Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In ...Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In this study,18 CNS strains with high proteolytic activity were isolated from Chinese Dong fermented pork(Nanx Wudl),and their technological and transcriptomic properties were investigated.After biochemical identification and genetic analysis,their technological properties,including nitrate reductase,catalase,antioxidant,and lipolytic activities and their growth under varying temperatures,salt concentrations,and p H levels were evaluated.Their aroma-producing potential was also determined in a model medium resembling fermented sausages.Transcriptomic analysis was performed using the most promising isolates.Biochemical identification and 16S rDNA sequencing revealed that the 18 Staphylococcus strains belonged to Staphylococcus xylosus,Staphylococcus saprophyticus,Staphylococcus carnosus,Staphylococcus sciuri,and Staphylococcus equorum.In terms of technological properties,16 strains showed a nitrate-reducing ability,while 11 strains had a lipolytic activity.All strains exhibited superoxide dismutase(SOD)and catalase activities;four strains displayed an SOD activity of>50%.They also tolerated 10%NaCl and 150 mg/kg of nitrite.They showed significant differences in ketone and acid production.The transcriptomic analysis of S.xylosus strains Sx3 and Sx6,which were selected because of their excellent enzymatic activities and aroma-producing ability,revealed the remarkable effect of genes related to pyruvate catabolism and amino acid metabolism on aroma generation.Therefore,this study provided valuable insights into the metabolic mechanisms underlying the technological properties of CNS and identified promising candidates as starter cultures in fermented sausage manufacturing.展开更多
Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides minin...Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data.In this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences.By functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to longevity.We have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide database.Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is reliable.This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.展开更多
Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 t...Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.展开更多
Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is ...Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.展开更多
The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic an...The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.展开更多
The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of...The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of A. alternata under fludioxonil fungicide stress, the fungus was cultured at the half-maximal effective concentration (EC₅₀) of fludioxonil. Transcriptomic and metabolomic profiles were analyzed using mycelia harvested under these conditions. Comparative analysis revealed 1,001 differentially expressed genes (DEGs) in the resistant strain (RS) relative to the wild-type strain (WT), comprising 628 upregulated and 373 downregulated genes. Concurrently, 524 differentially accumulated metabolites (DAMs) were identified, with 336 upregulated and 188 downregulated metabolites. KEGG pathway enrichment demonstrated pronounced upregulation in glycerophospholipid metabolism, α-linolenic acid metabolism, nucleic acid biosynthesis, and glycosylation processes. Conversely, arachidonic acid and galactose metabolism pathways were suppressed. Significant downregulation was observed in phosphatidylinositol signaling, aflatoxin biosynthesis, and cutin/suberin/wax biosynthesis pathways. Transcriptomic profiling further indicated that upregulated DEGs were predominantly associated with amino sugar/nucleotide sugar metabolism, ABC transporters, aflatoxin biosynthesis, and purine metabolism, while downregulated DEGs were enriched in N-glycan biosynthesis, endoplasmic reticulum protein processing, steroid biosynthesis, and riboflavin metabolism. Fludioxonil exerted substantial inhibitory effects on fungal growth, pathogenicity, and metabolic activity. Mechanistically, A. alternata counteracted fungicide-induced stress through modulation of its antioxidant defense system. This integrative multi-omics study delineates the dynamic gene expression and metabolic reprogramming in A. alternata under fludioxonil exposure, providing novel insights into potential molecular targets and informing the development of next-generation fungicidal strategies for phytopathogen control.展开更多
Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can d...Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can do air-breathing in some bimodal respiration fish.However,there is no comprehensive understanding of these two functions.In this study,the skin regeneration of loach(Paramisgurnus dabryanus)was investigated through morphological and histological observations.Then,original skins(OS)and the regenerated skins(RS)when their capillaries were the most abundant during healing,were collected for transcriptomic analysis.285,899,386 clean reads with a total length of 42.34 Gb were obtained.A total of 1282 differentially expressed genes(DEGs)were detected,including 1030 DEGs up-regulated and 252 DEGs down-regulated in the comparison of RS vs.OS.Fc gamma R-mediated phagocytosis(containing gelsolin(Gsn)),chemokine signaling pathway(containing C-C motif chemokine ligand 28(Ccl28)),and B cell receptor signaling pathway(containing CD80 molecule(Cd81))were closely related to skin immune response of the loach.PI3K-Akt signaling pathway[containing fibronectin 1(Fn1)and lysyl oxidase-like 2b(Loxl2b)],TGF-beta signaling pathway[containing thrombospondin 1(Thbs1)],ECM-receptor interaction[containing integrin alpha 7(Itga7),Itgb8,Itgb10 and Itgb5],and dilated cardiomyopathy[containing laminin subunit alpha1(Lama1)]were closely associated with skin air-breathing of the loach.This study is conducive to explore the molecular mechanisms of skin immune response during its regeneration and air-breathing of bimodal respiration fish.This study will benefit for the aquaculture of P.dabryanus and its related species.展开更多
Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for...Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for these effects have not yet been revealed.Methods:We used network pharmacology and single-cell transcriptomic analysis with molecular docking to elucidate the active components and targets of P.cuspidatum for hepatocellular carcinoma.Results:CDK1,ESR1,HSP90A11,and MAPK1 were shown to be the key targets of P.cuspidatum for hepatocellular carcinoma.P.cuspidatum was found to be likely correlated with the improved abnormal expression of CDK1 and ESR1 and the poor prognosis of HSP90AA1 and MAPK1.CDK1 was identified as the most potential antihepatocellular carcinoma target of P.cuspidatum.Among the active components of P.cuspidatum,physcion diglucoside was found to have the most potential to treat hepatocellular carcinoma by targeting CDK1.Conclusion:Our study provides novel insights into the anti-hepatocellular carcinoma pharmacological effects of P.cuspidatum,which could serve as a scientific basis for its development as a medicinal resource and the targeting of CDK1 for hepatocellular carcinoma treatment.展开更多
RNA sequencing(RNAseq)technology has become increasingly important in precision medicine and clinical diagnostics,and emerged as a powerful tool for identifying protein-coding genes,performing differential gene analys...RNA sequencing(RNAseq)technology has become increasingly important in precision medicine and clinical diagnostics,and emerged as a powerful tool for identifying protein-coding genes,performing differential gene analysis,and inferring immune cell composition.Human peripheral blood samples are widely used for RNAseq,providing valuable insights into individual biomolecular information.Blood samples can be classified as whole blood(WB),plasma,serum,and remaining sediment samples,including plasma-free blood(PFB)and serum-free blood(SFB)samples that are generally considered less useful byproducts during the processes of plasma and serum separation,respectively.However,the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear.In this study,we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis.We performed a comparative analysis of WB,PFB,and SFB samples for different applications.Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns,detection of differentially expressed genes,and immunological characterizations,suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis.Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research.展开更多
Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agricultur...Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.展开更多
tone fruits, also known as drupes, have evolved an extremely hard wood-like shell called a stone to protect the seeds. Recently, the market value of stoneless cultivars has risen dramatically, which highlights the nee...tone fruits, also known as drupes, have evolved an extremely hard wood-like shell called a stone to protect the seeds. Recently, the market value of stoneless cultivars has risen dramatically, which highlights the needto cultivate stoneless fruit. Therefore, determining the underlying mechanism of fruit stone development isurgently needed. By employing the stone-containing jujube cultivar 'Youhe' and two stoneless Chinese jujube cultivars, 'Wuhefeng' and 'Daguowuhe', we comprehensively studied the mechanism of fruit stone development in jujube. Anatomical analysis and lignin staining revealed that the stone cultivar 'Youhe' jujube exhibited much greater lignin accumulation in the endocarp than the two stoneless cultivars. Lignin accumulation may be the key factor in fruit stone formation. By analyzing the transcriptome data and identifying differentially expressed genes(DEGs), 49 overlapping DEGs were identified in the comparisons of 'Youhe' jujube vs. 'Wuhefeng' jujube and 'Youhe' jujube vs. 'Daguowuhe' jujube. ZjF6H1-3 and ZjPOD, which are involved in lignin synthesis, were identified among these DEGs. The overexpression and silencing of ZjF6H1-3 and ZjPOD in wild jujube seedlings further confirmed their roles in lignin synthesis. In addition, two bHLH transcription factors were included in the 49 overlapping DEGs, and bHLH transcription factor binding motifs were found in the promoters of ZjF6H1-3 and ZjPOD, indicating that bHLH transcription factors are also involved in lignin synthesis and stone formation in Chinese jujube. This study provides new insights into the molecular networks underlying fruit stone formation and can serve as an important reference for the molecular design and breeding of stoneless fruit cultivars of jujube and fruit trees.展开更多
Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of...Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of two chrysanthemum genotypes,'Nannonglihuang'(LH,N-efficient genotype)and'Nannongxuefeng"(XF,N-inefficient genotype),under low N(0.4 mmol L^(-1)N)and normal N(8 mmol L^(-1)N)treatments for 15 d and an N recovery treatment for 12 h(low N treatment for 15 d and then normal N treatment for 12 h)to understand the genetic factors impacting NUE in chrysanthemum.The two genotypes exhibited contrasting responses to the different N treatments.The N-efficient genotype LH had significant superiority in agronomic traits,N accumulation and glutamine synthase activity under both normal N and low N treatments.Low N treatment promoted root growth in LH,but inhibited root growth in XF.Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes,genes related to auxin and abscisic acid signal transduction in the roots of both genotypes,as well as genes related to gibberellin signal transduction in roots of LH.The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH.The expression levels of the NRT2.1,AMT1.1,and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments,suggesting that the genes related to N metabolism and hormone(auxin,abscisic acid,gibberellin,and cytokinin)signal transduction in roots of LH are more sensitive to different N treatments than those of XF.Co-expression network analysis(WGCNA)also identified hub genes like bZIP43,bHLH93,NPF6.3,IBR10,MYB62,PP2C,PP2C06 and NLP7,which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype.These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level,which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum,and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes.展开更多
Tetraploid oysters frequently exhibit growth and survival rates inferior to diploid and triploid oysters.Tetraploid Pacific oysters(Crassostrea gigas)are pivotal as broodstock in the triploid C.gigas industry.However,...Tetraploid oysters frequently exhibit growth and survival rates inferior to diploid and triploid oysters.Tetraploid Pacific oysters(Crassostrea gigas)are pivotal as broodstock in the triploid C.gigas industry.However,the high mortality of tetraploid C.gigas has occurred in production practice with the increasing temperature.The transcriptional patterns of high temperature-susceptible and-tolerant tetraploid C.gigas were compared in response to prolonged thermal treatment.The H was defined as oysters that have not been thermally treated.The susceptible and tolerant oysters after thermal treatment were designed as TS and TH,respectively.The survival rate of tetraploid C.gigas was low(6.33%±2.87%)after thermal treatment.A total of 5147,5250,and 433 differentially expressed genes(DEGs)were detected in TS vs.TH,TS vs.H,and TH vs.H groups,respectively.Functional enrichment analysis indicated that DEGs were notably enriched in various pathways,including the NF-kappa B signaling pathway,apoptosis,TNF signaling pathway,and arginine and proline metabolism,across both TS vs.TH and TS vs.H groups.Among the DEGs under thermal treatment in susceptible oysters,the translation regulation genes like eIF2a kinase 1,eIF2a kinase 3,MKNK1,and ATF-4 exhibited differential expressions.Susceptible oysters displayed a higher number of differentially expressed IAP genes compared to tolerant oysters,while the expression pattern of HSP genes differed between susceptible and tolerant oysters.This study underscores the contrasting response of susceptible and tolerant tetraploid C.gigas to thermal treatment,suggesting that high temperature-susceptible tetraploid C.gigas may be more responsive to rapid alterations in immune response and apoptosis compared to high temperature-tolerant tetraploid C.gigas.It is necessary to improve the high temperature tolerance of tetraploid C.gigas by selective breeding to promote the development of the triploid industry.展开更多
Herbivorous insects and pathogens cause severe damage to rice tissues,affecting yield and grain quality.Damaged cells trigger downstream defense responses through various signals.Extracellular ATP(eATP),a signaling mo...Herbivorous insects and pathogens cause severe damage to rice tissues,affecting yield and grain quality.Damaged cells trigger downstream defense responses through various signals.Extracellular ATP(eATP),a signaling molecule released during mechanical cell damage,is considered a constitutive damage-associated molecular pattern(DAMP),which is crucial for initiating plant defense responses.Thus,understanding how rice plants cope with DAMPs such as eATP is essential.Here,we found that exogenous ATP affected rice growth and development,cell wall composition,chloroplast development,and cell death.Subsequent global transcriptome analysis revealed that several pathways were involved in the eATP response,including genes related to cell surface receptors,cell wall organization,chlorophyll biosynthesis,heat and temperature stimulation,epigenetic regulation,and reactive oxygen species metabolism.Cell surface receptors,including members of the lectin receptor-like kinases(LecRKs),were found to participate in the eATP response.We further investigated ATP-induced genes in T-DNA activation mutants of OsLecRKs,demonstrating their involvement in eATP signaling in rice.This study confirms a DAMP-mediated transcriptional response in plants and provides novel candidates for advancing resistant rice breeding against insect herbivores and pathogens.展开更多
Chive(Allium ascalonicum L.),a seeding-vernalization-type vegetable,is prone to bolting.To explore the physiological and molecular mechanisms of its bolting,bolting-prone(‘BA’)and bolting-resistant(‘WA’)chives wer...Chive(Allium ascalonicum L.),a seeding-vernalization-type vegetable,is prone to bolting.To explore the physiological and molecular mechanisms of its bolting,bolting-prone(‘BA’)and bolting-resistant(‘WA’)chives were sampled at the vegetative growth,floral bud differentiation,and bud emergence stages.No bolting was observed in bolting-resistant‘WA’on the 130th day after planting,whereas the bolting reached 39.22%in bolting-prone‘BA’,which was significantly higher than that of‘WA’.The contents of gibberellins,abscisic acid,and zeatin riboside after floral bud differentiation in‘WA’were significantly less than in‘BA’,whereas the indoleacetic acid content in‘WA’was significantly higher than that in‘BA’before and after floral bud differentiation.The soluble sugar content and nitrate reductase activity in‘BA’were significantly higher than those in‘WA’before and during floral bud differentiation periods.However,they were significantly lower in‘BA’compared with in‘WA’after bolting due to the nutrient consumption required by reproductive growth.A transcriptome analysis determined that the differentially expressed genes related to bolting tolerance were enriched in the terms‘photoperiodism,flowering’,‘auxin-activated signaling pathway’,‘gibberellic acid mediated signaling pathway’,and‘carbohydrate metabolic process’,and this was generally consistent with the physiological data.Additionally,12 key differentially expressed genes(including isoform_203018,isoform_481005,isoform_716975,and isoform_564877)related to bolting tolerance were investigated.This research provides new information for breeding bolting-tolerant chives.展开更多
The insect fat body is comparable to the liver and adipose tissue in vertebrates,and plays a pivotal role in energy metabolism,nutrient storage,and reproduction.During metamorphosis,the fat body is disassembled via pr...The insect fat body is comparable to the liver and adipose tissue in vertebrates,and plays a pivotal role in energy metabolism,nutrient storage,and reproduction.During metamorphosis,the fat body is disassembled via programmed cell death and cell dissociation.After adult eclosion,the fat body is reconstructed either by repopulation from the remaining juvenile fat body cells or by differentiation from adult progenitor cells.This reconstruction is a prerequisite for initiating the extensive synthesis of vitellogenin(Vg),which is necessary for the maturation of eggs.Despite its significance,the underlying mechanisms of this reconstruction remain inadequately understood.Transcriptome analysis of the fat bodies from migratory locusts at 0-5 days post adult emergence revealed 79 genes associated with chromatin remodeling.Weighted gene co-expression network analysis indicated a positive correlation between chromatin remodeling and fat body reconstitution.Protein-protein interaction analysis revealed that brahma,which encodes the catalytic subunit of the SWI/SNF chromatin remodeling complex,is crucial for post-adult-eclosion fat body development.qRT-PCR analysis demonstrated that the levels of brahma mRNA in the fat body are progressively increased during the previtellogenic stage,then reach the peak and remain elevated in the vitellogenic phase.Furthermore,brahma is expressed in response to gonadotropic juvenile hormone(JH).Knockdown of brahma led to a marked reduction in Vg expression within the fat body,along with arrested ovarian growth.These findings shed light on the involvement of brahmamediated chromatin remodeling in JH-stimulated fat body reconstruction and reproduction of adult female locusts.展开更多
Wheat stripe rust,a devastating disease caused by the fungal pathogen Puccinia striiformis f.sp.tritici(Pst),poses a significant threat to global wheat production.Growing resistant cultivars is a crucial strategy for ...Wheat stripe rust,a devastating disease caused by the fungal pathogen Puccinia striiformis f.sp.tritici(Pst),poses a significant threat to global wheat production.Growing resistant cultivars is a crucial strategy for wheat stripe rust management.However,the underlying molecular mechanisms of wheat resistance to Pst remain incompletely understood.To unravel these mechanisms,we employed high-throughput RNA sequencing(RNA-Seq)to analyze the transcriptome of the resistant wheat cultivar Mianmai 46(MM46)at different time points(24,48,and 96 h)post-inoculation with the Pst race CYR33.The analysis revealed that Pst infection significantly altered the expression of genes involved in photosynthesis and energy metabolism,suggesting a disruption of host cellular processes.Conversely,the expression of several resistance genes was upregulated,indicating activation of defense responses.Further analysis identified transcription factors(TFs),pathogen-related(PR)proteins,and chitinase-encoding genes as key players in wheat resistance to Pst.These genes likely contribute to the activation of defense pathways,such as the oxidative burst,which involves the production of reactive oxygen species(ROS).The activities of antioxidant enzymes,including peroxidase(POD),superoxide dismutase(SOD),and catalase(CAT),were also upregulated,suggesting a role in mitigating oxidative damage caused by ROS.Our findings provide valuable insights into the molecular mechanisms underlying wheat resistance to Pst.By identifying key genes and pathways involved in this complex interaction,we can develop more effective strategies for breeding resistant wheat cultivars and managing this destructive disease.展开更多
Bistorta vivipara is a facultative reproductive plant capable of asexual reproduction through underground rhizomes and bulbils,as well as sexual reproduction via seeds.The phenomenon of vegetative organ vivipary is a ...Bistorta vivipara is a facultative reproductive plant capable of asexual reproduction through underground rhizomes and bulbils,as well as sexual reproduction via seeds.The phenomenon of vegetative organ vivipary is a complex biological process regulated by a network of genes.However,the developmental mechanism regulating bulbil vivipary in B.vivipara remains largely unexplored.This study investigated different developmental stages of B.vivipara using RNA sequencing and transcriptome analysis.Approximately 438 million high-quality reads were generated,with over 61.65%of the data mapped to the de novo transcriptome sequence.A total of 154,813 reads were matched in at least one public database,and 49,731 genes were differentially expressed across developmental stages.Functional analysis revealed significant enrichment of these genes in phenylpropanoid biosynthesis,plant hormone signal transduction,protein processing,starch and sucrose metabolism,and plant-pathogen interaction.Ninety-four genes involved in phytohormones,plant pigments,enzymes,and transcription factors were identified as potential candidates for inducing vegetative organ vivipary.These differentially expressed genes(DEGs),detected through comparative transcriptome analysis,may serve as candidate genes for bulbil vivipary in B.vivipara,establishing a foundation for future studies on the molecular mechanisms underlying vegetative organ vivipary.展开更多
Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk...Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk genes in the bagworm moth Eumeta variegata,a species that has recently been found to produce extraordinarily strong and tough silk.Using short-read transcriptomic analysis,we identified a partial sequence of the fibroin heavy chain gene and its product was found to have a C-terminal structure that is conserved within nonsaturniid species.This is in accordance with the presence of fibroin light chain/fibrohexamerin genes and it is suggested that the bagworm moth is producing silk composed of fibroin ternary complex.This indicates that the fibroin structure has been evolutionarily conserved longer than previously thought.Other than fibroins we identified candidates for sericin genes,expressed strongly in the middle region of the silk gland and encoding serine-rich proteins,and other silk genes,that are structurally conserved with other lepidopteran homologues.The bagworm moth is thus considered to be producing conventional lepidopteran type of silk.We further found a number of genes expressed in a specific region of the silk gland and some genes showed conserved expression with Bombyx mori counterparts.This is the first study allowing comprehensive silk gene identification and expression analysis in the lepidopteran Psychidae family and should contribute to the understanding of silk gene evolution as well as to the development of novel types of silk.展开更多
Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractil...Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractile properties in the genioglossus. To clarify the role of HIF-lot in contractile properties of the genioglossus, this study generated and compared high-throughput RNA-sequencing data from genioglossus between HIF-1α conditional knockout （KO） mice and littermate wild-type （WT） mice. Methods： KO mice were generated with cre-loxP strategy. Gene expression profile analysis was performed using gene enrichment analysis. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analyses of differently expressed messenger RNAs were performed to identify the related pathways and biological lhnctions. Six differentially expressed genes （DEGs） were validated by qualitative reverse transcription polymerase chain reaction. Results： A total of 142 （77 upregulated and 65 downregulated） transcripts were found to exhibit statistically significant difference between the HIF-la-KO and WT mice. GO and KEGG analyses indicated that DEGs included genes involved in ＂skeletal muscle cell differentiation,＂ ＂muscle organ development,＂ ＂glucose metabolic process,＂ ＂glycogen biosynthetic and metabolic process,＂ etc. Conclusion： This study might provide evidence that H IF-lot affects the expression of multiple genes involved in the myogenesis, muscle developrnent, and carbohydrate metabolism through transcriptome analysis in conditional HIE-1α-KO mice.展开更多
基金the financial support of the National Natural Science Foundation of China(32102016)the Taishan Industrial Experts Program。
文摘Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In this study,18 CNS strains with high proteolytic activity were isolated from Chinese Dong fermented pork(Nanx Wudl),and their technological and transcriptomic properties were investigated.After biochemical identification and genetic analysis,their technological properties,including nitrate reductase,catalase,antioxidant,and lipolytic activities and their growth under varying temperatures,salt concentrations,and p H levels were evaluated.Their aroma-producing potential was also determined in a model medium resembling fermented sausages.Transcriptomic analysis was performed using the most promising isolates.Biochemical identification and 16S rDNA sequencing revealed that the 18 Staphylococcus strains belonged to Staphylococcus xylosus,Staphylococcus saprophyticus,Staphylococcus carnosus,Staphylococcus sciuri,and Staphylococcus equorum.In terms of technological properties,16 strains showed a nitrate-reducing ability,while 11 strains had a lipolytic activity.All strains exhibited superoxide dismutase(SOD)and catalase activities;four strains displayed an SOD activity of>50%.They also tolerated 10%NaCl and 150 mg/kg of nitrite.They showed significant differences in ketone and acid production.The transcriptomic analysis of S.xylosus strains Sx3 and Sx6,which were selected because of their excellent enzymatic activities and aroma-producing ability,revealed the remarkable effect of genes related to pyruvate catabolism and amino acid metabolism on aroma generation.Therefore,this study provided valuable insights into the metabolic mechanisms underlying the technological properties of CNS and identified promising candidates as starter cultures in fermented sausage manufacturing.
基金funded by Shenzhen Science and Technology Innovation Commission(KCXFZ20201221173207022)。
文摘Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data.In this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences.By functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to longevity.We have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide database.Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is reliable.This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.
基金supported by the National Natural Science Foundation of China(Grant No.U23A20204)the“Wanjiang Scholar Program(Anhui Province)”.
文摘Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.
基金supported by the National Key Research and Development Program of China (2018YFD1000702/ 2018YFD1000700)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural SciencesOperating Expenses for Basic Scientific Research of Institute of Crop Science, Chinese Academy of Agricultural Sciences
文摘Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.
文摘The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.
基金supported by the Northeast Asia Biodiversity Research Center(grant number 411147021003).
文摘The predominant causal agent of poplar leaf blight is the pathogenic fungus Alternaria alternata (Fr.) Keissl., which exhibits host specificity toward Populus species. To elucidate the molecular response mechanisms of A. alternata under fludioxonil fungicide stress, the fungus was cultured at the half-maximal effective concentration (EC₅₀) of fludioxonil. Transcriptomic and metabolomic profiles were analyzed using mycelia harvested under these conditions. Comparative analysis revealed 1,001 differentially expressed genes (DEGs) in the resistant strain (RS) relative to the wild-type strain (WT), comprising 628 upregulated and 373 downregulated genes. Concurrently, 524 differentially accumulated metabolites (DAMs) were identified, with 336 upregulated and 188 downregulated metabolites. KEGG pathway enrichment demonstrated pronounced upregulation in glycerophospholipid metabolism, α-linolenic acid metabolism, nucleic acid biosynthesis, and glycosylation processes. Conversely, arachidonic acid and galactose metabolism pathways were suppressed. Significant downregulation was observed in phosphatidylinositol signaling, aflatoxin biosynthesis, and cutin/suberin/wax biosynthesis pathways. Transcriptomic profiling further indicated that upregulated DEGs were predominantly associated with amino sugar/nucleotide sugar metabolism, ABC transporters, aflatoxin biosynthesis, and purine metabolism, while downregulated DEGs were enriched in N-glycan biosynthesis, endoplasmic reticulum protein processing, steroid biosynthesis, and riboflavin metabolism. Fludioxonil exerted substantial inhibitory effects on fungal growth, pathogenicity, and metabolic activity. Mechanistically, A. alternata counteracted fungicide-induced stress through modulation of its antioxidant defense system. This integrative multi-omics study delineates the dynamic gene expression and metabolic reprogramming in A. alternata under fludioxonil exposure, providing novel insights into potential molecular targets and informing the development of next-generation fungicidal strategies for phytopathogen control.
基金supported by the National Natural Science Foundation of China (32172962 and 31872579)the Fundamental Research Funds for the Central Universities of China (Project Number:2662020SCPY002).
文摘Fish skin acts as the first immune barrier against pathogens from external environments.Recently,fish skin immunity research has gradually become a hot topic in aquaculture disease control.Interestingly,the skin can do air-breathing in some bimodal respiration fish.However,there is no comprehensive understanding of these two functions.In this study,the skin regeneration of loach(Paramisgurnus dabryanus)was investigated through morphological and histological observations.Then,original skins(OS)and the regenerated skins(RS)when their capillaries were the most abundant during healing,were collected for transcriptomic analysis.285,899,386 clean reads with a total length of 42.34 Gb were obtained.A total of 1282 differentially expressed genes(DEGs)were detected,including 1030 DEGs up-regulated and 252 DEGs down-regulated in the comparison of RS vs.OS.Fc gamma R-mediated phagocytosis(containing gelsolin(Gsn)),chemokine signaling pathway(containing C-C motif chemokine ligand 28(Ccl28)),and B cell receptor signaling pathway(containing CD80 molecule(Cd81))were closely related to skin immune response of the loach.PI3K-Akt signaling pathway[containing fibronectin 1(Fn1)and lysyl oxidase-like 2b(Loxl2b)],TGF-beta signaling pathway[containing thrombospondin 1(Thbs1)],ECM-receptor interaction[containing integrin alpha 7(Itga7),Itgb8,Itgb10 and Itgb5],and dilated cardiomyopathy[containing laminin subunit alpha1(Lama1)]were closely associated with skin air-breathing of the loach.This study is conducive to explore the molecular mechanisms of skin immune response during its regeneration and air-breathing of bimodal respiration fish.This study will benefit for the aquaculture of P.dabryanus and its related species.
基金Supported by National Training Program of Innovation and Entrepreneurship for Undergraduates(202410145118).
文摘Background and aims:Polygonum cuspidatum Sieb.et Zucc.(P.cuspidatum)and its active components have been clinically proven to have anti-hepatocellular carcinoma effects.However,the potential targets of P.cuspidatum for these effects have not yet been revealed.Methods:We used network pharmacology and single-cell transcriptomic analysis with molecular docking to elucidate the active components and targets of P.cuspidatum for hepatocellular carcinoma.Results:CDK1,ESR1,HSP90A11,and MAPK1 were shown to be the key targets of P.cuspidatum for hepatocellular carcinoma.P.cuspidatum was found to be likely correlated with the improved abnormal expression of CDK1 and ESR1 and the poor prognosis of HSP90AA1 and MAPK1.CDK1 was identified as the most potential antihepatocellular carcinoma target of P.cuspidatum.Among the active components of P.cuspidatum,physcion diglucoside was found to have the most potential to treat hepatocellular carcinoma by targeting CDK1.Conclusion:Our study provides novel insights into the anti-hepatocellular carcinoma pharmacological effects of P.cuspidatum,which could serve as a scientific basis for its development as a medicinal resource and the targeting of CDK1 for hepatocellular carcinoma treatment.
基金supported in part by the National Natural Science Foundation of China(31720103909 and 32170657)the National Key R&D Project of China(2018YFE0201603,2018YFE0201600,and 2021YFF1201305)+2 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)State Key Laboratory of Genetic Engineering(SKLGE-2117)the 111 Project(B13016).
文摘RNA sequencing(RNAseq)technology has become increasingly important in precision medicine and clinical diagnostics,and emerged as a powerful tool for identifying protein-coding genes,performing differential gene analysis,and inferring immune cell composition.Human peripheral blood samples are widely used for RNAseq,providing valuable insights into individual biomolecular information.Blood samples can be classified as whole blood(WB),plasma,serum,and remaining sediment samples,including plasma-free blood(PFB)and serum-free blood(SFB)samples that are generally considered less useful byproducts during the processes of plasma and serum separation,respectively.However,the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear.In this study,we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis.We performed a comparative analysis of WB,PFB,and SFB samples for different applications.Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns,detection of differentially expressed genes,and immunological characterizations,suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis.Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research.
基金Guangxi Science and Technology Base and Talent Special Fund,Project No.AD21220130Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain,Project No.20-065-7Guangxi Institute of Botany Fund,Project No.21014.
文摘Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.
基金supported by the Central Fund for Promoting Innovative Technology Development, China (236Z6801G)the Hebei Provincial Modern Seed Industry Technology Innovation Team-Dried Fruits, China (21326304D)the Construction of Innovative Teams for the Modern Agricultural Industry System in Hebei Province, China (HBCT2023120210, HBCT2024190203)。
文摘tone fruits, also known as drupes, have evolved an extremely hard wood-like shell called a stone to protect the seeds. Recently, the market value of stoneless cultivars has risen dramatically, which highlights the needto cultivate stoneless fruit. Therefore, determining the underlying mechanism of fruit stone development isurgently needed. By employing the stone-containing jujube cultivar 'Youhe' and two stoneless Chinese jujube cultivars, 'Wuhefeng' and 'Daguowuhe', we comprehensively studied the mechanism of fruit stone development in jujube. Anatomical analysis and lignin staining revealed that the stone cultivar 'Youhe' jujube exhibited much greater lignin accumulation in the endocarp than the two stoneless cultivars. Lignin accumulation may be the key factor in fruit stone formation. By analyzing the transcriptome data and identifying differentially expressed genes(DEGs), 49 overlapping DEGs were identified in the comparisons of 'Youhe' jujube vs. 'Wuhefeng' jujube and 'Youhe' jujube vs. 'Daguowuhe' jujube. ZjF6H1-3 and ZjPOD, which are involved in lignin synthesis, were identified among these DEGs. The overexpression and silencing of ZjF6H1-3 and ZjPOD in wild jujube seedlings further confirmed their roles in lignin synthesis. In addition, two bHLH transcription factors were included in the 49 overlapping DEGs, and bHLH transcription factor binding motifs were found in the promoters of ZjF6H1-3 and ZjPOD, indicating that bHLH transcription factors are also involved in lignin synthesis and stone formation in Chinese jujube. This study provides new insights into the molecular networks underlying fruit stone formation and can serve as an important reference for the molecular design and breeding of stoneless fruit cultivars of jujube and fruit trees.
基金supported by the National Key R&D Programof China(2020YFD1000400)the National Natural Science Foundation of China(32072603)+1 种基金the Jiangsu Agriculture Science and Technology Innovation Fund,China(CX(21)2004)the JBGS Project of Seed Industry Revitalization in Jiangsu Province,China(JBGS[2021]020).
文摘Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of two chrysanthemum genotypes,'Nannonglihuang'(LH,N-efficient genotype)and'Nannongxuefeng"(XF,N-inefficient genotype),under low N(0.4 mmol L^(-1)N)and normal N(8 mmol L^(-1)N)treatments for 15 d and an N recovery treatment for 12 h(low N treatment for 15 d and then normal N treatment for 12 h)to understand the genetic factors impacting NUE in chrysanthemum.The two genotypes exhibited contrasting responses to the different N treatments.The N-efficient genotype LH had significant superiority in agronomic traits,N accumulation and glutamine synthase activity under both normal N and low N treatments.Low N treatment promoted root growth in LH,but inhibited root growth in XF.Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes,genes related to auxin and abscisic acid signal transduction in the roots of both genotypes,as well as genes related to gibberellin signal transduction in roots of LH.The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH.The expression levels of the NRT2.1,AMT1.1,and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments,suggesting that the genes related to N metabolism and hormone(auxin,abscisic acid,gibberellin,and cytokinin)signal transduction in roots of LH are more sensitive to different N treatments than those of XF.Co-expression network analysis(WGCNA)also identified hub genes like bZIP43,bHLH93,NPF6.3,IBR10,MYB62,PP2C,PP2C06 and NLP7,which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype.These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level,which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum,and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes.
基金supported by grants from the National Key R&D Program of China(No.2022YFD2400305)the Key R&D Program of Shandong Province(Nos.2022LZ GCQY010,2021ZLGX03 and 2021TSGC1240)the China Agriculture Research System Project(No.CARS-49).
文摘Tetraploid oysters frequently exhibit growth and survival rates inferior to diploid and triploid oysters.Tetraploid Pacific oysters(Crassostrea gigas)are pivotal as broodstock in the triploid C.gigas industry.However,the high mortality of tetraploid C.gigas has occurred in production practice with the increasing temperature.The transcriptional patterns of high temperature-susceptible and-tolerant tetraploid C.gigas were compared in response to prolonged thermal treatment.The H was defined as oysters that have not been thermally treated.The susceptible and tolerant oysters after thermal treatment were designed as TS and TH,respectively.The survival rate of tetraploid C.gigas was low(6.33%±2.87%)after thermal treatment.A total of 5147,5250,and 433 differentially expressed genes(DEGs)were detected in TS vs.TH,TS vs.H,and TH vs.H groups,respectively.Functional enrichment analysis indicated that DEGs were notably enriched in various pathways,including the NF-kappa B signaling pathway,apoptosis,TNF signaling pathway,and arginine and proline metabolism,across both TS vs.TH and TS vs.H groups.Among the DEGs under thermal treatment in susceptible oysters,the translation regulation genes like eIF2a kinase 1,eIF2a kinase 3,MKNK1,and ATF-4 exhibited differential expressions.Susceptible oysters displayed a higher number of differentially expressed IAP genes compared to tolerant oysters,while the expression pattern of HSP genes differed between susceptible and tolerant oysters.This study underscores the contrasting response of susceptible and tolerant tetraploid C.gigas to thermal treatment,suggesting that high temperature-susceptible tetraploid C.gigas may be more responsive to rapid alterations in immune response and apoptosis compared to high temperature-tolerant tetraploid C.gigas.It is necessary to improve the high temperature tolerance of tetraploid C.gigas by selective breeding to promote the development of the triploid industry.
基金supported by the Brain Pool Program funded by the Ministry of Science and Information and Communication Technology through the National Research Foundation of Korea(Grant Nos.2022H1D3A2A01096185 and RS-2024-00410063)the Basic Science Research Program through the National Research Foundation of Korea(Grant No.RS-2023-00247376)+4 种基金the Cooperative Research Program for Agriculture Science and Technology Development,Korea(Grant No.RS-2022-RD010386)US National Science Foundation Plant Genome Program(Grant No.IOS-2048410)the US National Institute of General Medical Sciences of the National Institutes of Health(Grant No.R01GM121445)US Department of Agriculture’s National Institute of Food and Agriculture(Grant No.USDA-AFRI-2023-67013-39896)the National Science Foundation(Grant No.IOS-PGRP-2348319).
文摘Herbivorous insects and pathogens cause severe damage to rice tissues,affecting yield and grain quality.Damaged cells trigger downstream defense responses through various signals.Extracellular ATP(eATP),a signaling molecule released during mechanical cell damage,is considered a constitutive damage-associated molecular pattern(DAMP),which is crucial for initiating plant defense responses.Thus,understanding how rice plants cope with DAMPs such as eATP is essential.Here,we found that exogenous ATP affected rice growth and development,cell wall composition,chloroplast development,and cell death.Subsequent global transcriptome analysis revealed that several pathways were involved in the eATP response,including genes related to cell surface receptors,cell wall organization,chlorophyll biosynthesis,heat and temperature stimulation,epigenetic regulation,and reactive oxygen species metabolism.Cell surface receptors,including members of the lectin receptor-like kinases(LecRKs),were found to participate in the eATP response.We further investigated ATP-induced genes in T-DNA activation mutants of OsLecRKs,demonstrating their involvement in eATP signaling in rice.This study confirms a DAMP-mediated transcriptional response in plants and provides novel candidates for advancing resistant rice breeding against insect herbivores and pathogens.
基金funded by the‘National Key R&D Program Subject of China’(No.2021YFD1100301)the post subsidy project of National Key R&D Program,and the Guizhou Modern Agriculture Research System(GZMARS)-Plateau characteristic vegetable industry.
文摘Chive(Allium ascalonicum L.),a seeding-vernalization-type vegetable,is prone to bolting.To explore the physiological and molecular mechanisms of its bolting,bolting-prone(‘BA’)and bolting-resistant(‘WA’)chives were sampled at the vegetative growth,floral bud differentiation,and bud emergence stages.No bolting was observed in bolting-resistant‘WA’on the 130th day after planting,whereas the bolting reached 39.22%in bolting-prone‘BA’,which was significantly higher than that of‘WA’.The contents of gibberellins,abscisic acid,and zeatin riboside after floral bud differentiation in‘WA’were significantly less than in‘BA’,whereas the indoleacetic acid content in‘WA’was significantly higher than that in‘BA’before and after floral bud differentiation.The soluble sugar content and nitrate reductase activity in‘BA’were significantly higher than those in‘WA’before and during floral bud differentiation periods.However,they were significantly lower in‘BA’compared with in‘WA’after bolting due to the nutrient consumption required by reproductive growth.A transcriptome analysis determined that the differentially expressed genes related to bolting tolerance were enriched in the terms‘photoperiodism,flowering’,‘auxin-activated signaling pathway’,‘gibberellic acid mediated signaling pathway’,and‘carbohydrate metabolic process’,and this was generally consistent with the physiological data.Additionally,12 key differentially expressed genes(including isoform_203018,isoform_481005,isoform_716975,and isoform_564877)related to bolting tolerance were investigated.This research provides new information for breeding bolting-tolerant chives.
基金supported by the National Natural Science Foundation of China(32172389)the Excellent Youth Foundation of Henan Province,China(232300421029)the Key Research and Development Project of Henan Province,China(221111112200)。
文摘The insect fat body is comparable to the liver and adipose tissue in vertebrates,and plays a pivotal role in energy metabolism,nutrient storage,and reproduction.During metamorphosis,the fat body is disassembled via programmed cell death and cell dissociation.After adult eclosion,the fat body is reconstructed either by repopulation from the remaining juvenile fat body cells or by differentiation from adult progenitor cells.This reconstruction is a prerequisite for initiating the extensive synthesis of vitellogenin(Vg),which is necessary for the maturation of eggs.Despite its significance,the underlying mechanisms of this reconstruction remain inadequately understood.Transcriptome analysis of the fat bodies from migratory locusts at 0-5 days post adult emergence revealed 79 genes associated with chromatin remodeling.Weighted gene co-expression network analysis indicated a positive correlation between chromatin remodeling and fat body reconstitution.Protein-protein interaction analysis revealed that brahma,which encodes the catalytic subunit of the SWI/SNF chromatin remodeling complex,is crucial for post-adult-eclosion fat body development.qRT-PCR analysis demonstrated that the levels of brahma mRNA in the fat body are progressively increased during the previtellogenic stage,then reach the peak and remain elevated in the vitellogenic phase.Furthermore,brahma is expressed in response to gonadotropic juvenile hormone(JH).Knockdown of brahma led to a marked reduction in Vg expression within the fat body,along with arrested ovarian growth.These findings shed light on the involvement of brahmamediated chromatin remodeling in JH-stimulated fat body reconstruction and reproduction of adult female locusts.
基金funded by the National Natural Science Foundation of China(32502517)the Open Project Program of State Key Laboratory of Crop Stress Biology for Arid Areas(SKLCSRHPKF20)+1 种基金Collaborative Innovation Project of Department of Education of Anhui Provincial(GXXT-2019-033)Horizontal project-Breeding of high yield and multi resistant wheat varieties(2021122401).
文摘Wheat stripe rust,a devastating disease caused by the fungal pathogen Puccinia striiformis f.sp.tritici(Pst),poses a significant threat to global wheat production.Growing resistant cultivars is a crucial strategy for wheat stripe rust management.However,the underlying molecular mechanisms of wheat resistance to Pst remain incompletely understood.To unravel these mechanisms,we employed high-throughput RNA sequencing(RNA-Seq)to analyze the transcriptome of the resistant wheat cultivar Mianmai 46(MM46)at different time points(24,48,and 96 h)post-inoculation with the Pst race CYR33.The analysis revealed that Pst infection significantly altered the expression of genes involved in photosynthesis and energy metabolism,suggesting a disruption of host cellular processes.Conversely,the expression of several resistance genes was upregulated,indicating activation of defense responses.Further analysis identified transcription factors(TFs),pathogen-related(PR)proteins,and chitinase-encoding genes as key players in wheat resistance to Pst.These genes likely contribute to the activation of defense pathways,such as the oxidative burst,which involves the production of reactive oxygen species(ROS).The activities of antioxidant enzymes,including peroxidase(POD),superoxide dismutase(SOD),and catalase(CAT),were also upregulated,suggesting a role in mitigating oxidative damage caused by ROS.Our findings provide valuable insights into the molecular mechanisms underlying wheat resistance to Pst.By identifying key genes and pathways involved in this complex interaction,we can develop more effective strategies for breeding resistant wheat cultivars and managing this destructive disease.
基金supported by the National Natural Science Foundation of China(31960222)the Qinghai Provincial Major Science and Technology Special Funds(2023-NK-A3).
文摘Bistorta vivipara is a facultative reproductive plant capable of asexual reproduction through underground rhizomes and bulbils,as well as sexual reproduction via seeds.The phenomenon of vegetative organ vivipary is a complex biological process regulated by a network of genes.However,the developmental mechanism regulating bulbil vivipary in B.vivipara remains largely unexplored.This study investigated different developmental stages of B.vivipara using RNA sequencing and transcriptome analysis.Approximately 438 million high-quality reads were generated,with over 61.65%of the data mapped to the de novo transcriptome sequence.A total of 154,813 reads were matched in at least one public database,and 49,731 genes were differentially expressed across developmental stages.Functional analysis revealed significant enrichment of these genes in phenylpropanoid biosynthesis,plant hormone signal transduction,protein processing,starch and sucrose metabolism,and plant-pathogen interaction.Ninety-four genes involved in phytohormones,plant pigments,enzymes,and transcription factors were identified as potential candidates for inducing vegetative organ vivipary.These differentially expressed genes(DEGs),detected through comparative transcriptome analysis,may serve as candidate genes for bulbil vivipary in B.vivipara,establishing a foundation for future studies on the molecular mechanisms underlying vegetative organ vivipary.
基金This work was supported by grants-in-aid from the JST/JICA,SATREPS(Science and Technology Research Partnership for Sustainable Devel Devel opment)and Ministry of Agriculture,Forestry,and Fisheries,Japan.
文摘Lepidopteran insects produce cocoons with unique properties.The cocoons are made of silk produced in the larval tissue silk gland and our understanding of the silk genes is still very limited.Here,we investigated silk genes in the bagworm moth Eumeta variegata,a species that has recently been found to produce extraordinarily strong and tough silk.Using short-read transcriptomic analysis,we identified a partial sequence of the fibroin heavy chain gene and its product was found to have a C-terminal structure that is conserved within nonsaturniid species.This is in accordance with the presence of fibroin light chain/fibrohexamerin genes and it is suggested that the bagworm moth is producing silk composed of fibroin ternary complex.This indicates that the fibroin structure has been evolutionarily conserved longer than previously thought.Other than fibroins we identified candidates for sericin genes,expressed strongly in the middle region of the silk gland and encoding serine-rich proteins,and other silk genes,that are structurally conserved with other lepidopteran homologues.The bagworm moth is thus considered to be producing conventional lepidopteran type of silk.We further found a number of genes expressed in a specific region of the silk gland and some genes showed conserved expression with Bombyx mori counterparts.This is the first study allowing comprehensive silk gene identification and expression analysis in the lepidopteran Psychidae family and should contribute to the understanding of silk gene evolution as well as to the development of novel types of silk.
基金This study was supported by grants from the National Natural Science Foundation of China （No. 81271192 and No. 81600897）, and the Shanghai Science and Technology Committee of China （No. 15140903500）.
文摘Background： Chronic intermittent hypoxia is the most remarkable feature of obstructive sleep apnea/hypopnea syndrome and it can induce the change of hypoxia-inducible factor-1α （H IF-1α） expression and contractile properties in the genioglossus. To clarify the role of HIF-lot in contractile properties of the genioglossus, this study generated and compared high-throughput RNA-sequencing data from genioglossus between HIF-1α conditional knockout （KO） mice and littermate wild-type （WT） mice. Methods： KO mice were generated with cre-loxP strategy. Gene expression profile analysis was performed using gene enrichment analysis. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analyses of differently expressed messenger RNAs were performed to identify the related pathways and biological lhnctions. Six differentially expressed genes （DEGs） were validated by qualitative reverse transcription polymerase chain reaction. Results： A total of 142 （77 upregulated and 65 downregulated） transcripts were found to exhibit statistically significant difference between the HIF-la-KO and WT mice. GO and KEGG analyses indicated that DEGs included genes involved in ＂skeletal muscle cell differentiation,＂ ＂muscle organ development,＂ ＂glucose metabolic process,＂ ＂glycogen biosynthetic and metabolic process,＂ etc. Conclusion： This study might provide evidence that H IF-lot affects the expression of multiple genes involved in the myogenesis, muscle developrnent, and carbohydrate metabolism through transcriptome analysis in conditional HIE-1α-KO mice.
