Eclipta prostrata L.has been used in traditional medicine and known for its liver-protective properties for centuries.Wedelolactone(WEL)and demethylwedelolactone(DWEL)are the major coumarins found in E.prostrata L.How...Eclipta prostrata L.has been used in traditional medicine and known for its liver-protective properties for centuries.Wedelolactone(WEL)and demethylwedelolactone(DWEL)are the major coumarins found in E.prostrata L.However,the comprehensive characterization of these two compounds on non-alcoholic fatty liver disease(NAFLD)still remains to be explored.Utilizing a well-established zebrafish model of thioacetamide(TAA)-induced liver injury,the present study sought to investigate the impacts and mechanisms of WEL and DWEL on NAFLD through integrative spatial metabolomics with liver-specific transcriptomics analysis.Our results showed that WEL and DWEL significantly improved liver function and reduced the accumulation of fat in the liver.The biodistributions and metabolism of these two compounds in whole-body zebrafish were successfully mapped,and the discriminatory endogenous metabolites reversely regulated by WEL and DWEL treatments were also characterized.Based on spatial metabolomics and transcriptomics,we identified that steroid biosynthesis and fatty acid metabolism are mainly involved in the hepatoprotective effects of WEL instead of DWEL.Our study unveils the distinct mechanism of WEL and DWEL in ameliorating NAFLD,and presents a“multi-omics”platform of spatial metabolomics and liver-specific transcriptomics to develop highly effective compounds for further improved therapy.展开更多
The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field.Although bulk RNA sequencing and single-cell RNA sequencing(scRNA-seq)have provided insights into cel...The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field.Although bulk RNA sequencing and single-cell RNA sequencing(scRNA-seq)have provided insights into cell types and heterogeneity in the respiratory system,the relevant specific spatial localization and cellular interactions have not been clearly elucidated.Spatial transcriptomics(ST)has filled this gap and has been widely used in respiratory studies.This review focuses on the latest iterative technology of ST in recent years,summarizing how ST can be applied to the physiological and pathological processes of the respiratory system,with emphasis on the lungs.Finally,the current challenges and potential development directions are proposed,including high-throughput full-length transcriptome,integration of multi-omics,temporal and spatial omics,bioinformatics analysis,etc.These viewpoints are expected to advance the study of systematic mechanisms,including respiratory studies.展开更多
Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment ...Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment significantly decreased reactive oxygen species(ROS)and malondialdeh yde(MDA)contents in broccoli sprouts.On the the 8^(th)day,compared to tap water treatment,the the total glucosinolate content of broccoli sprouts with CHEW treatment increased by 10.6%and calcium content was dramatically enhanced from 14.4 mg/g DW to 22.7 mg/g DW.Comparative transcriptome and metabolome analyses revealed that CHEW treatment activated ROS and calcium signaling transduction pathways in broccoli sprouts and they interacted through MAPK cascades.Besides,CHEW treatment not only promoted the biosynthesis of amino acids,but also enhanced the expression of structural genes in glucosinolate synthesis through transcription factors(MYBs,bHLHs,WRKYs,etc.).The results of this study provided new insights into the regulatory network of glucosinolates biosynthesis in broccoli sprouts under CHEW treatment.展开更多
Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the im...Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the immune microenvironment has the potential to inform the development of therapeutic strategies for fungal infections.Methods:The study analyzed individual immune cell profiles in peripheral blood mononuclear cells from Candida albicans-infected mice and healthy control mice using single-cell transcriptomics,fluorescence quantitative PCR,and Western blotting.We investigated intergroup differences in the dynamics of immune cell subpopulation infiltration,pathway enrichment,and differentiation during Candida albicans infection.Results:Our findings indicate that infiltration of CD4^(+)naive cells,regulatory T(Treg)cells,and Microtubules(MT)-associated cells increased after infection,along with impaired T cell activity.Notably,CD4^(+) T cells and plasma cells were enhanced after infection,suggesting that antibody production is dependent on T cells.In addition,we screened 6 hub genes,transcription factor forkhead box protein 3(Foxp3),cytotoxic T-lymphocyte associated protein 4(CTLA4),Interleukin 2 Receptor Subunit Beta(Il2rb),Cd28,C-C Motif Chemokine Ligand 5(Ccl5),and Cd27 for alterations associated with CD4^(+) T cell differentiation.Conclusions:These results provide a comprehensive immunological landscape of the mechanisms of Candida albicans infection and greatly advance our understanding of adaptive immunity in fungal infections.展开更多
Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five differ...Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.展开更多
Cotton rose(Hibiscus mutabilis)is a well-known ornamental plant that produces large flowers of vibrant colors.However,metabolites in H.mutabilis flowers with vibrant color have not been fully understood.By performing ...Cotton rose(Hibiscus mutabilis)is a well-known ornamental plant that produces large flowers of vibrant colors.However,metabolites in H.mutabilis flowers with vibrant color have not been fully understood.By performing a combined analysis of metabolomics and transcriptomics data,we here explored mechanisms for the production of primary active compounds in this plant.Multivariate statistics unveiled differences in flavonoid metabolism between white and pink flowers,with pink flowers exhibiting a greater flavonoid abundance.The white-to-pink transition of cotton rose flowers may be attributed to pelargonidin-3-O-glucoside formation.On examining the expression of genes related to the structure of flavonoids,pink flowers were found to have a higher number of upregulated genes than white flowers,which resulted in higher flavonoid accumulation in the pink flowers.These results underscore the potential applications and development value of cotton rose flowers.Our study provides relevant insights into the regulation of key active components and the theoretical basis for the efficient utilization of cotton rose flowers.展开更多
Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network g...Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.展开更多
Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit.During the ripening process of tomato fruit,flavor and aroma metabolites,col...Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit.During the ripening process of tomato fruit,flavor and aroma metabolites,color,texture and plant hormones undergo significant changes.However,low temperatures delayed the ripening process of tomato fruit,inhibiting flavor compounds and ethylene production.Metabolomics and transcriptomics analyses of tomato fruit stored under low temperature(LT,5°C)and room temperature(RT,25°C)were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after harvest.The results of transcriptomics changes revealed that the differentially expressed genes(DEGs)involved in tomato fruit ripening,including several kinds of transcription factors(TFs)(TCP,WRKY,MYB and bZIP),enzymes involved in cell wall metabolism[beta-galactosidase(β-GAL),pectinesterase(PE)and pectate lyase(PL),cellulose and cellulose synthase(CESA)],enzymes associated with fruit flavor and aroma[acetyltransferase(AT),malic enzyme(ME),lipoxygenase(LOX),aldehyde dehydrogenase(ALDH),alcohol dehydrogenase(ADH)and hexokinase(HK)],genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1(ERF1),Auxin/indoleacetic acids protein(AUX/IAA),gibberellin regulated protein.Based on the above results,we constructed a regulatory network model of the effects of different temperatures during the fruit ripening process.According to the analysis of the metabolomics results,it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature,including,organic acids(L-tartaric acid,a-hydroxyisobutyric acid and 4-acetamidobutyric acid),sugars(melezitose,beta-Dlactose,D-sedoheptulose 7-phosphate,2-deoxyribose 1-phosphate and raffinose)and phenols(coniferin,curcumin and feruloylputrescine).This study revealed the effects of storage temperature on postharvest tomato fruit and provided a basis for further understanding of the molecular biology and biochemistry of fruit ripening.展开更多
Listeria monocytogenes is a worrisome food-borne pathogen threatening global food safety.Our previous study proved that lipopeptide brevilaterin B showed efficient antibacterial activity against L.monocytogenes by int...Listeria monocytogenes is a worrisome food-borne pathogen threatening global food safety.Our previous study proved that lipopeptide brevilaterin B showed efficient antibacterial activity against L.monocytogenes by interacting with the cell membrane.This research further explored the antibacterial mechanism of brevilaterin B against L.monocytogenes at the sub-minimum inhibition concentration via transcriptomic analysis.Brevilaterin B induced growth inhibition rather than direct membrane lysis in L.monocytogenes at the minimum inhibitory concentration.Transcriptomic analysis showed 1779 difference expressed genes,including 895 up-regulated and 884 down-regulated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that brevilaterin B influenced multiple pathways of L.monocytogenes,including peptidoglycan biosynthesis,membrane transport(ATP-binding cassette transports,ion transport),cellular metabolism(amino acid and lipid metabolism),ATP synthesis,and activation of the stress response(quorum sensing and bacterial chemotaxis).In conclusion,brevilaterin B affects gene expression related to biosynthesis,transport and stress response pathways on the membrane of L.monocytogenes.The present work provides the first transcriptomic assessment of the antibacterial mechanism of lipopeptide brevilaterin B at the gene level.展开更多
Hot pepper(Capsicum annuum L.)is consumed as one of the oldest domesticated crops all over the world.Although mutation breeding using radiation has been performed in hot peppers,little is known about the comparative a...Hot pepper(Capsicum annuum L.)is consumed as one of the oldest domesticated crops all over the world.Although mutation breeding using radiation has been performed in hot peppers,little is known about the comparative analysis of mutagenic effects at the molecular level by ion beam irradiation.To comprehend the response mechanism of hot pepper to the ion beam,we used a mutant with favorable economic characteristics induced by lithium-ion beam irradiation to investigate the biological effects.The results indicated that the lithium-ion beam had a positive effect on important agronomic traits,particularly yield unit,but had a negligible effect on the photosynthetic rate of hot pepper,with a specific influence on chlorophyll b rather than chlorophyll a.By RNA-Seq analysis,671 up-regulated and 376 down-regulated genes were identified as differentially expressed genes(DEGs)between irradiated and unirradiated hot pepper.Based on GO and KEGG network analysis,the auxin metabolic process was the common pathway in these two networks.A total of 118 potential reactive oxygen species(ROS)scavenging genes and 262 signal transduction genes were identified,suggesting a balance between antioxidant enzymes and enhanced ROS transduction.The amounts of 15 metabolite,involved in GABA pathways,secondary metabolism,carbohydrate metabolism,shikimate pathways,TCA cycles,nitrogen metabolism,glycerol metabolism and acetate pathways,were significantly changed in the ion beam irradiated sample.These results highlighted that the enriched pathways could play important roles in response to ion beam irradiation in hot pepper plants.In summary,these data provide valuable information for future research on ion beam irradiation and genomic studies in hot pepper.展开更多
The mature seed of Paris polyphylla var.chinensis(PPC)is morphophysiologically dormant and develops differently under warm and cold temperatures.To elucidate the molecular mechanisms underlying temperature-dependent r...The mature seed of Paris polyphylla var.chinensis(PPC)is morphophysiologically dormant and develops differently under warm and cold temperatures.To elucidate the molecular mechanisms underlying temperature-dependent regulation of PPC seed dormancy and germination,we investigated the dynamic changes in PPC seed transcript levels under warm and cold temperature stratifications(WS and CS,respectively)by time-resolved RNA sequencing,focusing on genes related to hormone metabolism and signaling and cell wall remodeling(CWRM)and encoding transcription factors/regulators(TFs/TRs).A total of 48765 and 47836 differentially expressed genes(DEGs)were associated with WS and CS,respectively.Of these,17581 and 16652 DEGs,respectively,unique to WS and CS,and 5386 were common to both temperature stratifications across nine analyzed growth stages.The expression of hormone metabolism and signaling,TF/TR,and CWRM genes were closely associated with temperature.More genes related to gibberellin(GA),cytokinin,auxin,and brassinosteroid biosynthetic were upregulated in WS as compared to CS seeds,while genes related to dormancy release and germination were downregulated in WS seeds.However,only GA and abscisic acid levels were altered in PPC seeds breaking morphophysiological dormancy(MPD).Overall,37 TF and five TR families were upregulated whereas 24 TF and 16 TR families were downregulated in WS as compared to CS seeds.Most CWRM families were highly expressed under WS as compared to CS,suggesting that they promote endosperm weakening and embryo growth of WS seeds and facilitate MPD release and germination.A coexpression analysis revealed positive correlations between TFs/TRs and DEGs involved in hormone metabolism and signaling and CWRM.These results provided a basis for investigating the interaction between the endosperm and underdeveloped embryo in the regulation of PPC seed germination and seedling emergence.展开更多
Michelia macclurei Dandy is a significant tree species that has extensive cultivation for forestry and horticulture purposes in southern China,owing to its economic and practical importance.Light quality influences pl...Michelia macclurei Dandy is a significant tree species that has extensive cultivation for forestry and horticulture purposes in southern China,owing to its economic and practical importance.Light quality influences plantlet growth and development during tissue culture.However,the growth characteristic and molecular regulation of M.macclurei under different light quality conditions are not well understood yet.In this study,we investigated the morphological,chlorophyll content,and transcriptomic responses of M.macclurei plantlets under different light-emitting diode(LED)qualities,including white,blue,and red light.The results showed that blue light significantly increased plant height(21.29%)and leaf number(18.65%),while red light decreased plant height and leaf number by 7.53%and 16.49%,respectively.In addition,the plantlets’chlorophyll content and etiolation rate were significantly reduced by blue and red light quality compared to white light.Compared to white light,blue light had a negative effect,leading to decreased rooting rate(64.28%),root number(72.72%),and root length(75.86%).Conversely,red light had a positive effect,resulting in increased rooting rate(24.99%),root number(109.58%),and root length(72.72%).Transcriptome analysis identified 54 differentially expressed genes(DEGs)in three groups that consisted of blue light vs.white light(BL-vs-WL),red light vs.white light(RL-vs-WL),and red light vs.blue light(RL-vs-BL).Specifically,21,7,and 41 DEGs were identified in the three groups,respectively.The DEGs found in the RL-vs-WL and BL-vs-WL groups were involved in plant hormone signaling,nitrogen metabolism,and phenylpropanoid biosynthesis pathways,which suggests that M.macclurei plantlets adapt to the changes of light quality via modulating gene expression.Overall,our study provides valuable insights for understanding the molecular and morphological responses of M.macclurei plantlets under different light qualities.展开更多
Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information.Upon data acquisition...Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information.Upon data acquisition,one major hurdle is the subsequent interpretation and visualization of the datasets acquired.To address this challenge,VR-Cardiomics is presented,which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets.By implementing the system in two separate immersive environments,fish tank virtual reality(FTVR)and head-mounted display virtual reality(HMD-VR),biologists can interact with the data in novel ways not previously possible,such as visually exploring the gene expression patterns of an organ,and comparing genes based on their 3D expression profiles.Further,a biologist-driven use-case is presented,in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.展开更多
The high-glucose tolerance of yeast is the main factor determining the efficiency of high-density alcohol fermentation.Zygosaccharomyces mellis LGL-1 isolated from honey could survive under 700 g/L high-glucose stress...The high-glucose tolerance of yeast is the main factor determining the efficiency of high-density alcohol fermentation.Zygosaccharomyces mellis LGL-1 isolated from honey could survive under 700 g/L high-glucose stress and its tolerant characteristics were identified in our previous study.This study was performed to explore and clarify the high-glucose tolerance mechanism of Z.mellis LGL-1.Comparative transcriptomic analysis was used to analyze the genes with differential expression in Z.mellis under high-glucose conditions of 300,500 and 700 g/L.With 300 g/L samples as reference,there were 937 and 2380 differentially expressed genes(DEGs)in the 500 and 700 g/L samples,respectively.Meanwhile,there was 825 significant DEGs in the 700 g/L samples compared with that of the 500 g/L samples.The result revealed that transcriptional changes in multiple metabolic pathways occur in response to high-glucose stress.q-RT PCR analysis further confirmed that several stress response pathways,such as the high osmolarity glycerol mitogen-activated protein kinase(HOG-MAPK)signal transduction pathway,trehalose synthesis pathway and oxidative stress response are closely related to high-glucose tolerance in Z.mellis.This study clarifies mechanisms of Z.mellis in response to high-glucose osmotic stress,providing theoretical basis for the process control of high-density alcohol fermentation.展开更多
Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome bac...Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome background. Transcriptomic analysis based on high-throughput RNA sequencing has been shown to be an efficient and powerful method for the discovery of relevant genes in non-model and genome reference-free organisms. Here, we constructed two c DNA libraries(control and Cd exposure groups) from the digestive gland of C. farreri and compared the transcriptomic data between them. A total of 227 673 transcripts were assembled into 105 071 unigenes, most of which shared high similarity with sequences in the NCBI non-redundant protein database. For functional classification, 24 493 unigenes were assigned to Gene Ontology terms. Additionally, Eu Karyotic Ortholog Groups and Kyoto Encyclopedia of Genes and Genomes analyses assigned 12 028 unigenes to 26 categories and 7 849 unigenes to five pathways, respectively. Comparative transcriptomics analysis identified 3 800 unigenes that were differentially expressed in the Cd-treated group compared with the control group. Among them, genes associated with heavy metal accumulation were screened, including metallothionein, divalent metal transporter, and metal tolerance protein. The functional genes and predicted pathways identified in our study will contribute to a better understanding of the metabolic and immune system in the digestive gland of C. farreri. In addition, the transcriptomic data will provide a comprehensive resource that may contribute to the understanding of molecular mechanisms that respond to marine pollutants in bivalves.展开更多
The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize th...The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.展开更多
The fermentation broth of Salinivibrio proteolyticus strain YCSC6 shows potent anti-parasitic activity against Uronema marinum,with activity varying in each fermentation stage.To investigate the biosynthetic mechanism...The fermentation broth of Salinivibrio proteolyticus strain YCSC6 shows potent anti-parasitic activity against Uronema marinum,with activity varying in each fermentation stage.To investigate the biosynthetic mechanism of anti-parasitic compounds in strain YCSC6,a comprehensive analysis of metabolomics and transcriptomics over four diff erent time points(12,24,48,and 72 h)was performed.Metabolomics detected 17943 metabolites with 1129 known metabolites.A trend analysis of the known metabolites showed that 575 metabolites,including 69 polyketides,were continuously enhanced,being the potential source of anti-parasitic agents.In addition,941 genes mapped to the same pathways of these metabolites,were screened through the association analysis of metabolites and genes.KEGG pathway enrichment of these genes showed 270 genes mapped to the biosynthesis of secondary metabolites and 192 genes mapped to the biosynthesis of antibiotics.This demonstrates the potent secondary metabolic capacity of strain YCSC6.Finally,a gene-metabolite correlation network was created based on the 575 continuously enhanced metabolites and 43 continuously up-regulated genes.This revealed 13 genes at the key position that mapped to a putative metabolic pathway associated with the biosynthesis of polyketides and caprylic acid,which contributes to the potent anti-parasitic activity of strain YCSC6.This comprehensive analysis of metabolomics and transcriptomics provides insights into the biosynthetic mechanisms of anti-parasitic compounds in strain YCSC6 and guides the exploitation of more anti-parasitic agents for aquaculture.展开更多
Revealing the structural characteristics,succession changes and functional genes of the microbial community in lactic acid bacteria-fermented food has been the focus of scientific research and industrial production fo...Revealing the structural characteristics,succession changes and functional genes of the microbial community in lactic acid bacteria-fermented food has been the focus of scientific research and industrial production for many years.In recent years,high-throughput sequencing technology has become an important tool for the research of lactic acid bacteria-fermented food microorganisms due to its advantages of high efficiency and being relatively cheap.In this paper,starting from the research on the genome,transcriptome and metabonomic levels of high-throughput sequencing technology,we reviewed the progress of transcriptomics in the study on microbial community structure,interaction,and functional gene mining of lactic acid bacteria-fermented food,and analyzed and discussed the main problems and development trends it faces,providing a certain reference for the scientific research and industrial production of fermented food in the future.展开更多
Background:The hypothesis was tested that insect meal(IM)as protein source influences intermediary metabolism of growing pigs.To test this,30 male,5-week-old crossbred pigs were randomly assigned to 3 groups of 10 pig...Background:The hypothesis was tested that insect meal(IM)as protein source influences intermediary metabolism of growing pigs.To test this,30 male,5-week-old crossbred pigs were randomly assigned to 3 groups of 10 pigs each with similar body weights(BW)and fed isonitrogenous diets either without(CON)or with 5%IM(IM5)or 10%IM(IM10)from Tenebrio molitor L.for 4 weeks and key metabolic tissues(liver,muscle,plasma)were analyzed using omics-techniques.Results:Most performance parameters did not differ across the groups,whereas ileal digestibilities of most amino acids were 6.7 to 15.6%-units lower in IM10 than in CON(P<0.05).Transcriptomics of liver and skeletal muscle revealed a total of 166 and 198,respectively,transcripts differentially expressed between IM10 and CON(P<0.05).Plasma metabolomics revealed higher concentrations of alanine,citrulline,glutamate,proline,serine,tyrosine and valine and a lower concentration of asparagine in IM10 than in CON(P<0.05).Only one out of fourteen quantifiable amino acid metabolites,namely methionine sulfoxide(MetS),in plasma was elevated by 45%and 71%in IM5 and IM10,respectively,compared to CON(P<0.05).Plasma concentrations of both,major carnitine/acylcarnitine species and bile acids were not different across groups.Lipidomics of liver and plasma demonstrated no differences in the concentrations of triacylglycerols,cholesterol and the main phospholipids,lysophospholipids and sphingolipids between groups.The percentages of all individual phosphatidylcholine(PC)and phosphatidylethanolamine(PE)species in the liver showed no differences between groups,except those with 6 double bonds(PC 38:6,PC 40:6,PE 38:6,PE 40:6),which were markedly lower in IM10 than in CON(P<0.05).In line with this,the percentage of C22:6n-3 in hepatic total lipids was lower in IM10 than in the other groups(P<0.05).Conclusions:Comprehensive analyzes of the transcriptome,lipidome and metabolome of key metabolic tissues indicate that partial or complete replacement of a conventional protein source by IM in the diet has only a weak impact on the intermediary metabolism of growing pigs.Thus,it is concluded that IM from Tenebrio molitor L.can be used as a dietary source of protein in pigs without causing adverse effects on metabolism.展开更多
Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study...Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, we used integrated transcriptomics and metabolomics analyses to investigate changes in gene/metabolite activity in a winter-hardy wheat cultivar of(cv. Jing 411) when subjected to sold stress. The 223 metabolites mainly enriched during cold acclimation included carbohydrates, flavonoids, and amino acids.Eight common metabolites had altered abundance following freezing treatment;six increased and two decreased. Transcriptome analysis revealed that 29,066 genes were differentially expressed in wheat crowns after cold acclimation compared to the nonacclimated control. Among them, 745 genes were up-regulated following freezing treatment, suggesting substantial change in expression of a large quantity of genes upon cold acclimation and freezing treatment, which impacts on the modified metabolites.Integrated analysis of gene expression and metabolite profiles revealed that the abscisic acid(ABA)/jasmonic acid(JA) phytohormone signaling and proline biosynthesis pathways were significantly modulated under cold acclimation and freezing treatments. Our results indicated that low-temperature stress induced substantial changes in both transcriptomes and metabolomes. Critical pathways associated with ABA/JA signaling and proline biosynthesis played important roles in regulating cold tolerance in wheat.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.:82273888)Natural Science Foundation of Shandong Province(Grant Nos.ZR2022QH257,ZR2020YQ60)+2 种基金Shandong Major Technological Innovation Project(Project No.:2021CXGC010508)Taishan Scholars Program of Shandong Province(Program Nos.:tsqn202103096,tsqn202211204)Shandong Province Science and Technology Small and Medium Enterprises Innovation Ability Enhancement Project(Project No.:2022TSGC2210).
文摘Eclipta prostrata L.has been used in traditional medicine and known for its liver-protective properties for centuries.Wedelolactone(WEL)and demethylwedelolactone(DWEL)are the major coumarins found in E.prostrata L.However,the comprehensive characterization of these two compounds on non-alcoholic fatty liver disease(NAFLD)still remains to be explored.Utilizing a well-established zebrafish model of thioacetamide(TAA)-induced liver injury,the present study sought to investigate the impacts and mechanisms of WEL and DWEL on NAFLD through integrative spatial metabolomics with liver-specific transcriptomics analysis.Our results showed that WEL and DWEL significantly improved liver function and reduced the accumulation of fat in the liver.The biodistributions and metabolism of these two compounds in whole-body zebrafish were successfully mapped,and the discriminatory endogenous metabolites reversely regulated by WEL and DWEL treatments were also characterized.Based on spatial metabolomics and transcriptomics,we identified that steroid biosynthesis and fatty acid metabolism are mainly involved in the hepatoprotective effects of WEL instead of DWEL.Our study unveils the distinct mechanism of WEL and DWEL in ameliorating NAFLD,and presents a“multi-omics”platform of spatial metabolomics and liver-specific transcriptomics to develop highly effective compounds for further improved therapy.
基金supported by the National Natural Science Foundation of China(82271629)the Central Funds Guiding the Local Science and Technology Development of Shenzhen(2021Szvup024)+1 种基金the Jiangsu Provincial Key Research and Development Program(BE2021664)the Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX23_0312)。
文摘The respiratory system's complex cellular heterogeneity presents unique challenges to researchers in this field.Although bulk RNA sequencing and single-cell RNA sequencing(scRNA-seq)have provided insights into cell types and heterogeneity in the respiratory system,the relevant specific spatial localization and cellular interactions have not been clearly elucidated.Spatial transcriptomics(ST)has filled this gap and has been widely used in respiratory studies.This review focuses on the latest iterative technology of ST in recent years,summarizing how ST can be applied to the physiological and pathological processes of the respiratory system,with emphasis on the lungs.Finally,the current challenges and potential development directions are proposed,including high-throughput full-length transcriptome,integration of multi-omics,temporal and spatial omics,bioinformatics analysis,etc.These viewpoints are expected to advance the study of systematic mechanisms,including respiratory studies.
基金supported by the National Natural Science Foundation of China(31972091)。
文摘Glucosinolates are important phytochemicals in Brassicaceae.We investigated the effect of CaCl_(2)-HCl electrolyzed water(CHEW)on glucosinolates biosynthesis in broccoli sprouts.The results showed that CHEW treatment significantly decreased reactive oxygen species(ROS)and malondialdeh yde(MDA)contents in broccoli sprouts.On the the 8^(th)day,compared to tap water treatment,the the total glucosinolate content of broccoli sprouts with CHEW treatment increased by 10.6%and calcium content was dramatically enhanced from 14.4 mg/g DW to 22.7 mg/g DW.Comparative transcriptome and metabolome analyses revealed that CHEW treatment activated ROS and calcium signaling transduction pathways in broccoli sprouts and they interacted through MAPK cascades.Besides,CHEW treatment not only promoted the biosynthesis of amino acids,but also enhanced the expression of structural genes in glucosinolate synthesis through transcription factors(MYBs,bHLHs,WRKYs,etc.).The results of this study provided new insights into the regulatory network of glucosinolates biosynthesis in broccoli sprouts under CHEW treatment.
基金supported by National Key Research and Development Program of China(2021YFC2301405)Chongqing Talent Program(No.CQYC202003220).
文摘Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the immune microenvironment has the potential to inform the development of therapeutic strategies for fungal infections.Methods:The study analyzed individual immune cell profiles in peripheral blood mononuclear cells from Candida albicans-infected mice and healthy control mice using single-cell transcriptomics,fluorescence quantitative PCR,and Western blotting.We investigated intergroup differences in the dynamics of immune cell subpopulation infiltration,pathway enrichment,and differentiation during Candida albicans infection.Results:Our findings indicate that infiltration of CD4^(+)naive cells,regulatory T(Treg)cells,and Microtubules(MT)-associated cells increased after infection,along with impaired T cell activity.Notably,CD4^(+) T cells and plasma cells were enhanced after infection,suggesting that antibody production is dependent on T cells.In addition,we screened 6 hub genes,transcription factor forkhead box protein 3(Foxp3),cytotoxic T-lymphocyte associated protein 4(CTLA4),Interleukin 2 Receptor Subunit Beta(Il2rb),Cd28,C-C Motif Chemokine Ligand 5(Ccl5),and Cd27 for alterations associated with CD4^(+) T cell differentiation.Conclusions:These results provide a comprehensive immunological landscape of the mechanisms of Candida albicans infection and greatly advance our understanding of adaptive immunity in fungal infections.
基金supported in part by the Priority Academic Program Development of Jiangsu Higher Education Institutions and the State Key Laboratory of Crop Genetics and Germplasm Enhancement,China(ZW201813)。
文摘Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.
基金supported by the college students’Innovation and Entrepreneurship Training Program of Chengdu University(S202311079115,CDUCX2024599).
文摘Cotton rose(Hibiscus mutabilis)is a well-known ornamental plant that produces large flowers of vibrant colors.However,metabolites in H.mutabilis flowers with vibrant color have not been fully understood.By performing a combined analysis of metabolomics and transcriptomics data,we here explored mechanisms for the production of primary active compounds in this plant.Multivariate statistics unveiled differences in flavonoid metabolism between white and pink flowers,with pink flowers exhibiting a greater flavonoid abundance.The white-to-pink transition of cotton rose flowers may be attributed to pelargonidin-3-O-glucoside formation.On examining the expression of genes related to the structure of flavonoids,pink flowers were found to have a higher number of upregulated genes than white flowers,which resulted in higher flavonoid accumulation in the pink flowers.These results underscore the potential applications and development value of cotton rose flowers.Our study provides relevant insights into the regulation of key active components and the theoretical basis for the efficient utilization of cotton rose flowers.
基金This work was financially supported by the grants from the National Key Research and Development Program of China(2021YFF1001204,2021YFD1201602)the MOE 111 Project(B08025)+2 种基金the MOA CARS-04 program,the Program of Jiangsu province(JBGS-2021-014)the Guangxi Scientific Research and Technology Development Plan(14125008-2-16)the Guidance Foundation of Sanya Institute of Nanjing Agricultural University(NAUSY-ZZ02,NAUSY-MS05).
文摘Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.
基金supported by the Young Investigator Fund of Beijing Academy of Agricultural and Forestry Sciences(Grant No.202016)the Special innovation ability construction fund of Beijing Academy of Agricultural and Forestry Sciences(Grant Nos.20210437,20210402 and 20200427)+4 种基金the Collaborative innovation center of Beijing Academy of Agricultural and Forestry Sciences(Grant No.201915)Special innovation ability construction fund of Beijing Vegetable Research Center,Beijing Academy of Agriculture and Forestry Sciences(Grant No.2020112)the National Natural Science Foundation of China(Grant Nos.31772022 and 32072284)the China Agriculture Research System of MOF and MARA(Grant No.CARS-23)Beijing Municipal Science and Technology Commission(Grant Nos.Z191100008619004,Z191100004019010 and Z181100009618033)。
文摘Tomato is one of the most important vegetable crops in the world and is a model plant used to study the ripening of climacteric fleshy fruit.During the ripening process of tomato fruit,flavor and aroma metabolites,color,texture and plant hormones undergo significant changes.However,low temperatures delayed the ripening process of tomato fruit,inhibiting flavor compounds and ethylene production.Metabolomics and transcriptomics analyses of tomato fruit stored under low temperature(LT,5°C)and room temperature(RT,25°C)were carried out to investigate the effects of storage temperature on the physiological changes in tomato fruit after harvest.The results of transcriptomics changes revealed that the differentially expressed genes(DEGs)involved in tomato fruit ripening,including several kinds of transcription factors(TFs)(TCP,WRKY,MYB and bZIP),enzymes involved in cell wall metabolism[beta-galactosidase(β-GAL),pectinesterase(PE)and pectate lyase(PL),cellulose and cellulose synthase(CESA)],enzymes associated with fruit flavor and aroma[acetyltransferase(AT),malic enzyme(ME),lipoxygenase(LOX),aldehyde dehydrogenase(ALDH),alcohol dehydrogenase(ADH)and hexokinase(HK)],genes associated with heat stress protein 70 and genes involved in the production of plant hormones such as Ethylene responsive factor 1(ERF1),Auxin/indoleacetic acids protein(AUX/IAA),gibberellin regulated protein.Based on the above results,we constructed a regulatory network model of the effects of different temperatures during the fruit ripening process.According to the analysis of the metabolomics results,it was found that the contents of many metabolites in tomato fruit were greatly affected by storage temperature,including,organic acids(L-tartaric acid,a-hydroxyisobutyric acid and 4-acetamidobutyric acid),sugars(melezitose,beta-Dlactose,D-sedoheptulose 7-phosphate,2-deoxyribose 1-phosphate and raffinose)and phenols(coniferin,curcumin and feruloylputrescine).This study revealed the effects of storage temperature on postharvest tomato fruit and provided a basis for further understanding of the molecular biology and biochemistry of fruit ripening.
基金financially supported by the National Natural Science Foundation of China(31771951,32072199,31801510)the Beijing Natural Science Foundation(KZ201810011016).
文摘Listeria monocytogenes is a worrisome food-borne pathogen threatening global food safety.Our previous study proved that lipopeptide brevilaterin B showed efficient antibacterial activity against L.monocytogenes by interacting with the cell membrane.This research further explored the antibacterial mechanism of brevilaterin B against L.monocytogenes at the sub-minimum inhibition concentration via transcriptomic analysis.Brevilaterin B induced growth inhibition rather than direct membrane lysis in L.monocytogenes at the minimum inhibitory concentration.Transcriptomic analysis showed 1779 difference expressed genes,including 895 up-regulated and 884 down-regulated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that brevilaterin B influenced multiple pathways of L.monocytogenes,including peptidoglycan biosynthesis,membrane transport(ATP-binding cassette transports,ion transport),cellular metabolism(amino acid and lipid metabolism),ATP synthesis,and activation of the stress response(quorum sensing and bacterial chemotaxis).In conclusion,brevilaterin B affects gene expression related to biosynthesis,transport and stress response pathways on the membrane of L.monocytogenes.The present work provides the first transcriptomic assessment of the antibacterial mechanism of lipopeptide brevilaterin B at the gene level.
基金supported by the China Atomic Energy Authority(Crop Varietal Improvement and Insect Pests Control by Nuclear Radiation)Key Technological Innovation Key Project of Agricultural Science and Technology Breakthrough in Heilongjiang Province-Breakthrough Variety Breeding and Industrial Application of Vegetables。
文摘Hot pepper(Capsicum annuum L.)is consumed as one of the oldest domesticated crops all over the world.Although mutation breeding using radiation has been performed in hot peppers,little is known about the comparative analysis of mutagenic effects at the molecular level by ion beam irradiation.To comprehend the response mechanism of hot pepper to the ion beam,we used a mutant with favorable economic characteristics induced by lithium-ion beam irradiation to investigate the biological effects.The results indicated that the lithium-ion beam had a positive effect on important agronomic traits,particularly yield unit,but had a negligible effect on the photosynthetic rate of hot pepper,with a specific influence on chlorophyll b rather than chlorophyll a.By RNA-Seq analysis,671 up-regulated and 376 down-regulated genes were identified as differentially expressed genes(DEGs)between irradiated and unirradiated hot pepper.Based on GO and KEGG network analysis,the auxin metabolic process was the common pathway in these two networks.A total of 118 potential reactive oxygen species(ROS)scavenging genes and 262 signal transduction genes were identified,suggesting a balance between antioxidant enzymes and enhanced ROS transduction.The amounts of 15 metabolite,involved in GABA pathways,secondary metabolism,carbohydrate metabolism,shikimate pathways,TCA cycles,nitrogen metabolism,glycerol metabolism and acetate pathways,were significantly changed in the ion beam irradiated sample.These results highlighted that the enriched pathways could play important roles in response to ion beam irradiation in hot pepper plants.In summary,these data provide valuable information for future research on ion beam irradiation and genomic studies in hot pepper.
基金supported by the CAMS Innovation Fund for Medical Sciences (CIFMS) (2017-I2M-3-013)the National Key Research and Development Program of China (Grant No. 2017YFC1700706)the National Natural Science Foundation of China (Grant No. 31471575).
文摘The mature seed of Paris polyphylla var.chinensis(PPC)is morphophysiologically dormant and develops differently under warm and cold temperatures.To elucidate the molecular mechanisms underlying temperature-dependent regulation of PPC seed dormancy and germination,we investigated the dynamic changes in PPC seed transcript levels under warm and cold temperature stratifications(WS and CS,respectively)by time-resolved RNA sequencing,focusing on genes related to hormone metabolism and signaling and cell wall remodeling(CWRM)and encoding transcription factors/regulators(TFs/TRs).A total of 48765 and 47836 differentially expressed genes(DEGs)were associated with WS and CS,respectively.Of these,17581 and 16652 DEGs,respectively,unique to WS and CS,and 5386 were common to both temperature stratifications across nine analyzed growth stages.The expression of hormone metabolism and signaling,TF/TR,and CWRM genes were closely associated with temperature.More genes related to gibberellin(GA),cytokinin,auxin,and brassinosteroid biosynthetic were upregulated in WS as compared to CS seeds,while genes related to dormancy release and germination were downregulated in WS seeds.However,only GA and abscisic acid levels were altered in PPC seeds breaking morphophysiological dormancy(MPD).Overall,37 TF and five TR families were upregulated whereas 24 TF and 16 TR families were downregulated in WS as compared to CS seeds.Most CWRM families were highly expressed under WS as compared to CS,suggesting that they promote endosperm weakening and embryo growth of WS seeds and facilitate MPD release and germination.A coexpression analysis revealed positive correlations between TFs/TRs and DEGs involved in hormone metabolism and signaling and CWRM.These results provided a basis for investigating the interaction between the endosperm and underdeveloped embryo in the regulation of PPC seed germination and seedling emergence.
基金funded and supported by Fundamental Research Funds of the Chinese Academy of Forestry,No.CAFYBB2017MB10.
文摘Michelia macclurei Dandy is a significant tree species that has extensive cultivation for forestry and horticulture purposes in southern China,owing to its economic and practical importance.Light quality influences plantlet growth and development during tissue culture.However,the growth characteristic and molecular regulation of M.macclurei under different light quality conditions are not well understood yet.In this study,we investigated the morphological,chlorophyll content,and transcriptomic responses of M.macclurei plantlets under different light-emitting diode(LED)qualities,including white,blue,and red light.The results showed that blue light significantly increased plant height(21.29%)and leaf number(18.65%),while red light decreased plant height and leaf number by 7.53%and 16.49%,respectively.In addition,the plantlets’chlorophyll content and etiolation rate were significantly reduced by blue and red light quality compared to white light.Compared to white light,blue light had a negative effect,leading to decreased rooting rate(64.28%),root number(72.72%),and root length(75.86%).Conversely,red light had a positive effect,resulting in increased rooting rate(24.99%),root number(109.58%),and root length(72.72%).Transcriptome analysis identified 54 differentially expressed genes(DEGs)in three groups that consisted of blue light vs.white light(BL-vs-WL),red light vs.white light(RL-vs-WL),and red light vs.blue light(RL-vs-BL).Specifically,21,7,and 41 DEGs were identified in the three groups,respectively.The DEGs found in the RL-vs-WL and BL-vs-WL groups were involved in plant hormone signaling,nitrogen metabolism,and phenylpropanoid biosynthesis pathways,which suggests that M.macclurei plantlets adapt to the changes of light quality via modulating gene expression.Overall,our study provides valuable insights for understanding the molecular and morphological responses of M.macclurei plantlets under different light qualities.
基金This project was partly funded by the Deutsche Forschungsgemeinschaft(DFG,German Research Foundation)-Project-ID 251654672-TRR 161by DFG Center of Excellence 2117“Centre for the Advanced Study of Collective Behaviour”(ID 422037984)M.R.was funded by an NH&MRC/Heart Foundation Career Development Fellowship and by an Australian Research Council Discovery Project DP190102771 Grant.
文摘Spatially resolved transcriptomics is an emerging class of high-throughput technologies that enable biologists to systematically investigate the expression of genes along with spatial information.Upon data acquisition,one major hurdle is the subsequent interpretation and visualization of the datasets acquired.To address this challenge,VR-Cardiomics is presented,which is a novel data visualization system with interactive functionalities designed to help biologists interpret spatially resolved transcriptomic datasets.By implementing the system in two separate immersive environments,fish tank virtual reality(FTVR)and head-mounted display virtual reality(HMD-VR),biologists can interact with the data in novel ways not previously possible,such as visually exploring the gene expression patterns of an organ,and comparing genes based on their 3D expression profiles.Further,a biologist-driven use-case is presented,in which immersive environments facilitate biologists to explore and compare the heart expression profiles of different genes.
基金Key-Area Research and Development Program of Guangdong Province(2018B020206001)Guangdong Provincial Agricultural Science and Technology Innovation and Extension Project in 2019(2019KJ101)+1 种基金National key research and development plan(2018YFC1604105)National Natural Science Foundation of China(81703053).
文摘The high-glucose tolerance of yeast is the main factor determining the efficiency of high-density alcohol fermentation.Zygosaccharomyces mellis LGL-1 isolated from honey could survive under 700 g/L high-glucose stress and its tolerant characteristics were identified in our previous study.This study was performed to explore and clarify the high-glucose tolerance mechanism of Z.mellis LGL-1.Comparative transcriptomic analysis was used to analyze the genes with differential expression in Z.mellis under high-glucose conditions of 300,500 and 700 g/L.With 300 g/L samples as reference,there were 937 and 2380 differentially expressed genes(DEGs)in the 500 and 700 g/L samples,respectively.Meanwhile,there was 825 significant DEGs in the 700 g/L samples compared with that of the 500 g/L samples.The result revealed that transcriptional changes in multiple metabolic pathways occur in response to high-glucose stress.q-RT PCR analysis further confirmed that several stress response pathways,such as the high osmolarity glycerol mitogen-activated protein kinase(HOG-MAPK)signal transduction pathway,trehalose synthesis pathway and oxidative stress response are closely related to high-glucose tolerance in Z.mellis.This study clarifies mechanisms of Z.mellis in response to high-glucose osmotic stress,providing theoretical basis for the process control of high-density alcohol fermentation.
基金Supported by the Shandong Provincial Post-Doctoral Special Fund Innovative Project(No.S43201403)the Post-Doctoral Applied Research Project of Qingdao City(No.Q51201413)the Shandong Provincial Natural Science Foundation,China(No.ZR2015PD004)
文摘Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome background. Transcriptomic analysis based on high-throughput RNA sequencing has been shown to be an efficient and powerful method for the discovery of relevant genes in non-model and genome reference-free organisms. Here, we constructed two c DNA libraries(control and Cd exposure groups) from the digestive gland of C. farreri and compared the transcriptomic data between them. A total of 227 673 transcripts were assembled into 105 071 unigenes, most of which shared high similarity with sequences in the NCBI non-redundant protein database. For functional classification, 24 493 unigenes were assigned to Gene Ontology terms. Additionally, Eu Karyotic Ortholog Groups and Kyoto Encyclopedia of Genes and Genomes analyses assigned 12 028 unigenes to 26 categories and 7 849 unigenes to five pathways, respectively. Comparative transcriptomics analysis identified 3 800 unigenes that were differentially expressed in the Cd-treated group compared with the control group. Among them, genes associated with heavy metal accumulation were screened, including metallothionein, divalent metal transporter, and metal tolerance protein. The functional genes and predicted pathways identified in our study will contribute to a better understanding of the metabolic and immune system in the digestive gland of C. farreri. In addition, the transcriptomic data will provide a comprehensive resource that may contribute to the understanding of molecular mechanisms that respond to marine pollutants in bivalves.
基金supported by the National Natural Science Foundation of China(32100342,U1902204,31771415,31801054)Bureau of Science and Technology of Yunnan Province(2015FA026)+1 种基金Youth Innovation Promotion AssociationWest Light Foundation of CAS(Y902401081)。
文摘The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.
基金Supported by the National Key R&D Program of China(No.2017YFC1404504)the Youth Talent Program Supported by Laboratory for Marine Fisheries Science and Food Production Processes,Pilot National Laboratory for Marine Science and Technology(No.2018-MFS-T16)。
文摘The fermentation broth of Salinivibrio proteolyticus strain YCSC6 shows potent anti-parasitic activity against Uronema marinum,with activity varying in each fermentation stage.To investigate the biosynthetic mechanism of anti-parasitic compounds in strain YCSC6,a comprehensive analysis of metabolomics and transcriptomics over four diff erent time points(12,24,48,and 72 h)was performed.Metabolomics detected 17943 metabolites with 1129 known metabolites.A trend analysis of the known metabolites showed that 575 metabolites,including 69 polyketides,were continuously enhanced,being the potential source of anti-parasitic agents.In addition,941 genes mapped to the same pathways of these metabolites,were screened through the association analysis of metabolites and genes.KEGG pathway enrichment of these genes showed 270 genes mapped to the biosynthesis of secondary metabolites and 192 genes mapped to the biosynthesis of antibiotics.This demonstrates the potent secondary metabolic capacity of strain YCSC6.Finally,a gene-metabolite correlation network was created based on the 575 continuously enhanced metabolites and 43 continuously up-regulated genes.This revealed 13 genes at the key position that mapped to a putative metabolic pathway associated with the biosynthesis of polyketides and caprylic acid,which contributes to the potent anti-parasitic activity of strain YCSC6.This comprehensive analysis of metabolomics and transcriptomics provides insights into the biosynthetic mechanisms of anti-parasitic compounds in strain YCSC6 and guides the exploitation of more anti-parasitic agents for aquaculture.
基金High-efficiency Ecological Agriculture Innovation Project of Taishan Industry Leading Talent Project(LJNY202001)Yantai Science and Technology Program(2019ZDCX013).
文摘Revealing the structural characteristics,succession changes and functional genes of the microbial community in lactic acid bacteria-fermented food has been the focus of scientific research and industrial production for many years.In recent years,high-throughput sequencing technology has become an important tool for the research of lactic acid bacteria-fermented food microorganisms due to its advantages of high efficiency and being relatively cheap.In this paper,starting from the research on the genome,transcriptome and metabonomic levels of high-throughput sequencing technology,we reviewed the progress of transcriptomics in the study on microbial community structure,interaction,and functional gene mining of lactic acid bacteria-fermented food,and analyzed and discussed the main problems and development trends it faces,providing a certain reference for the scientific research and industrial production of fermented food in the future.
基金This study was financially supported by the Deutsche Forschungsgemeinschaft(DFGGrant nos.RI 1537/6–1 and ED 70/14–1).
文摘Background:The hypothesis was tested that insect meal(IM)as protein source influences intermediary metabolism of growing pigs.To test this,30 male,5-week-old crossbred pigs were randomly assigned to 3 groups of 10 pigs each with similar body weights(BW)and fed isonitrogenous diets either without(CON)or with 5%IM(IM5)or 10%IM(IM10)from Tenebrio molitor L.for 4 weeks and key metabolic tissues(liver,muscle,plasma)were analyzed using omics-techniques.Results:Most performance parameters did not differ across the groups,whereas ileal digestibilities of most amino acids were 6.7 to 15.6%-units lower in IM10 than in CON(P<0.05).Transcriptomics of liver and skeletal muscle revealed a total of 166 and 198,respectively,transcripts differentially expressed between IM10 and CON(P<0.05).Plasma metabolomics revealed higher concentrations of alanine,citrulline,glutamate,proline,serine,tyrosine and valine and a lower concentration of asparagine in IM10 than in CON(P<0.05).Only one out of fourteen quantifiable amino acid metabolites,namely methionine sulfoxide(MetS),in plasma was elevated by 45%and 71%in IM5 and IM10,respectively,compared to CON(P<0.05).Plasma concentrations of both,major carnitine/acylcarnitine species and bile acids were not different across groups.Lipidomics of liver and plasma demonstrated no differences in the concentrations of triacylglycerols,cholesterol and the main phospholipids,lysophospholipids and sphingolipids between groups.The percentages of all individual phosphatidylcholine(PC)and phosphatidylethanolamine(PE)species in the liver showed no differences between groups,except those with 6 double bonds(PC 38:6,PC 40:6,PE 38:6,PE 40:6),which were markedly lower in IM10 than in CON(P<0.05).In line with this,the percentage of C22:6n-3 in hepatic total lipids was lower in IM10 than in the other groups(P<0.05).Conclusions:Comprehensive analyzes of the transcriptome,lipidome and metabolome of key metabolic tissues indicate that partial or complete replacement of a conventional protein source by IM in the diet has only a weak impact on the intermediary metabolism of growing pigs.Thus,it is concluded that IM from Tenebrio molitor L.can be used as a dietary source of protein in pigs without causing adverse effects on metabolism.
基金supported by the National Key Research and Development Program of China (2017YFD0101000)the Technology Innovation of Winter Wheat of Science and Technology Planning Project of Hebei Province (16226320D)
文摘Cold tolerance of crop plants influences survival and productivity under low-temperature conditions. Elucidation of molecular mechanisms underlying low temperature tolerance could be helpful in breeding. In this study, we used integrated transcriptomics and metabolomics analyses to investigate changes in gene/metabolite activity in a winter-hardy wheat cultivar of(cv. Jing 411) when subjected to sold stress. The 223 metabolites mainly enriched during cold acclimation included carbohydrates, flavonoids, and amino acids.Eight common metabolites had altered abundance following freezing treatment;six increased and two decreased. Transcriptome analysis revealed that 29,066 genes were differentially expressed in wheat crowns after cold acclimation compared to the nonacclimated control. Among them, 745 genes were up-regulated following freezing treatment, suggesting substantial change in expression of a large quantity of genes upon cold acclimation and freezing treatment, which impacts on the modified metabolites.Integrated analysis of gene expression and metabolite profiles revealed that the abscisic acid(ABA)/jasmonic acid(JA) phytohormone signaling and proline biosynthesis pathways were significantly modulated under cold acclimation and freezing treatments. Our results indicated that low-temperature stress induced substantial changes in both transcriptomes and metabolomes. Critical pathways associated with ABA/JA signaling and proline biosynthesis played important roles in regulating cold tolerance in wheat.
