For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism resp...For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.展开更多
Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilienc...Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilience through cross-generation plasticity.In this study,we analyzed larval growth and transcriptomic profiles in the Pacific oyster,Crassostrea gigas,a species of significant ecological relevance,under both control and elevated CO_(2)conditions experienced by their parental generation.Our findings indicate that the oyster populations exposed to OA exhibited a higher incidence of abnormalities during the D-shaped larval stage,followed by accelerated growth at the eyed stage.Through a comparative transcriptomic investigation of eyed larvae(25 d after fertilization),we observed that parental exposure to OA substantially influenced the gene expression in the offspring.Genes associated with lipid catabolism and shell formation were notably upregulated in oysters with parental OA exposure,potentially playing a role in cross-generational conditioning and conferring resilience to OA stressors.These results underscore the profound impact of OA on oyster larval development via cross-generational mechanisms and shed light on the molecular underpinnings of cross-generation plasticity.展开更多
This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.s...This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.展开更多
Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conve...Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.展开更多
Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile fla...Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile flavors of tomatoes is still not clear.Here,we integrated the metabolome and transcriptome of the volatile flavors in tomato fruit to explore the regulatory mechanism of volatile flavor formation,using wild and cultivated tomatoes with significant differences in flavors.A total of 35 volatile flavor compounds were identified,based on the solid phase microextraction-gas chromatography-mass spectrometry(SPME-GC-MS).The content of the volatiles,affecting fruit flavor,significantly increased in the transition from breaker to red ripe fruit stage.Moreover,the total content of the volatiles in wild tomatoes was much higher than that in the cultivated tomatoes.The content variations of all volatile flavors were clustered into 10 groups by hierarchical cluster and Pearson coefficient correlation(PCC)analysis.The fruit transcriptome was also patterned into 10 groups,with significant variations both from the mature green to breaker fruit stage and from the breaker to red ripe fruit stage.Combining the metabolome and the transcriptome of the same developmental stage of fruits by co-expression analysis,we found that the expression level of 1182 genes was highly correlated with the content of volatile flavor compounds,thereby constructing two regulatory pathways of important volatile flavors.One pathway is tetrahydrothiazolidine N-hydroxylase(SlTNH1)-dependent,which is regulated by two transcription factors(TFs)from the bHLH and AP2/ERF families,controlling the synthesis of 2-isobutylthiazole in amino acid metabolism.The other is lipoxygenase(Sl LOX)-dependent,which is regulated by one TF from the HD-Zip family,controlling the synthesis of hexanal and(Z)-2-heptenal in fatty acid metabolism.Dual-luciferase assay confirmed the binding of b HLH and AP2/ERF to their structural genes.The findings of this study provide new insights into volatile flavor formation in tomato fruit,which can be useful for tomato flavor improvement.展开更多
Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(...Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(qRT-PCR)is a powerful tool for gene expression analysis.The accuracy of qRT-PCR results largely depends on suitable reference genes.In this study,a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets,comprising 200 tissue samples,107 treated samples,and 140 samples from various moso bamboo(Phyllostachys edulis)forms.A total of 3444,1013,and 3962 stably expressed genes were identified from these three groups,respectively.Functional enrichment analysis revealed significant enrichment of these genes in pathways,including the spliceosome,proteasome,and oxidative phosphorylation.Eight candidate genes(ADPRE,GAPDH,TRX,TUBA,NRP,MBF,UNK,and CAM1),were selected for qRT-PCR validation using 112 samples.To assess their stability,five statistical methods(geNorm,NormFinder,BestKeeper,Delta-Ct,and RefFinder)were employed.The most suitable reference genes were ADPRE and GAPDH for different tissues,GAPDH and CAM1 for different treatments,and GAPDH and TRX for various moso bamboo forms.Overall,ADPRE and GAPDH were the most stable reference genes across all conditions,while TUBA and TRX were the least stable reference genes.In addition,a significant negative correlation was found between the Ct values of RT-qPCR and the log2TPM values from the transcriptome data(Ct=-1.534x+37.221),providing a potential method for estimating gene expression levels.The identified reference genes,particularly ADPRE and GAPDH,provide a robust set of references for gene expression studies in moso bamboo.展开更多
Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes h...Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.展开更多
Nanoplastics(less than 1µm in size,NPs)have emerged as a significant pollutant in aquatic environment,posing considerable threats to freshwater biota.However,the mechanisms through which NPs modulate the predatio...Nanoplastics(less than 1µm in size,NPs)have emerged as a significant pollutant in aquatic environment,posing considerable threats to freshwater biota.However,the mechanisms through which NPs modulate the predation responses of these organisms remain poorly elucidated.We investigated the impacts of polystyrene NPs,characterized by a representative particle size(diameter:50 nm;concentration:0–8μg/L),on the anti-predation defense mechanisms of mature rotifer Brachionus calyciflorus against predator of rotifer Asplanchna brightwellii,utilizing transcriptomics to unravel the underlying molecular pathways.Results reveal that the posterolateral spine length and type of B.calyciflorus serve as robust indicators of defensive morphology,even in the presence of NPs exposure.Specifically,increasing concentrations of NPs and predator cues suppressed the defensive responses,which was associated with morphological transformations.This suppression was associated with the down-regulation of the HIF-1αsignaling pathway,implicating potentially its role in modulating fight-or-flight responses.Furthermore,we identified functional crosstalk among multiple signaling pathways,including HIF-1α,PI3K-Akt,FoxO,and mTOR,in B.calyciflorus,which may underpin the organism's responses to polystyrene NP exposure.These findings contribute to the advancement of predictive models to assess the ecological risks posed by polystyrene NPs contamination in aquatic ecosystems.展开更多
Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the...Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the changes in the morphology,transcriptome,and proteome of gill tissue in yellowfin seabream infected with C.irritans,aiming to provide foundational data for further understanding the pathogenic mechanisms and control measures against this parasite.The main findings were as follows,after C.irritans infection,the structure of gill tissue in yellowfin seabream was damaged,with microvessels ruptured,some cells proliferating,and large amounts of mucus infiltrating.Transcriptome analysis revealed a total of 4299 differentially expressed genes,with 2367 up-regulated and 1932down-regulated.Further bioinformatics analysis of all differentially expressed genes identified nine immune-related genes,cox-2,mcama,tbx21,dcn,tnfb,cd74a,illb,ppib,and cd4-1 in A.latus.The reliability of the transcriptome data was validated by real time q PCR,which showed the same trend as the RNA-seq results.Proteome analysis found365 differential proteins,with 180 proteins up-regulated and 185 proteins down-regulated.Bioinformatics analysis identified three immune-related proteins,Myll,Gapdh,and Actn3b.These findings indicated that C.irritans disrupted the structure of gill tissue,impeded gas exchange and led to asphyxiation and death in affected fish.Transcriptome and proteome analyses showed that the expression of immune-related genes and proteins in yellowfin seabream,involved not only inflammatory responses and the activation and migration of immune cells but also potentially participated in tissue repair and defense regulation.These findings highlighted the complex immune regulatory network in response to C.irritans infection,offering references for prevention and control of white spot disease in yellowfin seabream.展开更多
Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perch...Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perchlorate on aquatic autotrophs such cyanobacterium are still unclear.Herein,Synechocystis sp.PCC6803(Synechocystis)was used to investigate the response mechanisms of perchlorate on cyanobacterium by integrating physiological and transcriptome analyses.Physiological results showed that perchlorate mainly damaged the photosystem of Synechocystis,and the inhibition degree of photosystem II(PSII)was severer than that of photosystem I(PSI).When the exposed cells were moved to a clean medium,the photosynthetic activities were slightly repaired but still lower than in the control group,indicating irreversible damage.Furthermore,perchlorate also destroyed the cellular ultrastructure and induced oxidative stress in Synechocystis.The antioxidant glutathione(GSH)content and the superoxide dismutase(SOD)enzyme activity were enhanced to scavenge harmful reactive oxygen(ROS)in Synechocystis.Transcriptome analysis revealed that the genes associated with“photosynthesis”and“electron transport”were significantly regulated.For instance,most genes related to PSI(e.g.,psaf,psaJ)and the“electron transport chain”were upregulated,whereas most genes related to PSII(e.g.,psbA3,psbD1,psbB,and psbC)were downregulated.Additionally,perchlorate also induced the expression of genes related to the antioxidant system(sod2,gpx,gst,katG,and gshB)to reduce oxidative damage.Overall,this study is the first to investigate the impacts andmechanisms of cyanobacterium under perchlorate stress,which is conducive to assessing the risk of perchlorate in aquatic environments.展开更多
Watermelon(Citrullus lanatus)is an economically important horticultural crop.However,it is susceptible to lowtemperature stress,which significantly challenges its production and supply.Despite the great economic impor...Watermelon(Citrullus lanatus)is an economically important horticultural crop.However,it is susceptible to lowtemperature stress,which significantly challenges its production and supply.Despite the great economic importance of watermelon,little is known about its response to low-temperature stress at the transcriptional level.In this study,we performed a time-course transcriptome analysis to systematically investigate the regulatory network of watermelon under low-temperature stress.Six low-temperature-responsive gene clusters representing six expression patterns were identified,revealing diverse regulation of metabolic pathways in watermelon under lowtemperature stress.Analysis of temporally specific differentially expressed genes revealed the time-dependent nature of the watermelon response to low temperature.Moreover,ClMYB14 was found to be a negative regulator of low-temperature tolerance as ClMYB14-OE lines were more susceptible to low-temperature stress.Co-expression network analysis demonstrated that ClMYB14 participates in the low-temperature response by regulating the unsaturated fatty acid pathway and heat shock transcription factor.This study provides substantial information for understanding the regulatory network of watermelon in response to low-temperature stress,and identifies candidate genes for the genetic improvement of watermelon with higher low-temperature tolerance.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
The Chinese seabass(Lateolabrax maculatus)is one of the most popular and valuable aquaculture species in China.Recently,the disease caused by Vibrio anguillarum has brought huge economic losses in the L.maculatus indu...The Chinese seabass(Lateolabrax maculatus)is one of the most popular and valuable aquaculture species in China.Recently,the disease caused by Vibrio anguillarum has brought huge economic losses in the L.maculatus industry.However,the immune response of L.maculatus after V.anguillarum infection remains unknown.In this study,the blood homeostasis,gut microbiota and transcriptomic profiling of L.maculatus after V.anguillarum infection were investigated.Our results indicated that the levels of superoxide dismutase(SOD),alanine aminotransferase(ALT)and total bilirubin(TBIL)increased,while the levels of blood glucose(BG),total protein(TP)and albumin(ALB)decreased after V.anguillarum infection.The analysis of the gut microbiota composition revealed that the dominant phyla was Firmicutes and Proteobacteria,and the relative abundance of genus Vibrio increased after V.anguillarum infection.Subsequently,the differentially expressed genes(DEGs)in the kidney and spleen after V.anguillarum infection were analyzed by transcriptome sequencing.The results indicated that immunity-related genes like TLR5,TLR8,TLR9,IL-1β,CCL3,IFNγ,CXCL11 and TNFαwere affected and the NOD-like receptor signaling pathway,cytokine-cytokine receptor interaction and Toll-like receptor signaling were activated.Thus,an effective immune and pro-flammatory response can help resist V.anguillarum infection.Our results provide a theoretical support for improving the disease resistance ability of L.maculatus.展开更多
Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought...Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought tolerance of five grape varieties was evaluated under high-temperature conditions to screen key genes for further exploration of resistance mechanisms. By comparing and analysing the morphological characteristics and physiological indicators associated with the response of grapevines to drought stress and integrating them with the membership function to assess the strength of their drought tolerance, the order of drought tolerance was found to be as follows: 420A>110R>Cabernet Sauvignon(CS)>Fercal>188-08. To further analyse the mechanism of differences in drought tolerance, transcriptomic sequencing was performed on the drought-tolerant cultivar 420A, the drought-sensitive cultivar 188-08 and the control cultivar CS. The functional analysis of differential metabolic pathways indicated that the differentially expressed genes were enriched mainly in biological process category, that 420A had higher antioxidant activity. Furthermore, differentially expressed transcription factors were analyzed in five grape varieties. Genes like Vv AGL15, Vv LBD41, and Vv MYB86 showed close associations with drought tolerance,indicating their potential role in regulating drought tolerance and research significance.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
Discovery and identification of robust biodetoxification strain is crucial for the sustainable and efficient operation of lignocellulosic biorefining process.Paecilomyces variotii FN89,a recently isolated mesophilic f...Discovery and identification of robust biodetoxification strain is crucial for the sustainable and efficient operation of lignocellulosic biorefining process.Paecilomyces variotii FN89,a recently isolated mesophilic filamentous fungi,was herein shown to be able to biodegrade lignocellulose-derived inhibitors including furfural(1.5 g/L),5-hydroxymethylfurfural(4 g/L),acetic acid(4 g/L),hydroxybenzaldehyde(0.2 g/L),syringaldehyde(0.2 g/L),and vanillin(1.5 g/L)efficiently and completely.P.variotii FN89 was adapted to mixed inhibitors and relatively low dissolved oxygen conditions,which can detoxify both the highly viscosity hydrolysate and solid biomass with the well preserve of fermentable sugars and no addition of any nutrients.Two biorefinery chains involving biodetoxification process were thus established to cope with different forms of pretreated biomass for cellulosic lactic acid production.The cellulosic lactic acid titers were above 100 g/L from 25%(w/w)solids loading pretreated wheat straw.The global transcriptome analysis of P.variotii FN89 in the presence of mixed inhibitors suggested that the glycolysis pathway and pentose phosphate pathway were repressed while tricarboxylic acid cycle was enhanced,ensuring the complete degradation of the inhibitors-derived intermediates and efficient energy supply.This study provided a unique and practical biodetoxification strain for lignocellulosic biorefinery,as well as enriched the knowledge of the molecular basis of lignocellulose-derived inhibitors tolerance and carbohydrates metabolism of P.variotii.展开更多
Citric acid is an important contributor to fruit flavor.The extremely significant differences in citric acid levels are observed among citrus species and varieties.The molecular basis of citric acid accumulation remai...Citric acid is an important contributor to fruit flavor.The extremely significant differences in citric acid levels are observed among citrus species and varieties.The molecular basis of citric acid accumulation remains largely unknown on the inter-species level.Here,we performed transcriptome analysis of five pairs of acidic and acidless variety fruits from kumquat(Citrus crassifolia),lemon(C.limon),pummelo(C.maxima),mandarin(C.reticulata),and sweet orange(C.sinensis)to investigate the common and specific genes related to citric acid accumulation in these citrus species.Transcript profiles of the citrate metabolism genes revealed that the mechanism of citric acid accumulation in kumquat differed from that in the other four species.The comparative analysis and weighted gene co-expression network analysis identified 61 candidate genes from lemon,pummelo,mandarin,and sweet orange.Vacuolar acidification regulated by CitPH4-CitAN1-CitPH5was a common mechanism underlying citric acid accumulation in these four species.In addition,gene network analysis indicated that CitPH4 was a central regulator,exhibiting a strong correlation with the genes involved in vacuolar trafficking and potassium(K^(+))transport.The co-expression and functional enrichment analyses showed that active sugar metabolism and increased citrate synthesis were mainly responsible for the accumulation of citric acid in kumquat.Twenty-four transcription factors were identified as candidate regulators,of which CitbHLH28 was found to regulate acidity level via transactivating CWINV2 and PK3 expressions.Overall,this study provides an insight into the mechanism of citric acid accumulation in citrus fruit and provides useful references for fruit quality improvement through acidity control in different citrus species.展开更多
Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explor...Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explored the adaptation mechanisms through comparative transcriptome sequencing and analysis of different tissues between seep mussels and vent mussels.We performed the comparative transcriptome sequencing and analysis for three tissue types(gill,mantle,and adductor muscle)of Bathymodiolus mussels collected from a cold seeping site Station S 11 and the 50-km away hydrothermal field Minami-Ensei Knoll in the Okinawa Trough.Results show that gene expression patterns had distinct tissue specificity.Compared with the non-endosymbiotic tissues(mantle and adductor muscle),the significantly strengthened gene functions in endosymbiotic gill included microbial recognition(fibrinogen C domain-containing protein 1-B-like(fibcd),fibrinogen-related protein 8(frp),peptidoglycan recognition proteins(pgrp),and C-type lectin(clec)),cell apoptosis and immunity(interferon regulatory factor 1/2-like 1(ir f),cathepsin D(ctsd),caspase 2(casp 2)),and antioxidant capacity(copper/zinc superoxide dismutase(czsod),glutathione peroxidase(gpx),selenoprotein(sel)),in both seep and vent individuals.Consistent with metal accumulation,high expression levels of genes related to heavy metal detoxification(cytochrome P 450(cyp),ferritin-like(ftl),metallothionein(mt),glutathione S-transferase(gst))were also observed in gill.Moreover,to adapt to high hydrostatic pressure in the deep sea,the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways associated with cellular community were significantly enriched in all three tissues,suggesting the regulation of cell structure and cell adhesion at transcriptional level.This study obtained gene expression profiles of deep-sea mussels subsisting at cold seep and hydrothermal vent sites,which could lay foundations for comprehensive investigations of molecular basis in adaptation of deep-sea mussels to the two extreme ecosystems.展开更多
Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of s...Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of soiny mullet(Liza haematocheila)larvae at 7 d and 14 d post 0.5μm MPs exposure were analyzed by DNBSEQ platform.A total number of 96585 unigenes were obtained with average length of 1925 bp.Approximately 72.48%(70004),76.80%(74176),and 62.94%(60787)unigenes were matched with the annotated sequences for non-redundant(NR),NCBI nucleotide(NT)and Swissprot database,respectively.Compared with control group,1336 differently expressed genes(DEGs)were identified at 7 d post MPs exposure.As the MPs exposure time extended to 14 d,the number of DEGs in the MPs exposure group reached to 3561.Further,KEGG enrichment analysis revealed that several immune-related pathways,such as interleukin(IL)-17 signaling pathway,tumor necrosis factor(TNF)signaling pathway,were affected by MPs exposure.In addition,apoptosis signaling pathway was also enriched under MPs exposure.These results demonstrated that MPs can alter the expressions of immune-related genes,providing basis for understanding the immune toxicity of MPs on fish and other vertebrates.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32072545,32272639 and 32260745)Zhejiang Provincial Natural Science Foundation of China(Grant Nos.LTGN23C150009 and LY22C150003)Zhejiang University Experimental Technology Research Project(Grant No.SYBJS202217).
文摘For red pear,the anthocyanin content is a crucial factor determining the fruit skin color,which affects consumer preferences.Low overnight temperatures promote anthocyanin accumulation,but the molecular mechanism responsible is unclear.In this study,‘Hongzaosu’pear(Pyrus pyrifolia×Pyrus communis)fruit were treated with a low nighttime temperature(LNT,16℃)or a warm nighttime temperature(WNT,26℃),with sampling conducted within two diurnal cycles.The results showed that LNT promoted anthocyanin accumulation in the fruit skin.The structural anthocyanin biosynthetic genes PpCHS,PpF3H,and PpUFGT exhibited a rhythmic increase in expression at night under LNT.To examine the underlying mechanism,RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations(24,48,72,or 96 h).Transcriptome analysis revealed 285 differentially expressed genes(DEGs)common to all pairwise comparisons of LNT-and WNT-treated calli of‘Clapp's Favorite’(P.communis)at the sampling time points.KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes,which are associated with anthocyanin biosynthesis.The transcription factor PpCDF5,which was responsive to LNT,was selected for further study.Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes PpMYB10,PpCHS,PpF3H,PpDFR,PpANS,and PpUFGT.The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the PpF3H promoter,which contains an AAAG motif.Overexpression of PpCDF5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation.The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.
基金Supported by the Key Research and Development Program of Shandong(No.2022LZGC015)the National Key R&D Program of China(No.2022YFD2401400)+1 种基金the Taishan Scholars Program,the National Key R&D Program of China(No.2022YFD2400304)the Agricultural Seed Project of Shandong Key R&D Program(No.2024LZGCQY003)。
文摘Atmospheric carbon dioxide(CO_(2))levels are escalating at an unprecedented rate,leading to the phenomenon of ocean acidification(OA).Parental exposure to acidification has the potential to enhance offspring resilience through cross-generation plasticity.In this study,we analyzed larval growth and transcriptomic profiles in the Pacific oyster,Crassostrea gigas,a species of significant ecological relevance,under both control and elevated CO_(2)conditions experienced by their parental generation.Our findings indicate that the oyster populations exposed to OA exhibited a higher incidence of abnormalities during the D-shaped larval stage,followed by accelerated growth at the eyed stage.Through a comparative transcriptomic investigation of eyed larvae(25 d after fertilization),we observed that parental exposure to OA substantially influenced the gene expression in the offspring.Genes associated with lipid catabolism and shell formation were notably upregulated in oysters with parental OA exposure,potentially playing a role in cross-generational conditioning and conferring resilience to OA stressors.These results underscore the profound impact of OA on oyster larval development via cross-generational mechanisms and shed light on the molecular underpinnings of cross-generation plasticity.
基金supported by the Natural Science Foundation of China(32272364)the Shanghai Education Committee Scientific Research Innovation Projects,China(2101070007800120)+2 种基金National Science Foundation for Distinguished Young Scholars(32025029)Shanghai Key Project in Synthetic Biology(23HC1400900)the Shanghai Engineering Research Center of 460 Food Microbiology Program(19DZ2281100).
文摘This study examined the potential response mechanisms of Ligilactobacillus salivarius AR612 to glucose stress through whole-genome and comparative transcriptome analysis.We obtained the basic genome information of L.salivarius AR612.The full genome length of L.salivarius AR612 was 1970245 bp,with a GC content of 33.01%and 1894 coding genes.Moreover,we identified many genes associated with genetic adaptations to various stress factors,including temperature,p H,osmotic pressure,bile salts,and oxidative stress.Physiological analysis revealed that the growth and morphology of AR612 changed significantly under glucose stress,with a decrease in the maximum growth and irregular cell morphology.Furthermore,a comparison of transcriptome data indicated that glucose stress induced changes in the number of differential genes.Moreover,AR612 could respond to extracellular glucose stress by changing the expression of genes related to cell morphology,carbohydrate metabolism,amino acid metabolism,fatty acid synthesis,and nucleotide metabolism.This study provides valuable theoretical insights for future research on the adaptation of L.salivarius AR612 to nutritional stress and its application in industrial processes.
基金supported by the National Natural Science Fund of China(Grant Nos.31872066 and 32272663)the Science and Technology Planning Project of Guangzhou(Grant No.2023B01J2002)+1 种基金the Key Research and Development Program of Hainan(Grant No.ZDYF2023XDNY052)the Seed Industry Engineering Project of Ministry of Agriculture and Rural Affairs of Guangdong(Grant Nos.2022-NPY-00-004 and 2022-NBH-00-001)。
文摘Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.
基金supported by the National Natural Science Foundation of China(Grant Nos.32120103010,32002050)Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences。
文摘Tomato is an important economic crop all over the world.Volatile flavors in tomato fruit are key factors influencing consumer liking and commercial quality.However,the regulatory mechanism controlling the volatile flavors of tomatoes is still not clear.Here,we integrated the metabolome and transcriptome of the volatile flavors in tomato fruit to explore the regulatory mechanism of volatile flavor formation,using wild and cultivated tomatoes with significant differences in flavors.A total of 35 volatile flavor compounds were identified,based on the solid phase microextraction-gas chromatography-mass spectrometry(SPME-GC-MS).The content of the volatiles,affecting fruit flavor,significantly increased in the transition from breaker to red ripe fruit stage.Moreover,the total content of the volatiles in wild tomatoes was much higher than that in the cultivated tomatoes.The content variations of all volatile flavors were clustered into 10 groups by hierarchical cluster and Pearson coefficient correlation(PCC)analysis.The fruit transcriptome was also patterned into 10 groups,with significant variations both from the mature green to breaker fruit stage and from the breaker to red ripe fruit stage.Combining the metabolome and the transcriptome of the same developmental stage of fruits by co-expression analysis,we found that the expression level of 1182 genes was highly correlated with the content of volatile flavor compounds,thereby constructing two regulatory pathways of important volatile flavors.One pathway is tetrahydrothiazolidine N-hydroxylase(SlTNH1)-dependent,which is regulated by two transcription factors(TFs)from the bHLH and AP2/ERF families,controlling the synthesis of 2-isobutylthiazole in amino acid metabolism.The other is lipoxygenase(Sl LOX)-dependent,which is regulated by one TF from the HD-Zip family,controlling the synthesis of hexanal and(Z)-2-heptenal in fatty acid metabolism.Dual-luciferase assay confirmed the binding of b HLH and AP2/ERF to their structural genes.The findings of this study provide new insights into volatile flavor formation in tomato fruit,which can be useful for tomato flavor improvement.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFD2200502)the National Natural Science Foundation of China(Grant No.31971736).
文摘Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life.The study of gene function has become an important part of bamboo breeding,whereas quantitative real-time PCR(qRT-PCR)is a powerful tool for gene expression analysis.The accuracy of qRT-PCR results largely depends on suitable reference genes.In this study,a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets,comprising 200 tissue samples,107 treated samples,and 140 samples from various moso bamboo(Phyllostachys edulis)forms.A total of 3444,1013,and 3962 stably expressed genes were identified from these three groups,respectively.Functional enrichment analysis revealed significant enrichment of these genes in pathways,including the spliceosome,proteasome,and oxidative phosphorylation.Eight candidate genes(ADPRE,GAPDH,TRX,TUBA,NRP,MBF,UNK,and CAM1),were selected for qRT-PCR validation using 112 samples.To assess their stability,five statistical methods(geNorm,NormFinder,BestKeeper,Delta-Ct,and RefFinder)were employed.The most suitable reference genes were ADPRE and GAPDH for different tissues,GAPDH and CAM1 for different treatments,and GAPDH and TRX for various moso bamboo forms.Overall,ADPRE and GAPDH were the most stable reference genes across all conditions,while TUBA and TRX were the least stable reference genes.In addition,a significant negative correlation was found between the Ct values of RT-qPCR and the log2TPM values from the transcriptome data(Ct=-1.534x+37.221),providing a potential method for estimating gene expression levels.The identified reference genes,particularly ADPRE and GAPDH,provide a robust set of references for gene expression studies in moso bamboo.
基金supported by the National Key R&D Program of China(2022YFD1201802)the Shandong Key R&D Program,China(2022CXGC010607)+2 种基金the Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202109)the Agricultural Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ASTIP2017-ICS)the Subproject of the Major Project of Science and Technology in Shanxi Province,China(202201140601025-1-02)。
文摘Southern corn rust(SCR)is an airborne fungal disease caused by Puccinia polysora Underw.(P.polysora)that adversely impacts maize quality and yields worldwide.Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.Using phenotypic SCR resistance-related data collected over two years and three geographical environments,a genome-wide association study was carried out in this work,which eventually identified 91 loci that were substantially correlated with SCR susceptibility.These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes(B73_RefGen_v4).Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection,with 2,586 and 797 differentially expressed genes(DEGs)ultimately being identified in the resistant Qi319and susceptible 8112 inbred lines following P.polysora infection,respectively,including 306 genes common to both lines.Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.One of these genes is ZmHCT9,which encodes the protein hydroxycinnamoyl transferase 9.This gene was up-regulated in susceptible inbred lines and linked to greater P.polysora resistance as confirmed through cucumber mosaic virus(CMV)-based virus induced-gene silencing(VIGS)system-mediated gene silencing.These data provide important insights into the genetic basis of the maize SCR response.They will be useful for for future research on potential genes related to SCR resistance in maize.
基金Supported by the earmarked fund for China Agriculture Research System(No.CARS-50)the Doctors Research Funding of Henan Normal University(No.20230246)。
文摘Nanoplastics(less than 1µm in size,NPs)have emerged as a significant pollutant in aquatic environment,posing considerable threats to freshwater biota.However,the mechanisms through which NPs modulate the predation responses of these organisms remain poorly elucidated.We investigated the impacts of polystyrene NPs,characterized by a representative particle size(diameter:50 nm;concentration:0–8μg/L),on the anti-predation defense mechanisms of mature rotifer Brachionus calyciflorus against predator of rotifer Asplanchna brightwellii,utilizing transcriptomics to unravel the underlying molecular pathways.Results reveal that the posterolateral spine length and type of B.calyciflorus serve as robust indicators of defensive morphology,even in the presence of NPs exposure.Specifically,increasing concentrations of NPs and predator cues suppressed the defensive responses,which was associated with morphological transformations.This suppression was associated with the down-regulation of the HIF-1αsignaling pathway,implicating potentially its role in modulating fight-or-flight responses.Furthermore,we identified functional crosstalk among multiple signaling pathways,including HIF-1α,PI3K-Akt,FoxO,and mTOR,in B.calyciflorus,which may underpin the organism's responses to polystyrene NP exposure.These findings contribute to the advancement of predictive models to assess the ecological risks posed by polystyrene NPs contamination in aquatic ecosystems.
基金Fujian Province Science and Technology Plan Project under contract No.2023N0011Xiamen Municipal Bureau of Marine Development Project under contract No.S24258。
文摘Cryptocaryon irritans is the parasite responsible for“white spot disease”in the yellowfin seabream Acanthopagrus latus,which has caused significant losses to the aquaculture industry.This experiment investigated the changes in the morphology,transcriptome,and proteome of gill tissue in yellowfin seabream infected with C.irritans,aiming to provide foundational data for further understanding the pathogenic mechanisms and control measures against this parasite.The main findings were as follows,after C.irritans infection,the structure of gill tissue in yellowfin seabream was damaged,with microvessels ruptured,some cells proliferating,and large amounts of mucus infiltrating.Transcriptome analysis revealed a total of 4299 differentially expressed genes,with 2367 up-regulated and 1932down-regulated.Further bioinformatics analysis of all differentially expressed genes identified nine immune-related genes,cox-2,mcama,tbx21,dcn,tnfb,cd74a,illb,ppib,and cd4-1 in A.latus.The reliability of the transcriptome data was validated by real time q PCR,which showed the same trend as the RNA-seq results.Proteome analysis found365 differential proteins,with 180 proteins up-regulated and 185 proteins down-regulated.Bioinformatics analysis identified three immune-related proteins,Myll,Gapdh,and Actn3b.These findings indicated that C.irritans disrupted the structure of gill tissue,impeded gas exchange and led to asphyxiation and death in affected fish.Transcriptome and proteome analyses showed that the expression of immune-related genes and proteins in yellowfin seabream,involved not only inflammatory responses and the activation and migration of immune cells but also potentially participated in tissue repair and defense regulation.These findings highlighted the complex immune regulatory network in response to C.irritans infection,offering references for prevention and control of white spot disease in yellowfin seabream.
基金supported by the Project of Chinese Manned Spaceflight(No.YYWT-0801-EXP-09)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA17010502)Jiangsu Province Ecological Environment Scientific Research Project(No.2022008).
文摘Perchlorate(ClO_(4)^(−))is a type of novel persistent inorganic pollutant that has gained increasing attention because of its high solubility,poor degradability,and widespread distribution.However,the impacts of perchlorate on aquatic autotrophs such cyanobacterium are still unclear.Herein,Synechocystis sp.PCC6803(Synechocystis)was used to investigate the response mechanisms of perchlorate on cyanobacterium by integrating physiological and transcriptome analyses.Physiological results showed that perchlorate mainly damaged the photosystem of Synechocystis,and the inhibition degree of photosystem II(PSII)was severer than that of photosystem I(PSI).When the exposed cells were moved to a clean medium,the photosynthetic activities were slightly repaired but still lower than in the control group,indicating irreversible damage.Furthermore,perchlorate also destroyed the cellular ultrastructure and induced oxidative stress in Synechocystis.The antioxidant glutathione(GSH)content and the superoxide dismutase(SOD)enzyme activity were enhanced to scavenge harmful reactive oxygen(ROS)in Synechocystis.Transcriptome analysis revealed that the genes associated with“photosynthesis”and“electron transport”were significantly regulated.For instance,most genes related to PSI(e.g.,psaf,psaJ)and the“electron transport chain”were upregulated,whereas most genes related to PSII(e.g.,psbA3,psbD1,psbB,and psbC)were downregulated.Additionally,perchlorate also induced the expression of genes related to the antioxidant system(sod2,gpx,gst,katG,and gshB)to reduce oxidative damage.Overall,this study is the first to investigate the impacts andmechanisms of cyanobacterium under perchlorate stress,which is conducive to assessing the risk of perchlorate in aquatic environments.
基金financed by the National Natural Science Foundation of China(31471894)the China Agriculture Research System of MOF and MARA(CARS-25)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAASASTIP-ZFRI)。
文摘Watermelon(Citrullus lanatus)is an economically important horticultural crop.However,it is susceptible to lowtemperature stress,which significantly challenges its production and supply.Despite the great economic importance of watermelon,little is known about its response to low-temperature stress at the transcriptional level.In this study,we performed a time-course transcriptome analysis to systematically investigate the regulatory network of watermelon under low-temperature stress.Six low-temperature-responsive gene clusters representing six expression patterns were identified,revealing diverse regulation of metabolic pathways in watermelon under lowtemperature stress.Analysis of temporally specific differentially expressed genes revealed the time-dependent nature of the watermelon response to low temperature.Moreover,ClMYB14 was found to be a negative regulator of low-temperature tolerance as ClMYB14-OE lines were more susceptible to low-temperature stress.Co-expression network analysis demonstrated that ClMYB14 participates in the low-temperature response by regulating the unsaturated fatty acid pathway and heat shock transcription factor.This study provides substantial information for understanding the regulatory network of watermelon in response to low-temperature stress,and identifies candidate genes for the genetic improvement of watermelon with higher low-temperature tolerance.
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received funding from the Natural Science Foundation of Shandong Province(No.ZR2023MC141)the Innovation and Entrepreneurship Training Program for College Students(No.202210435003)financial support was also provided by the‘First Class Fishery Discipline’Program and the Special Talent Program‘One Thing One Decision(Yishi Yiyi)’in Shandong Province,China。
文摘The Chinese seabass(Lateolabrax maculatus)is one of the most popular and valuable aquaculture species in China.Recently,the disease caused by Vibrio anguillarum has brought huge economic losses in the L.maculatus industry.However,the immune response of L.maculatus after V.anguillarum infection remains unknown.In this study,the blood homeostasis,gut microbiota and transcriptomic profiling of L.maculatus after V.anguillarum infection were investigated.Our results indicated that the levels of superoxide dismutase(SOD),alanine aminotransferase(ALT)and total bilirubin(TBIL)increased,while the levels of blood glucose(BG),total protein(TP)and albumin(ALB)decreased after V.anguillarum infection.The analysis of the gut microbiota composition revealed that the dominant phyla was Firmicutes and Proteobacteria,and the relative abundance of genus Vibrio increased after V.anguillarum infection.Subsequently,the differentially expressed genes(DEGs)in the kidney and spleen after V.anguillarum infection were analyzed by transcriptome sequencing.The results indicated that immunity-related genes like TLR5,TLR8,TLR9,IL-1β,CCL3,IFNγ,CXCL11 and TNFαwere affected and the NOD-like receptor signaling pathway,cytokine-cytokine receptor interaction and Toll-like receptor signaling were activated.Thus,an effective immune and pro-flammatory response can help resist V.anguillarum infection.Our results provide a theoretical support for improving the disease resistance ability of L.maculatus.
基金supported by the Major Innovation Project of Shandong Province, China (2022CXGC010605)the National Natural Science Foundation of China (32172518 and 32002023)+1 种基金the National Key R&D Program of China (2023YFD2301103)the Key R&D Projects in Ningxia Hui Autonomous Region, China (2022BBF02014)。
文摘Evaluating plant stress tolerance and screening key regulatory genes under the combined stresses of high temperature and drought are important for studying plant stress tolerance mechanisms. In this study, the drought tolerance of five grape varieties was evaluated under high-temperature conditions to screen key genes for further exploration of resistance mechanisms. By comparing and analysing the morphological characteristics and physiological indicators associated with the response of grapevines to drought stress and integrating them with the membership function to assess the strength of their drought tolerance, the order of drought tolerance was found to be as follows: 420A>110R>Cabernet Sauvignon(CS)>Fercal>188-08. To further analyse the mechanism of differences in drought tolerance, transcriptomic sequencing was performed on the drought-tolerant cultivar 420A, the drought-sensitive cultivar 188-08 and the control cultivar CS. The functional analysis of differential metabolic pathways indicated that the differentially expressed genes were enriched mainly in biological process category, that 420A had higher antioxidant activity. Furthermore, differentially expressed transcription factors were analyzed in five grape varieties. Genes like Vv AGL15, Vv LBD41, and Vv MYB86 showed close associations with drought tolerance,indicating their potential role in regulating drought tolerance and research significance.
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 National Key R&D Program of China(2023YFA0914400)the National Natural Science Foundation of China(32301269)+1 种基金the Yangfan Project of Science and Technology Committee of Shanghai Municipality(23YF1409900)the Key Technology R&D Program of the Science and Technology Commission of Shanghai Municipality(25HC2820200).
文摘Discovery and identification of robust biodetoxification strain is crucial for the sustainable and efficient operation of lignocellulosic biorefining process.Paecilomyces variotii FN89,a recently isolated mesophilic filamentous fungi,was herein shown to be able to biodegrade lignocellulose-derived inhibitors including furfural(1.5 g/L),5-hydroxymethylfurfural(4 g/L),acetic acid(4 g/L),hydroxybenzaldehyde(0.2 g/L),syringaldehyde(0.2 g/L),and vanillin(1.5 g/L)efficiently and completely.P.variotii FN89 was adapted to mixed inhibitors and relatively low dissolved oxygen conditions,which can detoxify both the highly viscosity hydrolysate and solid biomass with the well preserve of fermentable sugars and no addition of any nutrients.Two biorefinery chains involving biodetoxification process were thus established to cope with different forms of pretreated biomass for cellulosic lactic acid production.The cellulosic lactic acid titers were above 100 g/L from 25%(w/w)solids loading pretreated wheat straw.The global transcriptome analysis of P.variotii FN89 in the presence of mixed inhibitors suggested that the glycolysis pathway and pentose phosphate pathway were repressed while tricarboxylic acid cycle was enhanced,ensuring the complete degradation of the inhibitors-derived intermediates and efficient energy supply.This study provided a unique and practical biodetoxification strain for lignocellulosic biorefinery,as well as enriched the knowledge of the molecular basis of lignocellulose-derived inhibitors tolerance and carbohydrates metabolism of P.variotii.
基金financially supported by the National Natural Science Foundation of China(Grant No.31925034)the National Key Research and Development Program of China(Grant No.2022YFF1003100)+1 种基金the Foundation of Hubei Hongshan Laboratory(Grant No.2021hszd016)Key project of Hubei provincial Natural Science Foundation(Grant No.2021CFA017)。
文摘Citric acid is an important contributor to fruit flavor.The extremely significant differences in citric acid levels are observed among citrus species and varieties.The molecular basis of citric acid accumulation remains largely unknown on the inter-species level.Here,we performed transcriptome analysis of five pairs of acidic and acidless variety fruits from kumquat(Citrus crassifolia),lemon(C.limon),pummelo(C.maxima),mandarin(C.reticulata),and sweet orange(C.sinensis)to investigate the common and specific genes related to citric acid accumulation in these citrus species.Transcript profiles of the citrate metabolism genes revealed that the mechanism of citric acid accumulation in kumquat differed from that in the other four species.The comparative analysis and weighted gene co-expression network analysis identified 61 candidate genes from lemon,pummelo,mandarin,and sweet orange.Vacuolar acidification regulated by CitPH4-CitAN1-CitPH5was a common mechanism underlying citric acid accumulation in these four species.In addition,gene network analysis indicated that CitPH4 was a central regulator,exhibiting a strong correlation with the genes involved in vacuolar trafficking and potassium(K^(+))transport.The co-expression and functional enrichment analyses showed that active sugar metabolism and increased citrate synthesis were mainly responsible for the accumulation of citric acid in kumquat.Twenty-four transcription factors were identified as candidate regulators,of which CitbHLH28 was found to regulate acidity level via transactivating CWINV2 and PK3 expressions.Overall,this study provides an insight into the mechanism of citric acid accumulation in citrus fruit and provides useful references for fruit quality improvement through acidity control in different citrus species.
基金Supported by the National Natural Science Foundation of China(Nos.91858208,92358301)the Laoshan Laboratory(No.LSKJ 202203500),the China Postdoctoral Science Foundation of China(No.2019M663209)the Fundamental Research Funds for the Central Universities in China(No.19lGPY100)。
文摘Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explored the adaptation mechanisms through comparative transcriptome sequencing and analysis of different tissues between seep mussels and vent mussels.We performed the comparative transcriptome sequencing and analysis for three tissue types(gill,mantle,and adductor muscle)of Bathymodiolus mussels collected from a cold seeping site Station S 11 and the 50-km away hydrothermal field Minami-Ensei Knoll in the Okinawa Trough.Results show that gene expression patterns had distinct tissue specificity.Compared with the non-endosymbiotic tissues(mantle and adductor muscle),the significantly strengthened gene functions in endosymbiotic gill included microbial recognition(fibrinogen C domain-containing protein 1-B-like(fibcd),fibrinogen-related protein 8(frp),peptidoglycan recognition proteins(pgrp),and C-type lectin(clec)),cell apoptosis and immunity(interferon regulatory factor 1/2-like 1(ir f),cathepsin D(ctsd),caspase 2(casp 2)),and antioxidant capacity(copper/zinc superoxide dismutase(czsod),glutathione peroxidase(gpx),selenoprotein(sel)),in both seep and vent individuals.Consistent with metal accumulation,high expression levels of genes related to heavy metal detoxification(cytochrome P 450(cyp),ferritin-like(ftl),metallothionein(mt),glutathione S-transferase(gst))were also observed in gill.Moreover,to adapt to high hydrostatic pressure in the deep sea,the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways associated with cellular community were significantly enriched in all three tissues,suggesting the regulation of cell structure and cell adhesion at transcriptional level.This study obtained gene expression profiles of deep-sea mussels subsisting at cold seep and hydrothermal vent sites,which could lay foundations for comprehensive investigations of molecular basis in adaptation of deep-sea mussels to the two extreme ecosystems.
基金supported by the Major Projects of Natural Science Research for University and Colleges in Jiangsu Province(No.21KJA240001)the Key Research and Development Program of Jiangsu Province(No.BE2018348)+2 种基金partially by the Jiangsu Agricultural Science and Technology Innovation Fund(No.CX(22)3199)the Projects for the High-Quality Development of Fishery Industry of Yancheng City(No.YCSCYJ20210014)supported financially by the projects for‘Six Talents’of Jiangsu Province(No.NY115)。
文摘Microplastics(MPs)pollution has become a worldwide environmental problem.The study about the effects of microplastics on fish,especially on the fish immune system is limited.In the present study,the transcriptome of soiny mullet(Liza haematocheila)larvae at 7 d and 14 d post 0.5μm MPs exposure were analyzed by DNBSEQ platform.A total number of 96585 unigenes were obtained with average length of 1925 bp.Approximately 72.48%(70004),76.80%(74176),and 62.94%(60787)unigenes were matched with the annotated sequences for non-redundant(NR),NCBI nucleotide(NT)and Swissprot database,respectively.Compared with control group,1336 differently expressed genes(DEGs)were identified at 7 d post MPs exposure.As the MPs exposure time extended to 14 d,the number of DEGs in the MPs exposure group reached to 3561.Further,KEGG enrichment analysis revealed that several immune-related pathways,such as interleukin(IL)-17 signaling pathway,tumor necrosis factor(TNF)signaling pathway,were affected by MPs exposure.In addition,apoptosis signaling pathway was also enriched under MPs exposure.These results demonstrated that MPs can alter the expressions of immune-related genes,providing basis for understanding the immune toxicity of MPs on fish and other vertebrates.
