may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and provide insights into miRNA biogenesis and expression in plant somatic embryo development. [ABSTRACT FROM AUTHOR]

The efficient removal of uranium from aqueous solution remains of great challenge in securing water environment safety. In this paper, we reported a high temperature electrochemical method for the preparation of EuVO 4 with different morphologies from rare earth oxides and vanadate, which solved the problems of rare earth and vanadium recovery. The effects of pH, ionic strength, contact time, initial concentration and reaction temperature on the adsorption of U(VI) by prepared adsorbent were studied by static batch experiments. When the concentration of U(VI) standard is 100 mg g−1, the maximum adsorption capacity of EuVO 4 is 276.16 mg g−1. The adsorption mechanism was elucidated with zeta potential and XPS: 1) negatively charged EuVO 4 attracted UO 2 2+ by electrostatic attraction; 2) exposed Eu, V, and O atoms complexed with U(VI) through coordination; 3) the hybrid of Eu was complex, which accommodated different electrons to interact. In the multi-ion system with Al3+, Zn2+, Cu2+, Ni2+, Cr2+ and Mn2+, EuVO 4 also showed good selective adsorption properties for U(VI). Five adsorption and desorption cycle experiments demonstrated that EuVO 4 possessed good renewable performance. • Different morphologies of EuVO 4 were synthesized by high-temperature electrochemical method. • U(VI) sorption on EuVO 4 was studied using batch and spectroscopies. • The maximum adsorption capacity of EuVO 4 reached at 276.16 mg g−1. • EuVO 4 showed good selective adsorption property for U(Ⅵ) in the multi-ion system. [ABSTRACT FROM AUTHOR]

GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 μ m o l · L − 1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes. [ABSTRACT FROM AUTHOR]

B3 family transcription factors play an essential regulatory role in plant growth and development processes. This study performed a comprehensive analysis of the B3 family transcription factor in longan (Dimocarpus longan Lour.), and a total of 75 DlB3 genes were identified. DlB3 genes were unevenly distributed on the 15 chromosomes of longan. Based on the protein domain similarities and functional diversities, the DlB3 family was further clustered into four subgroups (ARF, RAV, LAV, and REM). Bioinformatics and comparative analyses of B3 superfamily expression were conducted in different light and with different temperatures and tissues, and early somatic embryogenesis (SE) revealed its specific expression profile and potential biological functions during longan early SE. The qRT-PCR results indicated that DlB3 family members played a crucial role in longan SE and zygotic embryo development. Exogenous treatments of 2,4-D (2,4-dichlorophenoxyacetic acid), NPA (N-1-naphthylphthalamic acid), and PP333 (paclobutrazol) could significantly inhibit the expression of the DlB3 family. Supplementary ABA (abscisic acid), IAA (indole-3-acetic acid), and GA3 (gibberellin) suppressed the expressions of DlLEC2, DlARF16, DlTEM1, DlVAL2, and DlREM40, but DlFUS3, DlARF5, and DlREM9 showed an opposite trend. Furthermore, subcellular localization indicated that DlLEC2 and DlFUS3 were located in the nucleus, suggesting that they played a role in the nucleus. Therefore, DlB3s might be involved in complex plant hormone signal transduction pathways during longan SE and zygotic embryo development. [ABSTRACT FROM AUTHOR]

Background: Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes. Results: Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA. Conclusion: Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other. [ABSTRACT FROM AUTHOR]

SUMMARY: Plant embryogenic calli (ECs) can undergo somatic embryogenesis to regenerate plants. This process is mediated by regulatory factors, such as transcription factors and specifically expressed genes, but the precise molecular mechanisms underlying somatic embryogenesis at the single‐cell level remain unclear. In this study, we performed high‐resolution single‐cell RNA sequencing analysis to determine the cellular changes in the EC of the woody plant species Dimocarpus longan (longan) and clarify the continuous cell differentiation trajectories at the transcriptome level. The highly heterogeneous cells in the EC were divided into 12 putative clusters (e.g., proliferating, meristematic, vascular, and epidermal cell clusters). We determined cluster‐enriched expression marker genes and found that overexpression of the epidermal cell marker gene GDSL ESTERASE/LIPASE‐1 inhibited the hydrolysis of triacylglycerol. In addition, the stability of autophagy was critical for the somatic embryogenesis of longan. The pseudo‐timeline analysis elucidated the continuous cell differentiation trajectories from early embryonic cell division to vascular and epidermal cell differentiation during the somatic embryogenesis of longan. Moreover, key transcriptional regulators associated with cell fates were revealed. We found that ETHYLENE RESPONSIVE FACTOR 6 was characterized as a heat‐sensitive factor that negatively regulates longan somatic embryogenesis under high‐temperature stress conditions. The results of this study provide new spatiotemporal insights into cell division and differentiation during longan somatic embryogenesis at single‐cell resolution. Significance Statement: Plant embryogenic calli can undergo somatic embryogenesis to regenerate plants. The single‐cell RNA‐seq results described herein provide new spatiotemporal insights into cell division and differentiation in the Dimocarpus longan (longan) embryogenic callus. The generated gene expression map will enable us to investigate how embryonic cells differentiate into vascular and epidermal cells. The results may provide the foundation for future molecular and cellular investigations into the mechanisms mediating longan somatic embryogenesis and zygotic embryogenesis. [ABSTRACT FROM AUTHOR]

Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana. [ABSTRACT FROM AUTHOR]

Atomic Force Microscopy (AFM) is one of the most popular and advanced tools for ultra high-resolution imaging and nanomanipulation of nano-scale matter. But AFM imaging typically takes a long time. High-speed and high-precision AFM measurement has attracted wide attention in recent several years. In traditional AFM, simple reduction in the number of measurement points may lose essential sample topography information. To resolve such problems, an AFM image reconstruction method based on Compressed Sensing (CS) theory is applied to reduce image acquisition time without cutting down the image quality. The benefit of using CS approach in AFM is shortening the imaging time, minimizing the interaction with the sample, and finally avoiding sample damage in AFM. Three kinds of testing samples with high and low frequency components were examined by a scanning electron microscope (SEM) and by AFM. An orthogonal Matching Pursuit (OMP) algorithm is employed to reconstruct an AFM image with different sampling rates. Subsequently the reconstruction results of sample topography images are analyzed and evaluated. Using the CS approach in AFM can greatly improve the AFM imaging process. Experimental results show that the obtained reconstructed images have different resolution and quality, depending on the surface morphology of the sample and sampling rates. [ABSTRACT FROM AUTHOR]

Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree. Its fruit quality and yield are affected by embryo development. As a plant seed germination marker gene, the germin-like protein (GLP) gene plays an important role in embryo development. However, the mechanism underlying the role of the GLP gene in somatic embryos is still unclear. Therefore, we conducted genome-wide identification of the longan GLP (DlGLP) gene and preliminarily verified the function of DlGLP1-5–1. Thirty-five genes were identified as longan GLP genes and divided into 8 subfamilies. Based on transcriptome data and qRT‒PCR results, DlGLP genes exhibited the highest expression levels in the root, and the expression of most DlGLPs was upregulated during the early somatic embryogenesis (SE) in longan and responded to high temperature stress and 2,4-D treatment; eight DlGLP genes were upregulated under MeJA treatment, and four of them were downregulated under ABA treatment. Subcellular localization showed that DlGLP5-8–2 and DlGLP1-5–1 were located in the cytoplasm and extracellular stroma/chloroplast, respectively. Overexpression of DIGLP1-5–1 in the globular embryos (GEs) of longan promoted the accumulation of lignin and decreased the H2O2 content by regulating the activities of ROS-related enzymes. The results provide a reference for the functional analysis of DlGLPs and related research on improving lignin accumulation in the agricultural industry through genetic engineering. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan) is a precious subtropical fruit with high nutritional value. The somatic embryogenesis (SE) affects the quality and yield of fruit. Apart from clonal propagation, SE has extensive applications in genetic improvement and mutation. Thus, understanding the molecular basis of embryogenesis in longan will help to develop strategies for mass production of quality planting material. Lysine acetylation (Kac) plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in plant early SE. In this study, the proteome and acetylome of longan embryogenic callus (ECs) and globular embryos (GEs) were investigated. In total, 7232 proteins and 14,597 Kac sites were identified, and this resulted in the discovery of 1178 differentially expressed proteins and 669 differentially expressed acetylated proteins. KEGG and GO analysis showed that glucose metabolism, carbon metabolism, fatty acid degradation, and oxidative phosphorylation pathways were influenced by Kac modification. Furthermore, sodium butyrate (Sb, a deacetylase inhibitor) led to reduced the proliferation and delayed the differentiation of ECs by regulating the homeostasis of reactive oxygen species (ROS) andindole-3-acetic acid (IAA). Our study provides a comprehensive proteomic and acetylomic analysis to aid in understanding the molecular mechanisms involved in early SE, representing a potential tool for genetic improvement of longan. • Kac is involved in the early regulation of longan embryogenesis with various regulatory pathways. • Sodium butyrate led to reduced the proliferation and delayed the differentiation of ECs by regulating the homeostasis of ROS and IAA. • Carbon metabolism, fatty acid degradation, and oxidative phosphorylation pathways were mainly influenced by Kac. [ABSTRACT FROM AUTHOR]

The early auxin responsive small auxin up-regulated RNA (SAUR) family is an important gene family in the auxin signal transduction pathway. This study focused on the regulatory mechanism of DlSAUR genes during early somatic embryogenesis (SE) and its response to hormone treatment and abiotic stress. Mining of the available Dimocarpus longan Lour. (D. longan) genome sequence yielded 68 putative SAUR genes. Transcript profiles based on RNA-seq data showed that most of the 24 detected DlSAUR genes were highly expressed in the globular embryos (GE) (10) and most of them responded to heat stress and 2,4-D treatment. The results of qRT-PCR showed that most of DlSAUR genes were up-regulated under auxin inhibitor N-1-naphthylphthalamic acid (NPA) and auxin indole-3-acetic acid (IAA) treatments. Moreover, NPA could promote longan SE. The assay for ATAC-seq data analysis showed that chromatin accessibility of 19 of the 24 DlSAUR genes were open during early SE, and most DlSAUR genes differentially expressed during early SE were not associated with H3K4me1 signal enrichment. The DlSAUR32 was selected for subcellular localization and RNA-seq analysis, which encode a cell nuclear-localized protein. Dual-luciferase assays and transient transformation showed that the transcription factors (TFs) DlWRKY75-1 and DlWRKY75-2 might bind to the DlSAUR32 promoters to inhibition gene transcription. Transient overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content in N. benthamiana leaves. Thus, the regulatory network composed of DlSAUR32 and its related TFs may regulate the early longan SE and be involved in the auxin response regulatory pathway of longan. • DlSAUR genes were sensitive to IAA and NPA treatments. • The regulatory network of transcription factors and DlSAUR genes was predicted. • DlWRKY75-1 and DlWRKY75-2 can significantly reduce the expression of DlSAUR32. • Overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content. [ABSTRACT FROM AUTHOR]

MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5’cDNA ends (RLM-RACE) were applied. Using degradome sequencing, 26 genes mainly involved in transcription factor, resistance protein and signal transduction protein synthesis were identified as potential miRNA targets, with 5 genes subsequently verified. Quantitative real-time PCR (qRT-PCR) revealed that the expression patterns of novel-miR1, novel-miR2, csn-miR160a, csn-miR162a, csn-miR394 and csn-miR396a were negatively correlated with catechin content. The expression of six miRNAs (csn-miRNA167a, csn-miR2593e, csn-miR4380a, csn-miR3444b, csn-miR5251 and csn-miR7777-5p.1) and their target genes involved in catechin biosynthesis were also analyzed by qRT-PCR. Negative and positive correlations were found between these miRNAs and catechin contents, while positive correlations were found between their target genes and catechin content. This result suggests that these miRNAs may negatively regulate catechin biosynthesis by down-regulating their biosynthesis-related target genes. Taken together, our results indicate that miRNAs are crucial regulators in tea, with the results of 5’-RLM-RACE and expression analyses revealing the important role of miRNAs in catechin anabolism. Our findings should facilitate future research to elucidate the function of miRNAs in catechin biosynthesis. [ABSTRACT FROM AUTHOR]

Strigolactones (SLs), a new class of plant hormones, are implicated in the regulation of various biological processes. However, the related family members and functions are not identified in longan (Dimocarpus longan Lour.). In this study, 23 genes in the CCD, D27, and SMXL family were identified in the longan genome. The phylogenetic relationships, gene structure, conserved motifs, promoter elements, and transcription factor-binding site predictions were comprehensively analysed. The expression profiles indicated that these genes may play important roles in longan organ development and abiotic stress responses, especially during early somatic embryogenesis (SE). Furthermore, GR24 (synthetic SL analogue) and Tis108 (SL biosynthesis inhibitor) could affect longan early SE by regulating the levels of endogenous IAA (indole-3-acetic acid), JA (jasmonic acid), GA (gibberellin), and ABA (abscisic acid). Overexpression of SMXL6 resulted in inhibition of longan SE by regulating the synthesis of SLs, carotenoids, and IAA levels. This study establishes a foundation for further investigation of SL genes and provides novel insights into their biological functions. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are widely involved in plant growth and development. However, the function of circRNAs in plant somatic embryogenesis (SE) remains elusive. Here, by using high-throughput sequencing, a total of 5029 circRNAs were identified in the three stages of longan (Dimocarpus longan Lour.) early SE. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed (DE) circRNA host genes were enriched in the 'non-homologous end-joining' (NHEJ) and 'butanoate metabolism' pathways. In addition, the reactive oxygen species (ROS) content during longan early SE was determined. The results indicated that ROS-induced DNA double-strand breaks may not depend on the NHEJ repair pathway. Correlation analyses of the levels of related metabolites (glutamate, γ-aminobutyrate and pyruvate) and the expression levels of circRNAs and their host genes involved in butanoate metabolism were performed. The results suggested that circRNAs may act as regulators of the expression of cognate mRNAs, thereby affecting the accumulation of related compounds. A competing endogenous RNA (ceRNA) network of DE circRNAs, DE mRNAs, DE long noncoding RNAs (lncRNAs) and DE microRNAs (miRNAs) was constructed. The results showed that the putative targets of the noncoding RNA (ncRNAs) were significantly enriched in the KEGG pathways 'mitogen-activated protein kinase signaling' and 'nitrogen metabolism'. Furthermore, the expression patterns of the candidate circRNAs, lncRNAs, miRNAs and mRNAs confirmed the negative correlation between miRNAs and ceRNAs. In addition, two circRNA overexpression vectors were constructed to further verify the ceRNA network correlations in longan early SE. Our study revealed the potential role of circRNAs in longan early SE, providing new insights into the intricate regulatory mechanism underlying plant SE. [ABSTRACT FROM AUTHOR]

Our aim in the experiment was to study the effects of methyl jasmonates (MeJA) on the active compounds of rosemary suspension cells, the metabolites' change of contents under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments promoted the accumulation of rosmarinic acid (RA), carnosic acid (CA), flavonoids, jasmonate (JA), gibberellin (GA), and auxin (IAA); but reduced the accumulations of abscisic acid (ABA), salicylic acid (SA), and aspartate (Asp). In addition, 50 and 100 μM MeJA promoted the accumulation of alanine (Ala) and glutamate (Glu), and 50 μM MeJA promoted the accumulation of linoleic acid and alpha-linolenic acid in rosemary suspension cells. Comparative RNA-sequencing analysis of different concentrations of MeJA showed that a total of 30, 61, and 39 miRNAs were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of the target genes of the differentially expressed miRNAs showed that plant hormone signal transduction, linoleic acid, and alpha-linolenic acid metabolism-related genes were significantly enriched. In addition, we found that miR160a-5p target ARF, miR171d_1 and miR171f_3 target DELLA, miR171b-3p target ETR, and miR156a target BRI1, which played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of 12 differentially expressed miRNAs and their target genes showed a high correlation between the RNA-seq and the qRT-PCR result. Amplification culture of rosemary suspension cells in a 5 L stirred bioreactor showed that cell biomass accumulation in the bioreactor was less than that in the shake flask under the same conditions, and the whole cultivation period was extended to 14 d. Taken together, MeJA promoted the synthesis of the active compounds in rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided an overall view of the miRNAs responding to MeJA in rosemary. [ABSTRACT FROM AUTHOR]

Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, we describe miRNAs which are upregulated in Oncidium orchid roots after colonization by the fungus. Growth promotion and vigorous root development were observed in Oncidium hybrid orchid, while seedlings were colonized by P. indica. We performed a genome-wide expression profiling of small RNAs in Oncidium orchid roots either colonized or not-colonized by P. indica. After sequencing, 24,570,250 and 24744,141 clean reads were obtained from two libraries. 13,736 from 17,036,953 unique sequences showed homology to either 86 miRNA families described in 41 plant species, or to 46 potential novel miRNAs, or to 51 corresponding miRNA precursors. The predicted target genes of these miRNAs are mainly involved in auxin signal perception and transduction, transcription, development and plant defense. The expression analysis of miRNAs and target genes demonstrated the regulatory functions they may participate in. This study revealed that growth stimulation of the Oncidium orchid after colonization by P. indica includes an intricate network of miRNAs and their targets. The symbiotic function of P. indica on Oncidium orchid resembles previous findings on Chinese cabbage. This is the first study on growth regulation and development of Oncidium orchid by miRNAs induced by the symbiotic fungus P. indica. [ABSTRACT FROM AUTHOR]

Drought is the stressor with a significant adverse impact on the yield stability of tea plants. HD-ZIP III transcription factors (TFs) play important regulatory roles in plant growth, development, and stress responses. However, whether and how HD-ZIP III TFs are involved in drought response and tolerance in tea plants remains unclear. Here, we identified seven HD-ZIP III genes (CsHDZ3–1 to CsHDZ3–7) in tea plant genome. The evolutionary analysis demonstrated that CsHDZ3 members were subjected to purify selection. Subcellular localization analysis revealed that all seven CsHDZ3s located in the nucleus. Yeast self-activation and dual-luciferase reporter assays demonstrated that CsHDZ3–1 to CsHDZ3–4 have trans-activation ability whereas CsHDZ3–5 to CsHDZ3–7 served as transcriptional inhibitors. The qRT-PCR assay showed that all seven CsHDZ3 genes could respond to simulated natural drought stress and polyethylene glycol treatment. Further assays verified that all CsHDZ3 genes can be cleaved by csn-miR166. Overexpression of csn-miR166 inhibited the expression of seven CsHDZ3 genes and weakened drought tolerance of tea leaves. In contrast, suppression of csn-miR166 promoted the expression of seven CsHDZ3 genes and enhanced drought tolerance of tea leaves. These findings established the foundation for further understanding the mechanism of CsHDZ3- miR166 modules' participation in drought responses and tolerance. [ABSTRACT FROM AUTHOR]

The photocatalytic reduction of soluble UO 2 2 + from radioactive wastewater is becoming an effective method to reduce radioactive pollution, while available catalysts are considerable limitation. Herein, the ZnS@g-C3N4 (ZSGCN) heterojunctions complexes were compounded as catalysts to reduce UO 2 2 + . The results from TEM, XRD, XPS, EIS, DRS and PL showed that the ZnS nanoparticles combined with graphite carbon nitride (GCN), which is the construction of heterojunctions broadened the absorption range of sunlight. The ZSGCN-5 presented the optimal photocatalytic reduction activity to UO 2 2 + , which was 4.34 times than that of pristine GCN. The ZSGCN-5 heterojunction becomes a promising photocatalyst for radioactive environment remediation. [ABSTRACT FROM AUTHOR]

DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing and transcriptome sequencing analyses for embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine content in EC, ICpEC and GE was 24.59, 19.65 and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene ontology and Kyoto encyclopedia of genes and genomes analysis of hypomethylated-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine treatment in EC promoted the formation of GE and enhanced the capability of longan SE. Our results suggest that DNA demethylation has important roles in longan SE development. [ABSTRACT FROM AUTHOR]

Longan (Dimocarpus longan Lour.) is an important commercial fruit tree in southern China. The embryogenesis of longan affects the quality and yield of fruit. A large number of alternative splicing events occurs during somatic embryogenesis (SE), which is regulated by serine/arginine-rich (SR) proteins. However, the functions of SR proteins in longan are poorly understood. In this study, 21 Dlo-SR gene family members belonging to six subfamilies were identified, among which Dlo-RSZ20a, Dlo-SR30, Dlo-SR17, Dlo-SR53 and Dlo-SR32 were localized in the nucleus, Dlo-RSZ20b, Dlo-RSZ20c, Dlo-RSZ20d, Dlo-SC18, Dlo-RS2Z29, Dlo-SCL41, and Dlo-SR33 were localized in chloroplasts, and Dlo-RS43, Dlo-SC33, Dlo-SC37, Dlo-RS2Z33, Dlo-RS2Z16, Dlo-RS2Z24, Dlo-SCL43, Dlo-SR112, and Dlo-SR59 were localized in the nucleus and chloroplasts. The Dlo-SR genes exhibited differential expression patterns in different tissues of longan. The transcript levels of Dlo-RSZ20a, Dlo-SC18, Dlo-RS2Z29, DLo-SR59, Dlo-SR53, and Dlo-SR17 were low in all analyzed tissues, whereas Dlo-RS43, Dlo-RS2Z16, Dlo-RS2Z24, and Dlo-SR30 were highly expressed in all tissues. To clarify their function during SE, the transcript levels of Dlo-SR genes were analyzed at different four stages of SE, comprising non-embryonic callus (NEC), friable-embryogenic callus (EC), incomplete compact pro-embryogenic culture (ICpEC) and globular embryo (GE). Interestingly, the transcript levels of Dlo-RS2Z29 and Dlo-SR112 were increased in embryogenic cells compared with the NEC stage, whereas transcript levels of Dlo-RSZ20a, Dlo-RS43, Dlo-SC37, and Dlo-RS2Z16 were especially increased at the GE stage compared with the other stages. Alternative splicing events of Dlo-SR mRNA precursors (pre-mRNAs) was detected during SE, with totals of 41, 29, 35, and 44 events detected during NEC, EC, ICpEC, and GE respectively. Protein–protein interaction analysis showed that SR proteins were capable of interaction with each other. The results indicate that the alternative splicing of Dlo-SR pre-mRNAs occurs during SE and that Dlo-SR proteins may interact to regulate embryogenesis of longan. [ABSTRACT FROM AUTHOR]

The Sm proteins are a conserved protein family with Sm motifs. The family includes Sm and Sm-like proteins, which play important roles in pre-mRNA splicing. Most research on the Sm proteins have been conducted in herbaceous plants, and less in woody plants such as Dimocarpus longan (longan). And the embryo development status significantly affects the quality and yield of longan. In this study, we conducted a genome-wide analysis of longan Sm genes (DlSm) to clarify their roles during somatic embryogenesis (SE) and identified 29 Sm genes. Phylogenetic analysis deduced longan Sm proteins clustered into 17 phylogenetic groups with the homologous Sm proteins of Arabidopsis thaliana. We also analyzed the gene structures, motif compositions, and conserved domains of the longan Sm proteins. The promoter sequences of the DlSm genes contained many light, endosperm development, hormone, and temperature response elements, which suggested their possible functions. In the non-embryogenic callus(NEC) and during early SE in longan, the alternative splicing(AS) events of DlSm genes indicated that these genes may influence SE development by changing gene structures and sequences. The kinetin(KT) hormone, and blue and white light treatments affected the differentiation and growth of longan embryonic callus(EC) probably by affecting the AS events of DlSm genes. Expression profiles showed the possible functional divergence among Sm genes, and different hormones and light qualities affected their expression levels. The expression trends of the DlSm genes determined by RNA sequencing as fragments per kilobase of exon model per million mapped reads (FPKM) and by real-time quantitative PCR(qRT-PCR) during early SE in longan showed that the expression of the DlSm genes was affected by the growth and differentiation of longan SE, and decreased as the somatic embryo differentiation progressed. The results will contributed to understanding the longan Sm gene family and provide a basis for future functional validation studies. [ABSTRACT FROM AUTHOR]

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan. [ABSTRACT FROM AUTHOR]

Background: The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.), which is an important tropical/subtropical evergreen fruit tree that produces a variety of bioactive compounds with rich nutritional and medicinal value. We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan. Results: A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. We identified 125 longan AP2/ERF genes and classified them into the ERF (101 members), AP2 (19 members), RAV (four members) families, and one Soloist. The AP2 and Soloist genes contained one to ten introns, whereas 87 genes in the ERF and RAV families had no introns. Hormone signaling molecules such as methyl jasmonate (MeJA), abscisic acid (ABA), gibberellin, auxin, and salicylic acid (SA), and stress response cis-acting element low-temperature (55) and defense (49) boxes also were identified. We detected diverse single nucleotide polymorphisms (SNPs) between the 'Hong He Zi' (HHZ) and 'SI JI MI' (SJM) cultivars. The number of insertions and deletions (InDels) was far fewer than SNPs. The AP2 family members exhibited more alternative splicing (AS) events in different developmental processes of longan than members of the other families. Expression pattern analysis revealed that some AP2/ERF members regulated early SE and developmental processes in longan seed, root, and flower, and responded to exogenous hormones such as MeJA, SA, and ABA, and 2,4-D, a synthetic auxin. Protein interaction predictions indicated that the Baby Boom (BBM) transcription factor, which was up-regulated at the transcriptional level in early SE, may interact with the LALF/AGL15 network. Conclusions: The comprehensive analysis of molecular evolution and expression patterns suggested that the AP2/ERF superfamily may plays an important role in longan, especially in early SE, and in seed, root, flower, and young fruit. This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement. [ABSTRACT FROM AUTHOR]

Background: Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). Results: RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1–1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2–1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. Conclusion: This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants. [ABSTRACT FROM AUTHOR]

Gerbera hybrida is one of the top five cut flowers across the world, it is host for the root rot causing parasite called Phytophthora cryptogea. In this study, plantlets of healthy and root-rot pathogen-infected G. hybrida were used as plant materials for transcriptome analyis using high-throughput Illumina sequencing technique. A total 108,135 unigenes were generated with an average length of 727 nt and N50 equal to 1274 nt out of which 611 genes were identified as DEGs by DESeq analyses. Among DEGs, 228 genes were up-regulated and 383 were down-regulated. Through this annotated data and Kyoto encyclopedia of genes and genomes (KEGG), molecular interaction network, transcripts accompanying with tyrosine metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction pathways were thoroughly observed considering expression pattern. The involvement of DEGs in tyrosine metabolism pathway was validated by real-time qPCR. We found that genes related with tyrosine metabolism were activated and up-regulated against stress response. The expression of GhTAT, GhAAT, GhHPD, GhHGD and GhFAH genes was significantly increased in the leaves and petioles at four and six dpi (days post inoculation) as compared with control. The study predicts the gene sequences responsible for the tyrosine metabolism pathway and its responses against root-rot resistance in gerbera plant. In future, identification of such genes is necessary for the better understanding of rot resistance mechanism and to develop a root rot resistance strategy for ornamental plants. [ABSTRACT FROM AUTHOR]

Superoxide dismutases (SODs), as a family of metalloenzymes related to the removal of reactive oxygen species (ROS), have not previously been investigated at genome-wide level in tea plant. In this study, 10 CsSOD genes were identified in tea plant genome, including 7 Cu/Zn-SODs (CSDs), 2 Fe-SODs (FSDs) and one Mn-SOD (MSD), and phylogenetically classified in three subgroups, respectively. Physico-chemical characteristic, conserved motifs and potential protein interaction analyses about CsSOD proteins were carried out. Exon-intron structures and codon usage bias about CsSOD genes were also examined. Exon-intron structures analysis revealed that different CsSOD genes contained various number of introns. On the basis of the prediction of regulatory miRNAs of CsSODs, a modification 5' RNA ligase-mediated (RLM)-RACE was performed and validated that csn-miR398a-3p-1 directly cleaves CsCSD4. By prediction of cis-acting elements, the expression patterns of 10 CsSOD genes and their regulatory miRNAs were detected under cold, drought, exogenous methyl jasmonate (MeJA) and gibberellin (GA3) treatments. The results showed that most of CsSODs except for CsFSD2 were induced under cold stress and CsCSDs may play primary roles under drought stress; exogenous GA3 and MeJA could also stimulated/inhibited distinct CsSODs at different stages. In addition, we found that csn-miR398a-3p-1 negatively regulated the expression of CsCSD4 may be a crucial regulatory mechanism under cold stress. This study provides a certain basis for the studies about stress resistance in tea plants, even provide insight into comprehending the classification, evolution, diverse functions and influencing factors of expression patterns for CsSOD genes. [ABSTRACT FROM AUTHOR]

Amaranth plants contain large amounts of betalains, including betaxanthins and betacyanins. Amaranthin is a betacyanin, and its molecular structure and associated metabolic pathway differ from those of betanin in beet plants. The chlorophyll, carotenoid, betalain, and flavonoid contents in amaranth leaves were analyzed. The abundance of betalain, betacyanin, and betaxanthin was 2–5-fold higher in the red leaf sectors than in the green leaf sectors. Moreover, a transcriptome database was constructed for the red and green sectors of amaranth leaves harvested from 30-day-old seedlings. 22 unigenes were selected to analyze the expression profiles in the two leaf sectors. The RNA-sequencing data indicated that many unigenes are involved in betalain metabolic pathways. The potential relationships between diverse metabolic pathways and betalain metabolism were analyzed. The validation of the expression of 22 selected unigenes in a qRT-PCR assay revealed the genes that were differentially expressed in the two leaf sectors. Betalains were biosynthesized in specific tissues of the red sectors of amaranth leaves. Almost all of the genes related to betalain metabolism were identified in the transcriptome database, and the expression profiles were different between the red sectors and green sectors in the leaf. Amaranth plants consist of diverse metabolic pathways, and the betalain metabolic pathway is linked to a group of other metabolic pathways. [ABSTRACT FROM AUTHOR]

BACKGROUND: The regulation of functional metabolites under light by structural genes and regulatory genes is understood but the roles of microRNAs in this pathway have rarely been reported and their regulation network is not yet clear. RESULTS: Blue light was most conducive to promoting the synthesis of some functional metabolites in longan embryonic callus (ECs). In this study, we sequenced three small RNA libraries of constructed longan ECs under different light qualities (dark, blue, and white). A total of 29 and 22 miRNAs were differentially expressed in the dark versus blue (DB) and dark versus white (DW) combinations, respectively. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, most of the differentially expressed miRNA target genes were involved in plant hormone signal transduction, mitogen‐activated protein kinase (MAPK) signaling, biosynthesis of unsaturated fatty acids, and so on. Cytoscape analysis of the target genes of miRNAs indicated that miR396b‐5p and miR5139 had the most target genes in DB. Moreover, this study also found that miR171f_3 targeted DELLA, miR390e targeted BRI1, miR396b‐5p targeted EBF1/2 and EIN3; these miRNAs participated in the blue light signaling network through their target genes and regulated the accumulation of longan functional metabolites. CONCLUSIONS: The results of the study revealed that the expressions of phase‐specific miRNAs vary with the change of functional metabolites in longan ECs. This study provides new insights into the molecular mechanisms that allow light to influence plant metabolism. © 2018 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Background: Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas. Result: Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana. Conclusions: In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas. [ABSTRACT FROM AUTHOR]

Background: Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. Results: In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). Conclusion: Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE. [ABSTRACT FROM AUTHOR]

Plant casein kinase II (CKII) plays an essential role in regulating plant growth and development, and responses to biotic and abiotic stresses. Here, we report the identification and characterization of the CKII family genes in Musa spp. cv. ‘Tianbaojiao’ (AAA group) and the wild banana (Musa itinerans). The 13 cDNA sequences of the CKII family members were identified both in ‘Tianbaojiao’ and wild banana, respectively. The differences between CKII α and CKII β members are corroborated through the subcellular localizations, phosphorylation sites and gene structures. The cloning of CKII β-like-2 gDNA sequences in wild banana and ‘Tianbaojiao’ and the analysis of gene structures showed MiCKIIβ-like-2b and MaCKIIβ-like-2 are likely alternatively spliced transcripts, which were derived from the alternative splicing events that involved exon deletion. The qPCR validation showed differential expression CKII family members in response to cold stress and also in all tested tissues (leaf, pseudostem and root) of wild banana. In particular, the normal transcript MiCKIIβ-like-2a was highly expressed in response to cold stress in wild banana; oppositely, the alternatively spliced transcript MiCKIIβ-like-2b was quite lowly expressed. The complex origin and long-term evolution of Musa lineage might explain the alternative splicing events of CKII β-like-2. [ABSTRACT FROM AUTHOR]

BPC 157, a pentadecapeptide with extensive healing effects, has recently been suggested to contribute to angiogenesis. However, the underlying mechanism is not yet clear. The present study aimed to explore the potential therapeutic effect and pro-angiogenic mechanism of BPC 157. As demonstrated by the chick chorioallantoic membrane (CAM) assay and endothelial tube formation assay, BPC 157 could increase the vessel density both in vivo and in vitro, respectively. BPC 157 could also accelerate the recovery of blood flow in the ischemic muscle of the rat hind limb as detected by laser Doppler scanning, indicating the promotion of angiogenesis. Histological analysis of the hind limb muscle confirmed the increased number of vessels and the enhanced vascular expression of vascular endothelial growth factor receptor 2 (VEGFR2) in rat with BPC 157 treatment. In vitro study using human vascular endothelial cells further confirmed the increased mRNA and protein expressions of VEGFR2 but not VEGF-A by BPC 157. In addition, BPC 157 could promote VEGFR2 internalization in vascular endothelial cells which was blocked in the presence of dynasore, an inhibitor of endocytosis. BPC 157 time dependently activated the VEGFR2-Akt-eNOS signaling pathway which could also be suppressed by dynasore. The increase of endothelial tube formation induced by BPC 157 was also inhibited by dynasore. This study demonstrates the pro-angiogenic effects of BPC 157 that is associated with the increased expression, internalization of VEGFR2, and the activation of VEGFR2-Akt-eNOS signaling pathway. BPC 157 promotes angiogenesis in CAM assay and tube formation assay. BPC 157 accelerates the blood flow recovery and vessel number in rats with hind limb ischemia. BPC 157 up-regulates VEGFR2 expression in rats with hind limb ischemia and endothelial cell culture. BPC 157 promotes VEGFR2 internalization in association with VEGFR2-Akt-eNOS activation. Key message: [ABSTRACT FROM AUTHOR]

• Fifty-three LysM gene family members were found in banana (Musa L.) genomes, and there were more members in Musa acuminata than in both Musa balbisiana and Musa itinerans. • Banana LysMs were expressed under low-temperature stresses, high-temperature stresses and root infestation by pathogens. • LysMs were highly conserved in the evolution of bananas, but they also show some differences among the genomes of three banana species. LysM (Lysin motif), in response to pathogenic molecular stresses, is a crucial signal recognition gene. To understand the molecular characteristics of banana LysM gene family members, we used a series of bioinformatics methods. Based on the genomic databases of Musa acuminata , Musa balbisiana and Musa itinerans , a total of 53 genes and 55 proteins were identified, with 21 genes and 23 proteins in the M.acuminata , 16 genes and 16 proteins in each of M.balbisiana and M.itinerans , respectively. According to the conserved structural domains, LysM can be divided into five classes, namely LysM&MltD , LYK , LYP , LysMn , and LysMe. The LysM gene was relatively highly conserved in the evolution of the three genomes of banana, and some differences occurred. Expression analysis revealed that MaLysM4-5 was relatively highly expressed under high-temperature stress, low-temperature stress and pathogen infection; at the same time, about one-third of the members were down-regulated under low-temperature stress and high-temperature stress, while the expression of MaLysM10-1 and MaLysM4-5 were up-regulated. After the banana wilt fungus Foc TR4 infected the banana roots, MaLysM1 was down-regulated and MaLysM11-1 was up-regulated. In conclusion, our study suggests that MaLysMs may be necessary in the response to high- and low-temperature stresses, as well as the banana wilt fungus infestation. Overall, this paper found that LysM genes may be involved in biotic and abiotic stresses in banana, and provided helpful information about LysM 's evolution, expression and properties, which will provide theoretical references for further studies on the functions of LysM genes and resistance breeding in the future. [ABSTRACT FROM AUTHOR]

• Fifty-three LysM gene family members were found in banana (Musa L.) genomes, and there were more members in Musa acuminata than in both Musa balbisiana and Musa itinerans. • Banana LysMs were expressed under low-temperature stresses, high-temperature stresses and root infestation by pathogens. • LysMs were highly conserved in the evolution of bananas, but they also show some differences among the genomes of three banana species. LysM (Lysin motif), in response to pathogenic molecular stresses, is a crucial signal recognition gene. To understand the molecular characteristics of banana LysM gene family members, we used a series of bioinformatics methods. Based on the genomic databases of Musa acuminata , Musa balbisiana and Musa itinerans , a total of 53 genes and 55 proteins were identified, with 21 genes and 23 proteins in the M.acuminata , 16 genes and 16 proteins in each of M.balbisiana and M.itinerans , respectively. According to the conserved structural domains, LysM can be divided into five classes, namely LysM&MltD , LYK , LYP , LysMn , and LysMe. The LysM gene was relatively highly conserved in the evolution of the three genomes of banana, and some differences occurred. Expression analysis revealed that MaLysM4-5 was relatively highly expressed under high-temperature stress, low-temperature stress and pathogen infection; at the same time, about one-third of the members were down-regulated under low-temperature stress and high-temperature stress, while the expression of MaLysM10-1 and MaLysM4-5 were up-regulated. After the banana wilt fungus Foc TR4 infected the banana roots, MaLysM1 was down-regulated and MaLysM11-1 was up-regulated. In conclusion, our study suggests that MaLysMs may be necessary in the response to high- and low-temperature stresses, as well as the banana wilt fungus infestation. Overall, this paper found that LysM genes may be involved in biotic and abiotic stresses in banana, and provided helpful information about LysM 's evolution, expression and properties, which will provide theoretical references for further studies on the functions of LysM genes and resistance breeding in the future. [ABSTRACT FROM AUTHOR]

• 327 CYP were found from the longan genome, and they exhibited a strong expansion with mainly tandem duplication (TD) events. • DlCYPs expressed higher in globular embryos (GE) compared with those in incomplete compact pro-embryogenic (ICpEC) stage and the embryogenic callus (EC) stage in longan. • DlCYPs had more AS events in ICpEC compared to those in EC and GE. Their transcript isoforms showed expression patterns during early SE in longan. Cytochrome P450 (CYP), a multi-gene superfamily, is involved in a broad range of physiological processes, including hormone responses and secondary metabolism throughout the plant life cycle. Longan (Dimocarpus longan), a subtropical and tropical evergreen fruit tree, its embryonic development is closely related to the yield and quality of fruits. And a large number of secondary metabolites, such as flavonoids and carotenoids, are also produced during the longan somatic embryogenesis (SE). It is important, therefore, to study potential functions of CYPs in longan. However, the knowledge of longan CYP s is still very limited. Here, a total of 327 DlCYPs were identified using the genome-search method, which could be classified into nine clans. The expansion of the DlCYP family was mainly caused by tandem duplication (TD) events. Promoter cis -acting elements analysis elucidated that DlCYPs played important roles in hormonal responses. A total of 246 DlCYPs exhibited six different expression patterns during the early SE based on longan transcriptomic data. Eight DlCYPs underwent alternative splicing (AS) events, and they might produce one to six isoforms. And the AS transcript of DlCYP97C1 might act as an alternative to the full-length transcript in ICpEC and GE stages. Finally, protein–protein interaction (PPI) networks and miRNA target prediction elucidated that DlCYPs might be involved in the phenylpropanoid metabolic pathway and primarily regulated and targeted by miR413. In summary, our results provided valuable inventory for understanding the classification and biological functions of DlCYPs and provided insight into further functional verification of DlCYPs during the longan early SE. [ABSTRACT FROM AUTHOR]

• A total of 69 core cell cycle genes (CCCs) family members were identified in the longan genome. • Either silencing of CKS or CYCD3;2 increased the expression of RB-E2F pathway-related genes. • Silencing of CYCD3;2 might lead to apoptosis in longan embryogenic callus. • ABA, 2,4-D and PEG4000 could increase the expression of all selected longan CCCs , while NaCl did not. Core cell cycle genes (CCCs) are essential regulators of cell cycle operation. In this study, a total of 69 CCCs family members, including 37 CYCs , 20 CDKs , five E2F/DPs , three KRPs , two RBs , one CKS and one Wee1 , were identified from the longan genome. Phylogenetic and motifs analysis showed the evolutionary conservation of CCCs. Transcriptome dataset showed that CCCs had various expression patterns during longan early somatic embryogenesis (SE). Either CKS or CYCD3;2 silencing increased the expression of RB-E2F pathway genes, and the silencing of CYCD3;2 might induce the process of apoptosis in longan embryogenic callus (EC) cells. In addition, The qRT-PCR results showed that the expression levels of CDKG2 , CYCD3;2 , CYCT1;2 , CKS and KRP1 were elevated by ABA, 2,4-D and PEG4000 treatments, while CDKG2 and CYCT1;2 were inhibited by NaCl treatment. In conclusion, our study provided valuable information for understanding the characterization and biological functions of longan CCCs. [ABSTRACT FROM AUTHOR]

Background: Obstructive sleep apnea (OSA) is known to be a risk factor of coronary artery disease. The chemotaxis and adhesion of monocytes to the endothelium in the early atherosclerosis is important. This study aimed to investigate the effect of intermittent hypoxia, the hallmark of OSA, on the chemotaxis and adhesion of monocytes. Methods: Peripheral blood was sampled from 54 adults enrolled for suspected OSA. RNA was prepared from the isolated monocytes for the analysis of C-C chemokine receptor 2 (CCR2). The effect of intermittent hypoxia on the regulation and function of CCR2 was investigated on THP-1 monocytic cells and monocytes. The mRNA and protein expression levels were investigated by RT/real-time PCR and western blot analysis, respectively. Transwell filter migration assay and cell adhesion assay were performed to study the chemotaxis and adhesion of monocytes. Results: Monocytic CCR2 gene expression was found to be increased in severe OSA patients and higher levels were detected after sleep. Intermittent hypoxia increased the CCR2 expression in THP-1 monocytic cells even in the presence of TNF-α and CRP. Intermittent hypoxia also promoted the MCP-1-mediated chemotaxis and adhesion of monocytes to endothelial cells. Furthermore, inhibitor for p42/44 MAPK or p38 MAPK suppressed the activation of monocytic CCR2 expression by intermittent hypoxia. Conclusions: This is the first study to demonstrate the increase of CCR2 gene expression in monocytes of severe OSA patients. Monocytic CCR2 gene expression can be induced under intermittent hypoxia which contributes to the chemotaxis and adhesion of monocytes. [ABSTRACT FROM AUTHOR]

Polyamines (PAs) play an important regulatory role in many basic cellular processes and physiological and biochemical processes. However, there are few studies on the identification of PA biosynthesis and metabolism family members and the role of PAs in the transition of plant embryogenic calli (EC) into globular embryos (GE), especially in perennial woody plants. We identified 20 genes involved in PA biosynthesis and metabolism from the third-generation genome of longan (Dimocarpus longan Lour.). There were no significant differences between longan and other species regarding the number of members, and they had high similarity with Citrus sinensis. Light, plant hormones and a variety of stress cis-acting elements were found in these family members. The biosynthesis and metabolism of PAs in longan were mainly completed by DlADC2, DlSAMDC2, DlSAMDC3, DlSPDS1A, DlSPMS, DlCuAOB, DlCuAO3A, DlPAO2 and DlPAO4B. In addition, 0.01 mmol∙L−1 1-aminocyclopropane-1-carboxylic acid (ACC), putrescine (Put) and spermine (Spm), could promote the transformation of EC into GE, and Spm treatment had the best effect, while 0.01 mmol∙L−1 D-arginine (D-arg) treatment inhibited the process. The period between the 9th and 11th days was key for the transformation of EC into GE in longan. There were higher levels of gibberellin (GA), salicylic acid (SA) and abscisic acid (ABA) and lower levels of indole-3-acetic acid (IAA), ethylene and hydrogen peroxide (H2O2) in this key period. The expression levels in this period of DlADC2, DlODC, DlSPDS1A, DlCuAOB and DlPAO4B were upregulated, while those of DlSAMDC2 and DlSPMS were downregulated. These results showed that the exogenous ACC, D-arg and PAs could regulate the transformation of EC into GE in longan by changing the content of endogenous hormones and the expression levels of PA biosynthesis and metabolism genes. This study provided a foundation for further determining the physicochemical properties and molecular evolution characteristics of the PA biosynthesis and metabolism gene families, and explored the mechanism of PAs and ethylene for regulating the transformation of plant EC into GE. [ABSTRACT FROM AUTHOR]

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes' change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary. [ABSTRACT FROM AUTHOR]

• 16 volatiles were identified as key odorants in postharvest jasmine flower (PJF). • A reference transcriptome of jasmine with 366,081 full-length isoforms was obtained. • Aroma formation of PJF depend on both de novo biosynthesis and glycoside hydrolysis. • HSPs may guarantee the normal fragrance release of PJF during flowering. Jasmine [ Jasminum sambac (L.) Aiton] flowers usually bloom and release their fragrance at night. However, the underlying regulatory mechanisms of aroma formation during flowering in postharvest jasmine are still poorly understood. Here, we profiled the volatile metabolome, multi-flux full-length sequencing, and transcriptome analysis to investigate volatile biosynthesis and global transcriptomic changes in postharvest flowering jasmine. A total of 102 volatiles were identified. Of these, 16 volatiles were considered key odorants of jasmine flowers. Linalool, α-farnesene, d -nerolidol, geraniol, α-cadinol, benyzl alcohol, benzaldehyde, benzyl acetate, benzyl benzoate, 3-hexen-1-ol benzoate, and (Z)-3-hexen-1-ol acetate play decisive roles in the typical jasmine fragrance, while benzeneacetaldehyde, benzoic acid, methyl anthranilate, methyl 2-(methylamino) benzoate, and (E)-2-hexenal modify the aroma of jasmine. Meanwhile, we built the first reference full-length transcriptome of postharvest jasmine flowers, which had 366,081 non-redundant isoforms. Among them, 280,326 (76.57 %) were annotated with at least one hit in the NT, NR, Swissprot, KEGG, KOG, Pfam, and GO databases. Combined with second-generation transcriptome analysis, we identified 52 differentially expressed transcripts (DETs) involved in terpenoid metabolic pathways and 28 DETs involved in phenylpropanoid/benzenoid metabolic pathway, and 31 β-glucosidase transcripts may be related to aroma formation of postharvest jasmine during flowering. In addition, the expression of 42 heat shock protein (HSP) transcripts was positively correlated with the content of 11 key odorants, as revealed by weighted gene co-expression network analysis (WGCNA). The present results advance the knowledge of the regulatory mechanism of aroma formation in postharvest jasmine during flowering and provide an abundant genetic resource for further studies on gene discovery in jasmine. [ABSTRACT FROM AUTHOR]

• A total of 18 CsZF-HDs were confirmed from tea plant genome. • CsZF-HD genes have spatio-temporal expression patterns in various tissues. • All the CsZF-HDs we detected differentially expressed under diverse treatments. • Some CsZF-HDs may be regulated by miRNAs under abiotic stresses and hormones stimuli. • The predicted eTM of csn-miR2673a may indirectly modulate CsZF-HD under SA treatment. In plants, zinc finger motif-associated homeodomain (ZF-HD) transcription factors (TFs) play indispensable roles in developmental processes and stress responses. However, the specific functions of members of the ZF-HD gene family in tea plants (Camellia sinensis) are poorly understood. We identified 18 CsZF-HD genes in tea at the whole-genome scale. These genes were phylogenetically classified into two major subfamilies: ZF-HD and MIF. Gene structural analyses showed that 13 of the 18 members have no introns. Analysis of transcriptome data revealed different spatio-temporal expression patterns of CsZF-HD genes in various tissues. On the basis of the cis -acting elements analysis, we detected the expression patterns of CsZF-HD genes under various abiotic and phytohormone treatments (drought, cold, exogenous SA, MeJA, ABA, and GA 3). Quantitative real time polymerase chain reaction (qRT-PCR) analyses confirmed the differential expression of CsZF-HDs under diverse stress and phytohormone treatments. The miRNAs that regulate CsZF-HD genes and their endogenous target mimics (eTMs) were predicted and investigated. The expression patterns of CsZF-HD10 and csn-miR172b-5p-3 were completely opposite under salicylic acid treatment. We also detected negative regulatory relationships between csn-miR2673a and CsZF-HD15 under salicylic acid treatment, between csn-miR399a-5 and CsZF-HD9 under abscisic acid treatment, and between csn-miR2673a and CsZF-HD3 under methyl jasmonate treatment during most sequential stages. The results indicate that the predicted eTM (LTCONS-00,013,981) of csn-miR2673a may indirectly modulate CsZF-HD expression by baiting relevant miRNAs under salicylic acid treatment. Together, these results lay the foundation for further research on the biological functions of CsZF-HDs. [ABSTRACT FROM AUTHOR]