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
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
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
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
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
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
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
Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied,the gene expression changes in the facial nerve trunk after injury are still unknown.In this study,we...Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied,the gene expression changes in the facial nerve trunk after injury are still unknown.In this study,we established an adult rat model of facial nerve crush injury by compressing the right lateral extracranial nerve trunk.Transcriptome sequencing,differential gene expression analysis,and cluster analysis of the injured facial nerve trunk were performed,and 39 intersecting genes with significant variance in expression were identified.Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the 39 intersecting genes revealed that these genes are mostly involved in leukocyte cell-cell adhesion and phagocytosis and have essential roles in regulating nerve repair.Quantitative real-time polymerase chain reaction assays were used to validate the expression of pivotal genes.Finally,nine pivotal genes that contribute to facial nerve recovery were identified,including Arhgap30,Akr1b8,C5ar1,Csf2ra,Dock2,Hcls1,Inpp5d,Sla,and Spi1.Primary Schwann cells were isolated from the sciatic nerve of neonatal rats.After knocking down Akr1b8 in Schwann cells with an Akr1b8-specific small interfering RNA plasmid,expression levels of monocyte chemoattractant protein-1 and interleukin-6 were decreased,while cell proliferation and migration were not obviously altered.These findings suggest that Akr1b8 likely regulates the interaction between Schwann cells and macrophages through regulation of cytokine expression to promote facial nerve regeneration.This study is the first to reveal a transcriptome change in the facial nerve trunk after facial nerve injury,thereby revealing the potential mechanism underlying repair of facial nerve injury.This study was approved by the Animal Ethics Committee of Nantong University,China in 2018(approval No.S20180923-007).展开更多
Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a na...Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a natural inhibitor of recombinant tissue plasminogen activator,neuroserpin inhibits the increased activity of tissue plasminogen activator in ischemic conditions and extends the therapeutic windows of tissue plasminogen activator for brain ischemia.However,the neuroprotective mechanism of neuroserpin against ischemic stroke remains unclear.In this study,we used a mouse model of middle cerebral artery occlusion and oxygen-glucose deprivation/reperfusion-injured cortical neurons as in vivo and in vitro ischemia-reperfusion models,respectively.The models were used to investigate the neuroprotective effects of neuroserpin.Our findings revealed that endoplasmic reticulum stress was promptly triggered following ischemia,initially manifesting as the acute activation of endoplasmic reticulum stress transmembrane sensors and the suppression of protein synthesis,which was followed by a later apoptotic response.Notably,ischemic stroke markedly downregulated the expression of neuroserpin in cortical neurons.Exogenous neuroserpin reversed the activation of multiple endoplasmic reticulum stress signaling molecules,the reduction in protein synthesis,and the upregulation of apoptotic transcription factors.This led to a reduction in neuronal death induced by oxygen/glucose deprivation and reperfusion,as well as decreased cerebral infarction and neurological dysfunction in mice with middle cerebral artery occlusion.However,the neuroprotective effects of neuroserpin were markedly inhibited by endoplasmic reticulum stress activators thapsigargin and tunicamycin.Our findings demonstrate that neuroserpin exerts neuroprotective effects on ischemic stroke by suppressing endoplasmic reticulum stress.展开更多
The flesh color of oriental melons is an important commercial trait that affects consumer preferences.To explore the mechanisms underlying the flesh color formation and regulation during fruit ripening,carotenoid-targ...The flesh color of oriental melons is an important commercial trait that affects consumer preferences.To explore the mechanisms underlying the flesh color formation and regulation during fruit ripening,carotenoid-targeted metabolomic and RNA-seq analysis were conducted between white-fleshed(WF)and orange-fleshed(OF)oriental melon cultivars at different stages.The carotenoid-targeted metabolomic analysis indicated thatβ-carotene was the major metabolite that caused differences in flesh color between the two cultivars.Additionally,through KEGG pathway enrichment and weighted gene co-expression network(WGCNA)analysis,metabolic pathways and related transcription factors that are associated with carotenoid metabolism were selected and transcriptome data was verified using RT-qPCR.Finally,the yeast one hybrid and luciferase activity showed that the transcription factor CmWRKY49 could directly bind to the CmPSY1 promoter to activate its expression in the’OF’cultivar.Transient overexpression of CmWRKY49 in’OF’cultivar increased theβ-carotene content,while theβ-carotene content decreased when it was silenced in the same cultivar.This study provides insights into the underlying regulatory network of carotenoid metabolism in oriental melon fruit.展开更多
Paris polyphylla Smith var.yunnanensis(Franch.) Hand.-Mazz.is a rhizomatous,herbaceous,perennial plant that has been used for more than a thousand years in traditional Chinese medicine.It is facing extinction due to o...Paris polyphylla Smith var.yunnanensis(Franch.) Hand.-Mazz.is a rhizomatous,herbaceous,perennial plant that has been used for more than a thousand years in traditional Chinese medicine.It is facing extinction due to overharvesting.Steroids are the major therapeutic components in Paris roots,the commercial value of which increases with age.To date,no genomic data on the species have been available.In this study,transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids.Using Illumina sequencing technology,we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information.Approximately 87,577 unique sequences,with an average length of 614 bases,were obtained from the root cells.Using bioinformatics methods,we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database.The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database.Of 3082 genes that were identified as significantly differentially expressed between roots of different ages,1518(49.25%) were upregulated and 1564(50.75%) were downregulated in the older root.Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids.These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P.polyphylla and facilitate saponin-rich plant development.展开更多
Close planting of dwarf varieties is currently the main cultivation direction for pear trees,and the screening of excellent dwarf varieties is an important goal for breeders.In this study,the dwarfing pear variety‘6...Close planting of dwarf varieties is currently the main cultivation direction for pear trees,and the screening of excellent dwarf varieties is an important goal for breeders.In this study,the dwarfing pear variety‘601D’and its vigorous mutant‘601T’were used to show their biological characteristics and further explore the dwarfing mechanism in‘601D’.The biological characteristics showed that‘601D’had a shorter internode length,a shorter and more compact tree body,thicker and broader leaves,lower stomata density,larger stomata size(dimension),and higher photosynthetic capacity.The biological characteristics of‘601T’showed notable contrasts.The results of endogenous hormone tests indicated that the contents of abscisic acid(ABA),ABA-glucosyl ester,and GA_(4) were higher in‘601D’,but the trans-zeatin content was lower.By transcriptomic analysis,significant differences were found in the biosynthetic and metabolic pathways of ABA.Related transcription factors such as bHLH,WRKY,and homeobox also participated in the regulation of plant dwarfing.We therefore examined three hormones with obvious differences with‘601T’,and found that only ABA could induce‘601T’to return to a dwarfing plant phenotype.Therefore,we conclude that the dwarfing of‘601D’is caused by an excessive accumulation of ABA.This study provides a new theoretical basis for breeding dwarf varieties.展开更多
Ayu （Plecoglossus altivelis） fish, which are an amphidromous species distributed in East Asia, live in brackish water （BW） during their larval stage and in fresh water （FW） during their adult stage. In this stud...Ayu （Plecoglossus altivelis） fish, which are an amphidromous species distributed in East Asia, live in brackish water （BW） during their larval stage and in fresh water （FW） during their adult stage. In this study, we found that FW-acclimated ayu larvae exhibited a slower growth ratio compared with that of BW-acclimated larvae. However, the mechanism underlying FW acclimation on growth suppression is poorly known. We employed transcriptome analysis to investigate the differential gene expression of FW acclimation by RNA sequencing. We identified 158 upregulated and 139 downregulated transcripts in FW-acclimated ayu larvae compared with that in BW-acclimated larvae. As determined by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway mapping, functional annotation of the genes covered diverse biological functions and processes, and included neuroendo- crinology, osmotic regulation, energy metabolism, and the cytoskeleton. Transcriptional expression of several differentially expressed genes in response to FW acclimation was further confirmed by real-time quantitative PCR. In accordance with transcriptome analysis, iodothyronine deiodinase （ID）, pro-opiom- elanocortin （POMC）, betaine-homocysteine S-meth- yltransferase 1 （BHMT）, fructose-bisphosphate aldolase B （aldolase B）, tyrosine aminotransferase （TAT）, and Na＋-K＋ ATPase （NKA） were upregulated after FW acclimation. Furthermore, the mRNA expressions of b-type natriurefic peptide （BNP） and transgelin were downregulated after FW acclimation. Our data indicate that FW acclimation reduced the growth rate of ayu larvae, which might result from the expression alteration of genes related to endocrine hormones, energy metabolism, and direct osmoregulation.展开更多
Toxoplasma gondii is a worldwide parasite that can infect almost all kinds of mammals and cause fatal toxoplasmosis in immunocompromised patients.Apoptosis is one of the principal strategies of host cells to clear pat...Toxoplasma gondii is a worldwide parasite that can infect almost all kinds of mammals and cause fatal toxoplasmosis in immunocompromised patients.Apoptosis is one of the principal strategies of host cells to clear pathogens and maintain organismal homeostasis,but the mechanism of cell apoptosis induced by T.gondii remains obscure.To explore the apoptosis influenced by T.gondii,Vero cells infected or uninfected with the parasite were subjected to apoptosis detection and subsequent dual RNA sequencing(RNA-seq).Using high-throughput Illumina sequencing and bioinformatics analysis,we found that pro-apoptosis genes such as DNA damage-inducible transcript 3(DDIT3),growth arrest and DNA damage-inducibleα(GADD45 A),caspase-3(CASP3),and high-temperature requirement protease A2(Htr A2)were upregulated,and anti-apoptosis genes such as poly(adenosine diphosphate(ADP)-ribose)polymerase family member 3(PARP3),B-cell lymphoma 2(Bcl-2),and baculoviral inhibitor of apoptosis protein(IAP)repeat containing 5(BIRC5)were downregulated.Besides,tumor necrosis factor(TNF)receptor-associated factor 1(TRAF1),TRAF2,TNF receptor superfamily member 10 b(TNFRSF10 b),disabled homolog2(DAB2)-interacting protein(DAB2 IP),and inositol 1,4,5-trisphosphate receptor type 3(ITPR3)were enriched in the upstream of TNF,TNF-related apoptosis-inducing ligand(TRAIL),and endoplasmic reticulum(ER)stress pathways,and TRAIL-receptor2(TRAIL-R2)was regarded as an important membrane receptor influenced by T.gondii that had not been previously considered.In conclusion,the T.gondii RH strain could promote and mediate apoptosis through multiple pathways mentioned above in Vero cells.Our findings improve the understanding of the T.gondii infection process through providing new insights into the related cellular apoptosis mechanisms.展开更多
Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been in...Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated.Here,the profiling of PA,(+)-catechin and(–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed.The levels of total PAs and catechin exhibited a decreased trend over jujube ripening,and epicatechin content of two jujube cultivars increased first and then declined.Transcriptome analysis revealed that the differentially expressed genes(DEGs)were mainly enriched in ribosome,glycolysis/gluconeogenesis,fructose and mannose metabolism.17 DEGs encoding PAL,CHS,CHI,CHS,F3'H,LAR,ANR,C4Hs,4CLs,FLSs,DFRs and UFGTs involved in PA biosynthesis were relatively abundant.The highly transcribed LAR gene may greatly contribute to epicatechin accumulation.A weighted gene co-expression network analysis(WGCNA)was performed,and a network module including 1620 genes highly correlated with content of Pas and catechin was established.We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module.Sixteen genes encoding 9 families of transcriptional factors(i.e.,MYB,bHLH,ERF,bZIP,NAC,SBP,MIKC,HB,WRKY)were considered as hub genes.The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data.These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.展开更多
In fruit production,the application of the plant growth regulator 1-(2-chloro-4-pyridyl)-3-phenylurea(CPPU)dulls the fruit aroma.Gas chromatography-mass spectrometry and transcriptome analyses were performed on CPPU-t...In fruit production,the application of the plant growth regulator 1-(2-chloro-4-pyridyl)-3-phenylurea(CPPU)dulls the fruit aroma.Gas chromatography-mass spectrometry and transcriptome analyses were performed on CPPU-treated and pollinated fruits to determine how CPPU affects the production of aroma in melon fruit.The results showed that the contents of two important esters(benzyl acetate and phenethyl acetate)in the CPPU-treated fruits were significantly lower than those in the pollinated fruits.Transcriptome sequencing data revealed that most differentially expressed genes were involved in“phenylalanine metabolism”pathway,and their expression was significantly decreased in the CPPU-treated fruits.Further analysis showed that the phenylalanine content in the CPPU-treated fruits was significantly higher than that in the pollinated fruits.In summary,CPPU application interferes with phenylalanine metabolism in melon fruits and affects the production of aromatic esters.展开更多
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 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 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.
文摘Although the transcriptional alterations inside the facial nucleus after facial nerve injury have been well studied,the gene expression changes in the facial nerve trunk after injury are still unknown.In this study,we established an adult rat model of facial nerve crush injury by compressing the right lateral extracranial nerve trunk.Transcriptome sequencing,differential gene expression analysis,and cluster analysis of the injured facial nerve trunk were performed,and 39 intersecting genes with significant variance in expression were identified.Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the 39 intersecting genes revealed that these genes are mostly involved in leukocyte cell-cell adhesion and phagocytosis and have essential roles in regulating nerve repair.Quantitative real-time polymerase chain reaction assays were used to validate the expression of pivotal genes.Finally,nine pivotal genes that contribute to facial nerve recovery were identified,including Arhgap30,Akr1b8,C5ar1,Csf2ra,Dock2,Hcls1,Inpp5d,Sla,and Spi1.Primary Schwann cells were isolated from the sciatic nerve of neonatal rats.After knocking down Akr1b8 in Schwann cells with an Akr1b8-specific small interfering RNA plasmid,expression levels of monocyte chemoattractant protein-1 and interleukin-6 were decreased,while cell proliferation and migration were not obviously altered.These findings suggest that Akr1b8 likely regulates the interaction between Schwann cells and macrophages through regulation of cytokine expression to promote facial nerve regeneration.This study is the first to reveal a transcriptome change in the facial nerve trunk after facial nerve injury,thereby revealing the potential mechanism underlying repair of facial nerve injury.This study was approved by the Animal Ethics Committee of Nantong University,China in 2018(approval No.S20180923-007).
基金supported in part by the National Key Research&Development Program of China,No.2022YFA1104900(to LS)the National Natural Science Foundation of China,Nos.82371175,82071535(both to LS),82101614(to YP)+5 种基金the International Science and Technology Cooperation Projects of Guangdong Province,No.2023A0505050121(to LS)Guangdong Basic and Applied Basic Research Foundation,Nos.2022B1515130007(to LS),2023A1515030012(to SZ),2022A1515010666(to WL)the Science and Technology Program of Guangzhou,Nos.202102070001(to LS),202201010041(to YP)Shenzhen Basic Research Grant,Nos.JCYJ20200109140414636,JCYJ20230807145103007(both to WL)awarded a Royal Society Newton Advanced Fellowship,No.AOMS-NAF0051003in collaboration with Zoltán Molnár,Department of Physiology,Anatomy and Genetics,University of Oxford(2017–2021)。
文摘Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a natural inhibitor of recombinant tissue plasminogen activator,neuroserpin inhibits the increased activity of tissue plasminogen activator in ischemic conditions and extends the therapeutic windows of tissue plasminogen activator for brain ischemia.However,the neuroprotective mechanism of neuroserpin against ischemic stroke remains unclear.In this study,we used a mouse model of middle cerebral artery occlusion and oxygen-glucose deprivation/reperfusion-injured cortical neurons as in vivo and in vitro ischemia-reperfusion models,respectively.The models were used to investigate the neuroprotective effects of neuroserpin.Our findings revealed that endoplasmic reticulum stress was promptly triggered following ischemia,initially manifesting as the acute activation of endoplasmic reticulum stress transmembrane sensors and the suppression of protein synthesis,which was followed by a later apoptotic response.Notably,ischemic stroke markedly downregulated the expression of neuroserpin in cortical neurons.Exogenous neuroserpin reversed the activation of multiple endoplasmic reticulum stress signaling molecules,the reduction in protein synthesis,and the upregulation of apoptotic transcription factors.This led to a reduction in neuronal death induced by oxygen/glucose deprivation and reperfusion,as well as decreased cerebral infarction and neurological dysfunction in mice with middle cerebral artery occlusion.However,the neuroprotective effects of neuroserpin were markedly inhibited by endoplasmic reticulum stress activators thapsigargin and tunicamycin.Our findings demonstrate that neuroserpin exerts neuroprotective effects on ischemic stroke by suppressing endoplasmic reticulum stress.
基金supported by China Agriculture Research System of MOF and MARA(Grant No.CARS-25).
文摘The flesh color of oriental melons is an important commercial trait that affects consumer preferences.To explore the mechanisms underlying the flesh color formation and regulation during fruit ripening,carotenoid-targeted metabolomic and RNA-seq analysis were conducted between white-fleshed(WF)and orange-fleshed(OF)oriental melon cultivars at different stages.The carotenoid-targeted metabolomic analysis indicated thatβ-carotene was the major metabolite that caused differences in flesh color between the two cultivars.Additionally,through KEGG pathway enrichment and weighted gene co-expression network(WGCNA)analysis,metabolic pathways and related transcription factors that are associated with carotenoid metabolism were selected and transcriptome data was verified using RT-qPCR.Finally,the yeast one hybrid and luciferase activity showed that the transcription factor CmWRKY49 could directly bind to the CmPSY1 promoter to activate its expression in the’OF’cultivar.Transient overexpression of CmWRKY49 in’OF’cultivar increased theβ-carotene content,while theβ-carotene content decreased when it was silenced in the same cultivar.This study provides insights into the underlying regulatory network of carotenoid metabolism in oriental melon fruit.
基金supported by the National Natural Science Foundation of China(81473310,31260075,31560085)
文摘Paris polyphylla Smith var.yunnanensis(Franch.) Hand.-Mazz.is a rhizomatous,herbaceous,perennial plant that has been used for more than a thousand years in traditional Chinese medicine.It is facing extinction due to overharvesting.Steroids are the major therapeutic components in Paris roots,the commercial value of which increases with age.To date,no genomic data on the species have been available.In this study,transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids.Using Illumina sequencing technology,we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information.Approximately 87,577 unique sequences,with an average length of 614 bases,were obtained from the root cells.Using bioinformatics methods,we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database.The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database.Of 3082 genes that were identified as significantly differentially expressed between roots of different ages,1518(49.25%) were upregulated and 1564(50.75%) were downregulated in the older root.Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids.These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P.polyphylla and facilitate saponin-rich plant development.
基金funded by the National Key Research and Development Program of China(2018YFD1000100)the Agricultural Improved Variety Project Program of Shandong Province,China(2019LZGC008)the National Key Research and Development Program of China(2019YFD1001404-3)。
文摘Close planting of dwarf varieties is currently the main cultivation direction for pear trees,and the screening of excellent dwarf varieties is an important goal for breeders.In this study,the dwarfing pear variety‘601D’and its vigorous mutant‘601T’were used to show their biological characteristics and further explore the dwarfing mechanism in‘601D’.The biological characteristics showed that‘601D’had a shorter internode length,a shorter and more compact tree body,thicker and broader leaves,lower stomata density,larger stomata size(dimension),and higher photosynthetic capacity.The biological characteristics of‘601T’showed notable contrasts.The results of endogenous hormone tests indicated that the contents of abscisic acid(ABA),ABA-glucosyl ester,and GA_(4) were higher in‘601D’,but the trans-zeatin content was lower.By transcriptomic analysis,significant differences were found in the biosynthetic and metabolic pathways of ABA.Related transcription factors such as bHLH,WRKY,and homeobox also participated in the regulation of plant dwarfing.We therefore examined three hormones with obvious differences with‘601T’,and found that only ABA could induce‘601T’to return to a dwarfing plant phenotype.Therefore,we conclude that the dwarfing of‘601D’is caused by an excessive accumulation of ABA.This study provides a new theoretical basis for breeding dwarf varieties.
基金Foundation items： The project was supported by the Program for the National Natural Science Foundation of China （31201970） and the KC Wong Magna Fund in Ningbo University
文摘Ayu （Plecoglossus altivelis） fish, which are an amphidromous species distributed in East Asia, live in brackish water （BW） during their larval stage and in fresh water （FW） during their adult stage. In this study, we found that FW-acclimated ayu larvae exhibited a slower growth ratio compared with that of BW-acclimated larvae. However, the mechanism underlying FW acclimation on growth suppression is poorly known. We employed transcriptome analysis to investigate the differential gene expression of FW acclimation by RNA sequencing. We identified 158 upregulated and 139 downregulated transcripts in FW-acclimated ayu larvae compared with that in BW-acclimated larvae. As determined by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway mapping, functional annotation of the genes covered diverse biological functions and processes, and included neuroendo- crinology, osmotic regulation, energy metabolism, and the cytoskeleton. Transcriptional expression of several differentially expressed genes in response to FW acclimation was further confirmed by real-time quantitative PCR. In accordance with transcriptome analysis, iodothyronine deiodinase （ID）, pro-opiom- elanocortin （POMC）, betaine-homocysteine S-meth- yltransferase 1 （BHMT）, fructose-bisphosphate aldolase B （aldolase B）, tyrosine aminotransferase （TAT）, and Na＋-K＋ ATPase （NKA） were upregulated after FW acclimation. Furthermore, the mRNA expressions of b-type natriurefic peptide （BNP） and transgelin were downregulated after FW acclimation. Our data indicate that FW acclimation reduced the growth rate of ayu larvae, which might result from the expression alteration of genes related to endocrine hormones, energy metabolism, and direct osmoregulation.
基金supported by the National Natural Science Foundation of China(Nos.81802037,81871684)the Qingshan Lake United Fund of Zhejiang Province(No.LQY19H190002)+2 种基金the Zhejiang Provincial Natural Science Foundation of China(No.LY22H190003)the Zhejiang Provincial Program for the Cultivation of High-level Innovative Health Talentsthe Basic Scientific Research Funds of Department of Education of Zhejiang Province(Nos.KYZD202104 and KYYB202101),China。
文摘Toxoplasma gondii is a worldwide parasite that can infect almost all kinds of mammals and cause fatal toxoplasmosis in immunocompromised patients.Apoptosis is one of the principal strategies of host cells to clear pathogens and maintain organismal homeostasis,but the mechanism of cell apoptosis induced by T.gondii remains obscure.To explore the apoptosis influenced by T.gondii,Vero cells infected or uninfected with the parasite were subjected to apoptosis detection and subsequent dual RNA sequencing(RNA-seq).Using high-throughput Illumina sequencing and bioinformatics analysis,we found that pro-apoptosis genes such as DNA damage-inducible transcript 3(DDIT3),growth arrest and DNA damage-inducibleα(GADD45 A),caspase-3(CASP3),and high-temperature requirement protease A2(Htr A2)were upregulated,and anti-apoptosis genes such as poly(adenosine diphosphate(ADP)-ribose)polymerase family member 3(PARP3),B-cell lymphoma 2(Bcl-2),and baculoviral inhibitor of apoptosis protein(IAP)repeat containing 5(BIRC5)were downregulated.Besides,tumor necrosis factor(TNF)receptor-associated factor 1(TRAF1),TRAF2,TNF receptor superfamily member 10 b(TNFRSF10 b),disabled homolog2(DAB2)-interacting protein(DAB2 IP),and inositol 1,4,5-trisphosphate receptor type 3(ITPR3)were enriched in the upstream of TNF,TNF-related apoptosis-inducing ligand(TRAIL),and endoplasmic reticulum(ER)stress pathways,and TRAIL-receptor2(TRAIL-R2)was regarded as an important membrane receptor influenced by T.gondii that had not been previously considered.In conclusion,the T.gondii RH strain could promote and mediate apoptosis through multiple pathways mentioned above in Vero cells.Our findings improve the understanding of the T.gondii infection process through providing new insights into the related cellular apoptosis mechanisms.
基金supported by Major scientific and technological projects of Xinjiang Production and Construction Corps(2017DB006 and 2020KWZ-012)。
文摘Proanthocyanidin(PA)is an important bioactive compound with multiple physiological benefits in jujube(Ziziphus jujube Mill.).However,the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated.Here,the profiling of PA,(+)-catechin and(–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed.The levels of total PAs and catechin exhibited a decreased trend over jujube ripening,and epicatechin content of two jujube cultivars increased first and then declined.Transcriptome analysis revealed that the differentially expressed genes(DEGs)were mainly enriched in ribosome,glycolysis/gluconeogenesis,fructose and mannose metabolism.17 DEGs encoding PAL,CHS,CHI,CHS,F3'H,LAR,ANR,C4Hs,4CLs,FLSs,DFRs and UFGTs involved in PA biosynthesis were relatively abundant.The highly transcribed LAR gene may greatly contribute to epicatechin accumulation.A weighted gene co-expression network analysis(WGCNA)was performed,and a network module including 1620 genes highly correlated with content of Pas and catechin was established.We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module.Sixteen genes encoding 9 families of transcriptional factors(i.e.,MYB,bHLH,ERF,bZIP,NAC,SBP,MIKC,HB,WRKY)were considered as hub genes.The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data.These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.
基金the China Agriculture Research System of MOF and MARA(CARS-25)the Special Fund for Agro-scientific Research in the Public Interest,China(201203080)+1 种基金the Fundamental Research Funds for the Central Universities,China(2662018PY039)the Hubei Provincial Natural Science Foundation of China(2019CFA017).
文摘In fruit production,the application of the plant growth regulator 1-(2-chloro-4-pyridyl)-3-phenylurea(CPPU)dulls the fruit aroma.Gas chromatography-mass spectrometry and transcriptome analyses were performed on CPPU-treated and pollinated fruits to determine how CPPU affects the production of aroma in melon fruit.The results showed that the contents of two important esters(benzyl acetate and phenethyl acetate)in the CPPU-treated fruits were significantly lower than those in the pollinated fruits.Transcriptome sequencing data revealed that most differentially expressed genes were involved in“phenylalanine metabolism”pathway,and their expression was significantly decreased in the CPPU-treated fruits.Further analysis showed that the phenylalanine content in the CPPU-treated fruits was significantly higher than that in the pollinated fruits.In summary,CPPU application interferes with phenylalanine metabolism in melon fruits and affects the production of aromatic esters.
