Genome-wide identification and expression pattern analysis of the GRF transcription factor family in Astragalus mongholicus.

BACKGROUND: Astragalus membranaceus is a plant of the Astragalus genus, which is used as a traditional Chinese herbal medicine with extremely high medicinal and edible value. Astragalus mongholicus, as one of the representative medicinal materials with the same origin of medicine and food, has a rising market demand for its raw materials, but the quality is different in different production areas. Growth-regulating factors (GRF) are transcription factors unique to plants that play important roles in plant growth and development. Up to now, there is no report about GRF in A. mongholicus. METHODS AND RESULTS: This study conducted a genome-wide analysis of the AmGRF gene family, identifying a total of nine AmGRF genes that were classified into subfamily V based on phylogenetic relationships. In the promoter region of the AmGRF gene, we successfully predicted cis-elements that respond to abiotic stress, growth, development, and hormone production in plants. Based on transcriptomic data and real-time quantitative polymerase chain reaction (qPCR) validation, the results showed that AmGRFs were expressed in the roots, stems, and leaves, with overall higher expression in leaves, higher expression of AmGRF1 and AmGRF8 in roots, and high expression levels of AmGRF1 and AmGRF9 in stems. CONCLUSIONS: The results of this study provide a theoretical basis for the further exploration of the functions of AmGRFs in plant growth and development.

Cloning, Expression Characteristics of Farnesyl Pyrophosphate Synthase Gene from Platycodon grandiflorus and Functional Identification in Triterpenoid Synthesis.

Platycodon grandiflorus is a medicinal plant whose main component is platycodins, which have a variety of pharmacological effects and nutritional values. The farnesyl pyrophosphate synthase (FPS) is a key enzyme in the isoprenoid biosynthesis pathway, which catalyzes the synthesis of farnesyl diphosphate (FPP). In this study, we cloned the FPS gene from P. grandiflorus (PgFPS) with an ORF of 1260 bp, encoding 419 amino acids with a deduced molecular weight and theoretical pI of 46,200.98 Da and 6.52, respectively. The squalene content of overexpressed PgFPS in tobacco leaves and yeast cells extract was 1.88-fold and 1.21-fold higher than that of the control group, respectively, and the total saponin content was also increased by 1.15 times in yeast cells extract, which verified the biological function of PgFPS in terpenoid synthesis. After 48 h of MeJA treatment and 6 h of ethephon treatment, the expression of the PgFPS gene in roots and stems reached its peak, showing a 3.125-fold and 3.236-fold increase compared to the untreated group, respectively. Interestingly, the expression of the PgFPS gene in leaves showed a decreasing trend after exogenous elicitors treatment. The discovery of this enzyme will provide a novel perspective for enhancing the efficient synthesis of platycodins.

Genome-Wide Analysis of the HSF Gene Family Reveals Its Role in Astragalus mongholicus under Different Light Conditions.

Astragalus mongholicus is a traditional Chinese medicine (TCM) with important medicinal value and is widely used worldwide. Heat shock (HSF) transcription factors are among the most important transcription factors in plants and are involved in the transcriptional regulation of various stress responses, including drought, salinity, oxidation, osmotic stress, and high light, thereby regulating growth and developmental processes. However, the HFS gene family has not yet been identified in A. mongholicus, and little is known regarding the role of HSF genes in A. mongholicus. This study is based on whole genome analysis of A. mongholicus, identifying a total of 22 AmHSF genes and analyzing their physicochemical properties. Divided into three subgroups based on phylogenetic and gene structural characteristics, including subgroup A (12), subgroup B (9), and subgroup C (1), they are randomly distributed in 8 out of 9 chromosomes of A. mongholicus. In addition, transcriptome data and quantitative real time polymerase chain reaction (qRT-PCR) analyses revealed that AmHSF was differentially transcribed in different tissues, suggesting that AmHSF gene functions may differ. Red and blue light treatment significantly affected the expression of 20 HSF genes in soilless cultivation of A. mongholicus seedlings. AmHSF3, AmHSF3, AmHSF11, AmHSF12, and AmHSF14 were upregulated after red light and blue light treatment, and these genes all had light-corresponding cis-elements, suggesting that AmHSF genes play an important role in the light response of A. mongholicus. Although the responses of soilless-cultivated A. mongholicus seedlings to red and blue light may not represent the mature stage, our results provide fundamental research for future elucidation of the regulatory mechanisms of HSF in the growth and development of A. mongholicus and its response to different light conditions.

Identification of the lateral organ boundary domain gene family and its preservation by exogenous salicylic acid in Cerasus humilis.

The gene family known as the Lateral Organ Boundary Domain (LBD) is responsible for producing transcription factors unique to plants, which play a crucial role in controlling diverse biological activities, including their growth and development. This research focused on examining Cerasus humilis'ChLBD gene, owing to its significant ecological, economic, and nutritional benefits. Examining the ChLBD gene family's member count, physicochemical characteristics, phylogenetic evolution, gene configuration, and motif revealed 41 ChLBD gene family members spread across 8 chromosomes, with ChLBD gene's full-length coding sequences (CDSs) ranging from 327 to 1737 base pairs, and the protein sequence's length spanning 109 (ChLBD30)-579 (ChLBD35) amino acids. The molecular weights vary from 12.068 (ChLBD30) to 62.748 (ChLBD35) kDa, and the isoelectric points span from 4.74 (ChLBD20) to 9.19 (ChLBD3). Categorizing them into two evolutionary subfamilies: class I with 5 branches, class II with 2, the majority of genes with a single intron, and most members of the same subclade sharing comparable motif structures. The results of collinearity analysis showed that there were 3 pairs of tandem repeat genes and 12 pairs of fragment repeat genes in the Cerasus humilis genome, and in the interspecific collinearity analysis, the number of collinear gene pairs with apples belonging to the same family of Rosaceae was the highest. Examination of cis-acting elements revealed that methyl jasmonate response elements stood out as the most abundant, extensively dispersed in the promoter areas of class 1 and class 2 ChLBD. Genetic transcript analysis revealed that during Cerasus humilis' growth and maturation, ChLBD developed varied control mechanisms, with ChLBD27 and ChLBD40 potentially playing a role in managing color alterations in fruit ripening. In addition, the quality of calcium fruit will be affected by the environment during transportation and storage, and it is particularly important to use appropriate means to preserve the fruit. The research used salicylic acid-treated Cerasus humilis as the research object and employed qRT-PCR to examine the expression of six ChLBD genes throughout storage. Variations in the expression of the ChLBD gene were observed when exposed to salicylic acid, indicating that salicylic acid could influence ChLBD gene expression during the storage of fruits. This study's findings lay the groundwork for additional research into the biological role of the LBD gene in Cerasus humilis. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01438-5.

CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation.

Oxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers and bilayers. These studies investigate how the tail length and polar functional groups of OxPLs impact membrane properties, how oxidized membranes can be stabilized, and how membrane integrity is generally affected by oxidized lipids. In addition, for oxPL-containing membrane modeling and simulation, CHARMM-GUI Membrane Builder has been extended to support a variety of oxPLs, accelerating the simulation system building process for these biologically relevant lipid bilayers.

Identification and expression analysis of TPS family gene in Cannabis sativa L.

Terpene synthases (TPSs) regulate plant growth, development, and stress response. TPS genes have been identified in Arabidopsis thaliana and Zea mays. Cannabis sativa TPS genes were identified and analyzed using bioinformatics. Genomic data were downloaded from Plant Transcription Factor Database and National Center for Biotechnology Information database, and TPS genes were predicted, analyzed, and visualized using ExPASy, PlantCare, and other online websites along with TBtools, MEGA software, and other software. To verify its role, quantitative real-time polymerase chain reaction (qRT-PCR) tests were conducted. The Cannabis sativa TPS family comprises 41 elements distributed over 8 chromosomes and a single scaffold segment. The isoelectric point varied between 4.96 and 7.03, while the molecular weight spanned from 20705.90 to 102324.64 Da. The majority of genes were found in the cytoplasm and chloroplasts, with the remainder situated in the peroxisome, nucleus, plasma membrane, and mitochondria. Several cis-acting components associated with stress response were present in the gene's upstream promoter region. Data from RNA sequencing and qRT-PCR revealed specific expression of TPS genes in all five organs of female Cannabis sativa plants. Collinearity analysis showed 4 homologous gene pairs between the Cannabis sativa and Arabidopsis thaliana, with many pairs of homologous genes in other species, which was consistent with the dicotyledons evolutionary relationship. Furthermore, some genes may participate in Cannabis sativa growth and development and play a role in secondary metabolite synthesis. Therefore, bioinformatics analysis of the Cannabis sativa TPS gene family provides a theoretical basis for future research on the volatile terpene compounds of Cannabis sativa.

Safety and efficacy of apatinib in combination with chemotherapy with or without immunotherapy versus chemotherapy alone as first-line treatment for advanced gastric cancer.

The specific first-line regimen for advanced gastric cancer (GC) is still controversial. The benefit of apatinib for first-line treatment of advanced GC remains unknown and needs to be further explored. Eighty-two patients with advanced GC treated in our institution from October 2017 to March 2023 were retrospectively reviewed. All individuals had her-2 negative GC and had received at least two cycles of first-line treatment, including 44 patients in the combination treatment group (apatinib in combination with chemotherapy with or without immunotherapy) and 38 patients in the simple chemotherapy group. We evaluated the efficacy and safety of apatinib in combination with chemotherapy with or without immunotherapy in the first-line treatment of advanced GC by comparing the efficacy, progression-free survival (PFS), and adverse events in two groups of patients. The median PFS of the simple chemotherapy group was 9.25 months (95% confidence interval (CI), 6.1-11.2 months), and that of the combination treatment group was 10.9 months (95% CI, 7.9-15.8 months), which was 1.65 months longer than the simple chemotherapy group. Statistically significant differences are shown (P = 0.022). The objective response rate (ORR) of the combination treatment group was 65.9%, and 36.8% in the simple chemotherapy group. Statistically significant differences are shown (P = 0.014). No serious (Grade IV) adverse events occurred in either group. Our study indicates that apatinib in combination with chemotherapy with or without immunotherapy as first-line treatment for advanced GC exhibits good anti-tumor activity and is well tolerated by patients.

Inhibition of cannabinoid degradation enhances hippocampal contextual fear memory and exhibits anxiolytic effects.

Recent studies have demonstrated the pivotal involvement of endocannabinoids in regulating learning and memory, but the conclusions obtained from different paradigms or contexts are somewhat controversial, and the underlying mechanisms remain largely elusive. Here, we show that JZL195, a dual inhibitor of fatty acid amide hydrolase and monoacylglycerol lipase, can enhance the performance of mice in a contextual fear conditioning task and increase the time spent in open arms in the elevated zero maze (EZM). Although the effect of JZL195 on fear memory could not be inhibited by antagonists of cannabinoid receptors, the effect on the EZM seems to be mediated by CB1R. Simultaneously, hippocampal neurons are hyperactive, and theta oscillation power is significantly increased during the critical period of memory consolidation upon treatment with JZL195. These results suggest the feasibility of targeting the endocannabinoid system for the treatment of various mental disorders.

Antiviral drug recognition and elevator-type transport motions of CNT3.

Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic distribution and cellular entry are human nucleoside transporters. Here, we establish that the human concentrative nucleoside transporter 3 (CNT3) interacts with antiviral drugs used in the treatment of coronavirus infections. We report high-resolution single-particle cryo-electron microscopy structures of bovine CNT3 complexed with antiviral nucleosides N4-hydroxycytidine, PSI-6206, GS-441524 and ribavirin, all in inward-facing states. Notably, we found that the orally bioavailable antiviral molnupiravir arrests CNT3 in four distinct conformations, allowing us to capture cryo-electron microscopy structures of drug-loaded outward-facing and drug-loaded intermediate states. Our studies uncover the conformational trajectory of CNT3 during membrane transport of a nucleoside analog antiviral drug, yield new insights into the role of interactions between the transport and the scaffold domains in elevator-like domain movements during drug translocation, and provide insights into the design of nucleoside analog antiviral prodrugs with improved oral bioavailability.

The complete chloroplast genome sequence of Jacobaea cannabifolia.

Jacobaea cannabifolia is a widely used medicinal plant. The total length of the chloroplast genome was 151,390 bp, and it comprised a large single-copy (LSC, 83,432 bp) region, a small single-copy (SSC, 18,304 bp) region, and a pair of inverted repeats (IRs, 49,654 bp). A total of 130 coding genes were annotated, including 88 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. A phylogenetic tree was showed that J. cannabifolia and other species of the same genus clustered together.

Interactive effects of climate-atmospheric cycling on aquatic communities and ecosystem shifts in mountain lakes of southeastern Tibetan Plateau.

Recent climate warming and atmospheric reactive nitrogen (Nr) deposition are affecting a broad spectrum of physical, ecological and human systems that may be irreversible on a century time scale and have the potential to cause regime shifts in ecological systems. These changes may alter the limnological conditions with important but still unclear effects on lake ecosystems. We present changes in cladoceran with comparisons to diatom assemblages over the past ~200 years from high-resolution, well-dated sediment cores retrieved from six high mountain lakes in the southeastern (SE) margin of the Tibetan Plateau. Our findings suggest that warming and the exponential increase of atmospheric Nr deposition are the major drivers of ecological regime changes. Shifts in cladoceran and diatom communities in high alpine lakes began over a century ago and intensified since 1950 CE, indicating a regional-scale response to anthropogenic climate warming. Zooplankton in the forest lakes showed asynchronous trajectories, with increased Nr deposition as a significant explanatory factor. Forest lakes with higher dissolved organic carbon (DOC) concentrations partially buffered the impacts of Nr deposition with little structural change, while lakes with low DOC display symptoms of resilience loss related to Nr deposition. Biological community compositional turnover in subalpine lakes has shown marked shifts, equivalent to those of low-elevation lakes strongly affected by direct human impacts. This suggests that local effects override climatic forcing and that lake basin features modified by anthropogenic activity act as basin-specific filters of common forcing. Our results indicate that snow and glacial meltwaters along with nutrient enrichment related to climate warming and atmospheric Nr deposition, represent major threats for lake ecosystems, even in remote areas. We reveal that climate and atmospheric contaminants will further impact ecological conditions and alter aquatic food webs in higher altitude biomes if climate and anthropogenic forcing continue.

Spatio-temporal variation and environmental drivers of chlorophyll a concentration and diatom community in four small urban lakes of Kunming, China.

Chlorophyll a (Chla) and diatom community structure are two indicators of lake water quality. In this study, we investigated the environmental parameters, chlorophyll a, and diatom community of four small urban lakes in Kunming (Beitan, Beihu, Nanhu and Longtan lakes in the campus of Yunnan Normal University) between March 2017 and December 2019. The results showed that the concentrations of total nitrogen (TN), total phosphorus (TP), and Chla in the four lakes showed significant seasonal fluctuation. The Chla concentration in Nanhu Lake, which had the highest nutrient level among the four lakes, was significantly higher than that in the other three lakes and largely affected by TN. In comparison, water temperature significantly contributed to the increases in Chla concentration in the other three lakes. Water temperature and TN were significantly correlated with Chla across the four lakes. Diatom assemblages in Beitan, Nanhu, and Longtan lakes were dominated by planktonic diatoms, and benthic diatoms were dominant in the shallowest lake Beihu, suggesting that water depth significantly affected the proportion of planktonic diatoms and dominant taxa. Water depth, TN, TP, transparency, and water temperature affected the spatio-temporal changes of diatom community structure, with water temperature as the major factor in causing the seasonal variation in diatom community, and TN and TP as the major drivers for community variation among lakes within the same season.

A review of the botany, phytochemistry, traditional uses, pharmacology, toxicology, and quality control of the Astragalus memeranaceus.

Astragali Radix (Huangqi) is mainly distributed in the Northern Hemisphere, South America, and Africa and rarely in North America and Oceania. It has long been used as an ethnomedicine in the Russian Federation, Mongolia, Korea, Kazakhstan, and China. It was first recorded in the Shennong Ben Cao Jing and includes the effects of reinforcing healthy qi, dispelling pathogenic factors, promoting diuresis, reducing swelling, activating blood circulation, and dredging collaterals. This review systematically summarizes the botanical characteristics, phytochemistry, traditional uses, pharmacology, and toxicology of Astragalus to explore the potential of Huangqi and expand its applications. Data were obtained from databases such as PubMed, CNKI, Wan Fang Data, Baidu Scholar, and Google Scholar. The collected material also includes classic works of Chinese herbal medicine, Chinese Pharmacopoeia, Chinese Medicine Dictionary, and PhD and Master's theses. The pharmacological effects of the isoflavone fraction in Huangqi have been studied extensively; The pharmacological effects of Huangqi isoflavone are mainly reflected in its anti-inflammatory, anti-tumor, anti-oxidant, anti-allergic, and anti-diabetic properties and its ability to treat several related diseases. Additionally, the medicinal uses, chemical composition, pharmacological activity, toxicology, and quality control of Huangqi require further elucidation. Here, we provide a comprehensive review of the botany, phytochemistry, traditional uses, pharmacology, toxicology, and quality control of Astragalus to assist future innovative research and to identify and develop new drugs involving Huangqi.

Sediment geochemical records of water quality deterioration in lake Jiren, a remote alpine lake on the southeastern margin of the Tibetan Plateau.

Limited human activities in catchments make remote alpine lakes valuable sites for studying the evolution of lake environments in response to climate change and atmospheric deposition; however, this issue remains rarely studied owing to the scarcity of monitoring data. In this study, water quality evolution in Lake Jiren, a remote alpine lake on the southeastern margin of the Tibetan Plateau, over the past two centuries was reconstructed through geochemical analyses of aliphatic hydrocarbons, major and trace elements, and organic matter (OM) pyrolysis products in a dated sediment core, and the associated drivers were identified by temporally comparing the geochemical results with document records. All geochemical data demonstrated that the lake water remained relatively pure until 1947, after which the n-alkane and αß-hopane proxies indicated eutrophication and petroleum contamination. The OM pyrolysis proxy hydrocarbon index indicated more eutrophic conditions after 1957. Concurrently, hypolimnetic deoxygenation increased, as indicated by redox-sensitive proxies, such as the enrichment factors (EFs) of molybdenum (Mo). These proxies recorded further intensification of deoxygenation after 1976. The EFs for other trace elements indicated cadmium contamination after 1967. The greater anthropogenic emissions of reactive nitrogen, petroleum products, and heavy metals in East and South Asia since approximately 1950 and the subsequent atmospheric transport of these materials to the lake might be the basic driver of water quality deterioration. Eutrophication induced by nitrogen deposition was responsible for increased hypolimnetic deoxygenation by enhancing phytoplankton productivity and OM input. The further intensification of deoxygenation was attributed to climate warming since the 1970s, as prolonged water column stratification under this condition decreased oxygen input from the epilimnion to the lake bottom. These findings may be beneficial for understanding the natural and anthropogenic effects on the water quality of alpine lakes and help in the environmental management of Lake Jiren and other alpine lakes.

Vogesella aquatica sp. nov. and Vogesella margarita sp. nov., isolated from rivers in Southwest China.

Eight Gram-stain-negative, aerobic, short rod-shaped and motile strains (DC21WT, LYT5WT, LYT10W, LYT16W, LYT22W, LYT23W, LYT24W and SH7W) were isolated from rivers in Southwest China. Comparisons based on the 16S rRNA gene sequences showed that strain DC21WT shared the highest 16S rRNA gene sequence similarity (99.6 %) with Vogesella mureinivorans 389T, strain LYT5WT shared 99.2 % with Vogesella fluminis Npb-07T, and the other isolated strains took Vogesella indigofera DSM 3303T as their most similar strain, respectively. The phylogenetic trees reconstructed based on the 16S rRNA gene sequences also supported that strains V. mureinivorans 389T, V. fluminis Npb-07T and V. indigofera DSM 3303T were the closest neighbours of the isolated strains. The phylogenomic tree showed similar phylogenetic relationships among these strains. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains DC21WT, LYT5WT and other related strains were less than 93.7 and 53.7 %, respectively. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains LYT10W, LYT16W, LYT22W, LYT23W, LYT24W, SH7W and V. indigofera DSM 3303T ranged from 94.8 to 97.2 % and from 59.8 to 74.9 %, respectively. Although these values were located in the transition region of species demarcation, their similar phenotypic, biochemical and genotypic characteristics supported that these six strains should be assigned to the species V. indigofera. Comparative genomic analyses showed that only V. indigofera DSM 3303T harboured 19 genes encoding the Type VI secretion system. Combining above descriptions, strains DC21WT and LYT5WT should represent two independent novel species of the genus Vogesella, for which the names Vogesella aquatica sp. nov. (type strain DC21WT=GDMCC 1.3220T=KCTC 92556T) and Vogesella margarita sp. nov. (type strains LYT5WT=GDMCC 1.3213T=KCTC 92549T) are proposed, respectively.

The complete chloroplast genome of Aegle marmelos and its phylogenetic analysis.

Aegle marmelos (L.) Correa 1800, a plant belonging to the Rutaceae family, is extensively used in Tibetan medicine. We employed Illumina HiSeq reads to assemble the complete chloroplast (cp) genome of A. marmelos, which spans 144,538 bp. The genome comprises 114 genes, including 75 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. It is characterized by four regions: The large single-copy (LSC) region (74,253 bp), the inverted repeat A (IRa) region (26,015 bp), the small single-copy (SSC) region (18,255 bp), and the inverted repeat B (IRb) region (26,015 bp). Phylogenomic analysis demonstrated a close relationship between A. marmelos and Citrus. The assembly of The cp genome in this study serves as a foundation for conservation efforts and phylogenetic investigations of A. marmelos, paving the way for future experimentation.

Asticcacaulis aquaticus sp. nov., Asticcacaulis currens sp. nov. and Asticcacaulis machinosus sp. nov., isolated from streams in PR China.

Three Gram-stain-negative, aerobic, rod-shaped, stalked and motile strains with a polar flagellum (BYS171WT, DXS10WT and LKC15WT) were isolated from streams in PR China. Comparisons based on 16S rRNA gene sequences showed that strains BYS171WT and DXS10WT had the highest 16S rRNA gene sequence similarities (98.1 and 98.6 %, respectively) to Asticcacaulis excentricus CB 48T, and strain LKC15WT showed 99.6 % similarity to Asticcacaulis endophyticus ZFGT-14T. These three strains showed 16S rRNA gene sequence similarities of less than 96.9 % to other species of the genus Asticcacaulis. A phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains BYS171WT and DXS10WT took A. excentricus CB 48T as their closest neighbour, and strain LKC15WT formed a tight cluster with A. endophyticus ZFGT-14T. The phylogenomic tree also showed that these three strains belong to the genus Asticcacaulis and form a distinct clade with the species of the genus Asticcacaulis. The major cellular fatty acids of these three strains were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and 11-methyl C18 : 1 ω7c. Their polar lipids mainly consisted of phosphatidylglycerol, unidentified glycolipids and nitrogen-containing phosphoglycolipids. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains BYS171WT, DXS10WT, LKC15WT and other related strains were less than 87.2 % and 34.0 %, respectively, indicating that these three strains should represent three independent novel species of the genus Asticcacaulis, for which the names Asticcacaulis aquaticus sp. nov. (type strain BYS171WT=GDMCC 1.3226T=KCTC 92612T), Asticcacaulis currens sp. nov. (type strain DXS10WT=GDMCC 1.3224T=KCTC 92543T) and Asticcacaulis machinosus sp. nov. (type strain LKC15WT=GDMCC 1.3225T=KCTC 92544T) are proposed.

Genome-wide identification of the NAC transcription factors family and regulation of metabolites under salt stress in Isatis indigotica.

NAC (NAM, ATAF1/2 and CUC2) transcription factors (TFs) are a class of TFs families unique to plants, which not only play an important role in the growth and developmental stages of plants but also function in response to stress and regulation of secondary metabolite biosynthesis. However, there are few studies on NAC genes in the medicinal plant Isatis indigotica. In this study, 96 IiNAC genes were identified based on the whole-genome data of I. indigotica, distributed in seven chromosomes and three contigs. IiNAC genes were structurally conserved and divided into 15 subgroups. Cis-elements were identified in the promoter region of the IiNAC gene in response to plant growth and development, abiotic stresses and hormones. In addition, transcriptome and metabolome data of I. indigotica leaves under salt stress were analyzed to construct a network of IiNAC gene co-expression and metabolite association. Ten differentially expressed IiNAC genes were co-expressed with 109 TFs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that most of these genes were associated with plant growth and development and abiotic stress responses. Eleven IiNAC genes were positively associated with 72 metabolites. Eleven IiNAC genes were positively or negatively associated with 47 metabolites through 37 TFs. Commonly associated secondary metabolites include two terpenoids, abscisic acid and bilobalide, two flavonoids, dihydrokaempferol and syringaldehyde, a coumarin, 7-methoxycoumarin, an alkaloid, lupinine, and quinone dihydrotanshinone I. This study provides important data to support the identification of the NAC gene family in I. indigotica and the regulatory functions of IiNAC genes in metabolites under salt stress.

Sunlight irradiation promotes both the chemodiversity of terrestrial DOM and the biodiversity of bacterial community in a subalpine lake.

Alpine lake habitats are evolving into subalpine lakes under the scenario of climate change, where the vegetation are promoted due to increasing temperature and precipitation. The abundant terrestrial dissolved organic matter (TDOM) leached from watershed soil into subalpine lakes would undergo strong photochemical reaction due to the high altitude, with the potential to alter DOM composition and affect the bacterial communities. To reveal the transformation of TDOM by both photochemical and microbial processes in a typical subalpine lake, Lake Tiancai (located 200 m below the tree line) was chosen. TDOM was extracted from the surrounding soil of Lake Tiancai and then subjected to the photo/micro-processing for 107 days. The transformation of TDOM was analyzed by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and fluorescence spectroscopy, and the shift of bacterial communities was analyzed using 16s rRNA gene sequencing technology. Dissolved organic carbon and light-absorbing components (a350) decay accounted for approximately 40% and 80% of the original, respectively, in the sunlight process, but both less than 20% in the microbial process for 107 days. The photochemical process promoted the chemodiversity as there were ∼7000 molecules after sunlight irradiation, compared to ∼3000 molecules in the original TDOM. Light promoted the production of highly unsaturated molecules and aliphatics, which were significantly associated with Bacteroidota, suggesting that light may influence bacterial communities by regulating the DOM molecules. Carboxylic-rich alicyclic molecules were generated in both photochemical and biological processes, suggesting TDOM was converted to a stable pool over time. Our finding on the transformation of terrestrial DOM and the alternation of bacterial community under the simultaneously photochemical and microbial processes will help to reveal the response of the carbon cycle and lake system structure to climate change for high-altitude lakes.

Identification and characterization of Dof genes in Cerasus humilis.

Introduction: Dof genes encode plant-specific transcription factors, which regulate various biological processes such as growth, development, and secondary metabolite accumulation. Methods: We conducted whole-genome analysis of Chinese dwarf cherry (Cerasus humilis) to identify ChDof genes and characterize the structure, motif composition, cis-acting elements, chromosomal distribution, and collinearity of these genes as well as the physical and chemical properties, amino acid sequences, and phylogenetic evolution of the encoded proteins. Results: The results revealed the presence of 25 ChDof genes in C. humilis genome. All 25 ChDof genes could be divided into eight groups, and the members of the same group had similar motif arrangement and intron-exon structure. Promoter analysis showed that cis-acting elements responsive to abscisic acid, low temperature stress, and light were dominant. Transcriptome data revealed that most ChDof genes exhibited tissue-specific expression. Then, we performed by qRT-PCR to analyze the expression patterns of all 25 ChDof genes in fruit during storage. The results indicated that these genes exhibited different expression patterns, suggesting that they played an important role in fruit storage. Discussion: The results of this study provide a basis for further investigation of the biological function of Dof genes in C. humilis fruit.