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
Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in broilers.Therefore,it is an important task for poultry breeders to breed broilers with low abdominal fat.Abdominal ...Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in broilers.Therefore,it is an important task for poultry breeders to breed broilers with low abdominal fat.Abdominal fat deposition is a highly complex biological process,and its molecular basis remains elusive.In this study,we performed transcriptome analysis to compare gene expression profiles at different stages of abdominal fat deposition to identify the key genes and pathways involved in abdominal fat accumulation.We found that abdominal fat weight(AFW)increased gradually from day 35(D35)to 91(D91),and then decreased at day 119(D119).Accordingly,after detecting differentially expressed genes(DEGs)by comparing gene expression profiles at D35 vs.D63 and D35 vs.D91,and identifying gene modules associated with fat deposition by weighted gene co-expression network analysis(WGCNA),we performed intersection analysis of the detected DEGs and WGCNA gene modules and identified 394 and 435 intersecting genes,respectively.The results of the Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses showed that the steroid hormone biosynthesis and insulin signaling pathways were co-enriched in all intersecting genes,steroid hormones have been shown that regulated insulin signaling pathway,indicating the importance of the steroid hormone biosynthesis pathway in the development of broiler abdominal fat.We then identified 6 hub genes(ACTB,SOX9,RHOBTB2,PDLIM3,NEDD9,and DOCK4)related to abdominal fat deposition.Further analysis also revealed that there were direct interactions between 6 hub genes.SOX9 has been shown to bind to proteins required for steroid hormone receptor binding,and RHOBTB2 indirectly regulates the steroid hormones biosynthesis through cyclin factor,and ultimately affect fat deposition.Our results suggest that the genes RHOBTB2 and SOX9 play an important role in fat deposition in broilers,by regulating steroid hormone synthesis.These findings provide new targets and directions for further studies on the mechanisms of fat deposition in chicken.展开更多
The fish brain is crucial for adjusting to environmental changes.Metabolic changes play a vital role in the adaptation to salinity change in aquatic animals.However,few studies have evaluated the responses of the fish...The fish brain is crucial for adjusting to environmental changes.Metabolic changes play a vital role in the adaptation to salinity change in aquatic animals.However,few studies have evaluated the responses of the fish brain to salinity changes.To evaluate the response to various salinities,spotted scat(Scatophagus argus)was cultured in water with salinity levels of 5(low salinity:LS),25(control group:Ctrl),and 35(high salinity group:HS)for 22 days.The brain transcriptome was analyzed.In total,1698 differentially expressed genes(DEGs)were identified between the HS and Ctrl groups,and 841 DEGs were identified between the LS and Ctrl groups.KEGG analysis showed that the DEGs in the HS vs.Ctrl comparison were involved in steroid biosynthesis,terpenoid backbone biosynthesis,fatty acid biosynthesis,ascorbate and aldarate metabolism,other types of O-glycan biosynthesis,and fatty acid metabolism.Glyoxylate and dicarboxylate metabolism,one carbon pool by folate,steroid biosynthesis,and cysteine and methionine metabolism were significantly enriched in the LS vs.Ctrl comparison.Additionally,the genes related to metabolism(acc,fas,hmgcr,hmgcs1,mvd,soat1,nsdhl,sqle,cel,fdft1,dnmt3a and mtr)were significantly up-regulated in the HS vs.Ctrl comparison.The genes related to metabolism(lipa,sqle,acc,fas,bhmt,mpst,dnmt3a,mtr,hao2,LOC111225351 and hmgcs1)were significantly up-regulated,while hmgcr and soat1 were significantly down-regulated in the LS vs.Ctrl compparison.These results suggest that salinity stress affects signaling pathways and genes’expressions involved in metabolic processes in the brain,and the differences in metabolism play an important role in adaptation to hyperhaline or hypohaline environments in spotted scat.This research provides a comprehensive overview of transcriptional changes in the brain under hyperhaline or hypohaline conditions,which is helpful to understand the mechanisms underlying salinity adaptation in euryhaline fishes.展开更多
Free cholesterol has been considered to be a critical risk factor of nonalcoholic fatty liver disease(NAFLD).It remains unknown whether dietary intake of condensed tannins(CTs)have distinguishable effects to alleviate...Free cholesterol has been considered to be a critical risk factor of nonalcoholic fatty liver disease(NAFLD).It remains unknown whether dietary intake of condensed tannins(CTs)have distinguishable effects to alleviate liver damage caused by a high cholesterol diet.Male C57BL/6 mice were fed a high cholesterol diet for 6 weeks,and given CTs treatment at a dosage of 200 mg/(kg·day)at the same time.The results indicated that compared with mice fed a normal diet,a high cholesterol diet group resulted in significant weight loss,dysregulation of lipid metabolism in blood and liver,and oxidative stress in the liver,but CTs treatment dramatically reversed these negative effects.Hematoxylin and eosin(H&E)staining and frozen section observation manifested that CTs treatment could effectively reduce the deposition of liver cholesterol and tissue necrosis caused by high cholesterol intake.CTs alleviated liver injury mainly by regulating the expression of related genes in cholesterol metabolism pathway and AMPK phosphorylation.Our results confirmed that CTs have remarkable cholesterol lowering and anti-liver injury effects in vivo.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
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
MADS-box transcription factors show highly diverse regulatory functions in a wide variety of organisms. In this study, we characterized a MADS-box gene （BpMADS12） from the white birch （Betula platyphylla Suk）. Thi...MADS-box transcription factors show highly diverse regulatory functions in a wide variety of organisms. In this study, we characterized a MADS-box gene （BpMADS12） from the white birch （Betula platyphylla Suk）. This gene is a member of the suppressor of overexpression of CO 1/tomato MADS 3 class of MADS-box genes. We generated lines overexpressing BpMADS12 and found that these had higher levels of lignin compared to that observed in nontransgenic lines. Transcriptome anal- ysis revealed numerous changes in gene expression patterns. In total, 8794 differentially expressed genes were identified, including 5006 upregulated unigenes and 3788 downregulated unigenes in BpMADS-overexpression lines. Differentially expressed genes involved in the pathways for lignin and brassinosteroid biosynthesis were significantly enriched and may have contributed to phenotypic changes. The results from a quantitative RT-PCR analysis were consistent those obtained with the transcriptome analysis.Our transcriptome analysis, in combination with measure- ment of lignin level, indicated that BpMADS12 promotes lignin synthesis through regulation of key enzymes in response to brassinosteroid signaling. These results suggest that this MADS-box protein is crucial to all subsequent structural events and provide a good foundation for studies aiming to elucidate the developmental mechanisms underlying formation of wood.展开更多
The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for comm...The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for common bean breeding genetic research.Although model plants and crops are studied to comprehend the molecular mechanisms and genetic basis of plant phenotypes,the molecular mechanism of phenotypic variation in common beans remains underexplored.We here used the mutant‘nts’as material for transcriptome sequencing analysis.This mutant was obtained through 60Co-γirradiation from the common bean variety‘A18’.Differentially expressed genes were mainly enriched in GO functional entries such as cell wall organization,auxin response and transcription factor activity.Metabolic pathways significantly enriched in KEGG analysis included plant hormone signal transduction pathways,phenylpropanoid biosynthesis pathways,and fructose and mannose metabolic pathways.AUX1(Phvul.001G241500),the gene responsible for auxin transport,may be the key gene for auxin content inhibition.In the plant hormone signal transduction pathway,AUX1 expression was downregulated and auxin transport across the membrane was blocked,resulting in stunted growth of the mutant‘nts’.The results provide important clues for revealing the molecular mechanism of‘nts’phenotype regulation in bean mutants and offer basic materials for breeding beneficial phenotypes of bean varieties.展开更多
Perfluorooctanoic acid(PFOA)is a widespread synthetic persistent organic pollutant that may enrich along the food chain and affect the growth,development,reproduction,and lipid metabolism of aquatic organisms,particul...Perfluorooctanoic acid(PFOA)is a widespread synthetic persistent organic pollutant that may enrich along the food chain and affect the growth,development,reproduction,and lipid metabolism of aquatic organisms,particularly the benthic organisms.How-ever,the toxic effects of PFOA on the half-smooth tongue sole Cynoglossus semilaevis,a commercial benthic fish in China,have rarely been reported.Because juvenile fish are sensitive to environmental pollutants,in the present study,histological assessment and tran-scriptome sequencing were performed to determine the short-term impact of PFOA on juvenile half-smooth tongue soles.Histologi-cal analysis showed that PFOA exposure caused hepatocyte rupture,intestinal villi breakage,increased goblet cell count,and brain ab-normal.Transcriptome results showed that some interesting signaling pathways,such as glycolysis/gluconeogenesis,PPAR signaling pathway and GABAergic synapse signaling pathway,were enriched after PFOA exposure.In addition,some metabolic,immune and neural genes were differentially expressed,which including ependymin,hbb1-like and gad 1,and they were up-regulated after 14 days of exposure.Transcriptome results also indicated that half-smooth tongue sole might improve energy metabolism in response to PFOA toxicity after 7 days of exposure.These findings provide a basis for studying the ecological effects of PFOA on marine benthic fishes.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
The neural regeneration process is driven by a wide range of molecules and pathways. Adherens junctions are critical cellular junctions for the integrity of peripheral nerves. However, few studies have systematically ...The neural regeneration process is driven by a wide range of molecules and pathways. Adherens junctions are critical cellular junctions for the integrity of peripheral nerves. However, few studies have systematically characterized the transcript changes in the adherens junction pathway following injury. In this study, a rat model of sciatic nerve crush injury was established by forceps. Deep sequencing data were analyzed using comprehensive transcriptome analysis at 0, 1, 4, 7, and 14 days after injury. Results showed that most individual molecules in the adherens junctions were either upregulated or downregulated after nerve injury. The m RNA expression of ARPC1 B, ARPC3, TUBA8, TUBA1 C, CTNNA2, ACTN3, MET, HGF, NME1 and ARF6, which are involved in the adherens junction pathway and in remodeling of adherens junctions, was analyzed using quantitative real-time polymerase chain reaction. Most of these genes were upregulated in the sciatic nerve stump following peripheral nerve injury, except for CTNNA2, which was downregulated. Our findings reveal the dynamic changes of key molecules in adherens junctions and in remodeling of adherens junctions. These key genes provide a reference for the selection of clinical therapeutic targets for peripheral nerve injury.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
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
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 rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say th...The rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell.With this disruptive technology,it is now possible to mine heterogeneity between tissue types and within cells like never before.This enables more rapid identification of rare and novel cell types,simultaneous characterization of multiple different cell types and states,more accurate and integrated understanding of their roles in life processes,and more.However,we are only at the beginning of unlocking the full potential of scRNA-seq applications.This is particularly true for plant sciences,where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome.In this review,we compare and evaluate recent pioneering studies using the A rabidopsis root model,which has established new paradigms for scRNA-seq studies in plants.We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale.In addition,we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.展开更多
High-temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening. We used the Affymetrix 22K Barley1 GeneChip microarray to investig...High-temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening. We used the Affymetrix 22K Barley1 GeneChip microarray to investigate the response of developing barley （Hordeum vulgare） seeds, termed caryopses, after 0.5, 3, and 6 h of heat stress exposure; 958 induced and 1122 repressed genes exhibited spatial and temporal expression patterns that provide a detailed insight into the caryopses＇ early heat stress responses. Down-regulation of genes related to storage compound biosynthesis and cell growth provides evidence for a rapid impairment of the caryopsis＇ development. Increased levels of sugars and amino acids were indicative for both production of compatible solutes and feedback-induced accumulation of substrates for storage compound biosynthesis. Metadata analysis identified embryo and endosperm as primary locations of heat stress responses, indicating a strong impact of short-term heat stress on central developmental functions of the caryopsis. A comparison with heat stress responses in Arabidopsis shoots and drought stress responses in barley caryopses identified both conserved and presumably heat- and caryopsis-specific stress-responsive genes. Summarized, our data provide an important basis for further investigation of gene functions in order to aid an improved heat tolerance and reduced losses of yield in barley as a model for cereal crops.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 that β-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 the β-carotene content,while the β-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
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
Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptom...Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.展开更多
Objectives:Peach(Prunus persica L.)is an ancient fruit tree that originated from China.It is the climacteric fruit belonging to genus Prunus in family Rosaceae.Ethylene,which is produced during ripening,accelerates fr...Objectives:Peach(Prunus persica L.)is an ancient fruit tree that originated from China.It is the climacteric fruit belonging to genus Prunus in family Rosaceae.Ethylene,which is produced during ripening,accelerates fruit softening,and therefore peaches cannot be stored for a long time.Materials and Methods:To study the mechanism of fruit late ripening,transcriptome analysis of the fruit of a late-ripening mutant of'Jinghong'peach was performed to identify genes and pathways involved in fruit late ripening.Results:A total of 1805,1511,and 2309 genes were found to be differentially expressed in W2_vs_M1,W3_vs_M2,and W3_vs_M3,respectively.Functional enrichment analysis of the differentially expressed genes showed they were related to carotenoid biosynthesis,starch and sucrose metabolism plant hormone signal transduction,flavonoid biosynthesis,and photosynthesis.The expression trends of ripening-related genes that encode transcription factors and plant hormone signal transduction-related genes that encode enzymes were similar.Conclusions:It will help to elucidate the transcriptional regulatory network of fruit development in the spontaneous late-ripening mutant of‘Jinghong’peach and provide a theoretical basis for understanding the molecular regulatory mechanism of fruit ripening.展开更多
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funded by the grants from the Beijing Natural Science Foundation,China(6202028)the National Natural Science Foundation of China(32172723)+2 种基金the State Key Laboratory of Animal Nutrition,China(2004DA125184G2109)the Agricultural Science and Technology Innovation Program,China(ASTIP-IAS04)the China Agriculture Research System of MOF and MARA(CARS-41).
文摘Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in broilers.Therefore,it is an important task for poultry breeders to breed broilers with low abdominal fat.Abdominal fat deposition is a highly complex biological process,and its molecular basis remains elusive.In this study,we performed transcriptome analysis to compare gene expression profiles at different stages of abdominal fat deposition to identify the key genes and pathways involved in abdominal fat accumulation.We found that abdominal fat weight(AFW)increased gradually from day 35(D35)to 91(D91),and then decreased at day 119(D119).Accordingly,after detecting differentially expressed genes(DEGs)by comparing gene expression profiles at D35 vs.D63 and D35 vs.D91,and identifying gene modules associated with fat deposition by weighted gene co-expression network analysis(WGCNA),we performed intersection analysis of the detected DEGs and WGCNA gene modules and identified 394 and 435 intersecting genes,respectively.The results of the Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses showed that the steroid hormone biosynthesis and insulin signaling pathways were co-enriched in all intersecting genes,steroid hormones have been shown that regulated insulin signaling pathway,indicating the importance of the steroid hormone biosynthesis pathway in the development of broiler abdominal fat.We then identified 6 hub genes(ACTB,SOX9,RHOBTB2,PDLIM3,NEDD9,and DOCK4)related to abdominal fat deposition.Further analysis also revealed that there were direct interactions between 6 hub genes.SOX9 has been shown to bind to proteins required for steroid hormone receptor binding,and RHOBTB2 indirectly regulates the steroid hormones biosynthesis through cyclin factor,and ultimately affect fat deposition.Our results suggest that the genes RHOBTB2 and SOX9 play an important role in fat deposition in broilers,by regulating steroid hormone synthesis.These findings provide new targets and directions for further studies on the mechanisms of fat deposition in chicken.
基金funded by the National Natural Science Foundation of China(Nos.31972775 and 32172971).
文摘The fish brain is crucial for adjusting to environmental changes.Metabolic changes play a vital role in the adaptation to salinity change in aquatic animals.However,few studies have evaluated the responses of the fish brain to salinity changes.To evaluate the response to various salinities,spotted scat(Scatophagus argus)was cultured in water with salinity levels of 5(low salinity:LS),25(control group:Ctrl),and 35(high salinity group:HS)for 22 days.The brain transcriptome was analyzed.In total,1698 differentially expressed genes(DEGs)were identified between the HS and Ctrl groups,and 841 DEGs were identified between the LS and Ctrl groups.KEGG analysis showed that the DEGs in the HS vs.Ctrl comparison were involved in steroid biosynthesis,terpenoid backbone biosynthesis,fatty acid biosynthesis,ascorbate and aldarate metabolism,other types of O-glycan biosynthesis,and fatty acid metabolism.Glyoxylate and dicarboxylate metabolism,one carbon pool by folate,steroid biosynthesis,and cysteine and methionine metabolism were significantly enriched in the LS vs.Ctrl comparison.Additionally,the genes related to metabolism(acc,fas,hmgcr,hmgcs1,mvd,soat1,nsdhl,sqle,cel,fdft1,dnmt3a and mtr)were significantly up-regulated in the HS vs.Ctrl comparison.The genes related to metabolism(lipa,sqle,acc,fas,bhmt,mpst,dnmt3a,mtr,hao2,LOC111225351 and hmgcs1)were significantly up-regulated,while hmgcr and soat1 were significantly down-regulated in the LS vs.Ctrl compparison.These results suggest that salinity stress affects signaling pathways and genes’expressions involved in metabolic processes in the brain,and the differences in metabolism play an important role in adaptation to hyperhaline or hypohaline environments in spotted scat.This research provides a comprehensive overview of transcriptional changes in the brain under hyperhaline or hypohaline conditions,which is helpful to understand the mechanisms underlying salinity adaptation in euryhaline fishes.
基金supported by the National Basic Research Program of China(2013CB127106)。
文摘Free cholesterol has been considered to be a critical risk factor of nonalcoholic fatty liver disease(NAFLD).It remains unknown whether dietary intake of condensed tannins(CTs)have distinguishable effects to alleviate liver damage caused by a high cholesterol diet.Male C57BL/6 mice were fed a high cholesterol diet for 6 weeks,and given CTs treatment at a dosage of 200 mg/(kg·day)at the same time.The results indicated that compared with mice fed a normal diet,a high cholesterol diet group resulted in significant weight loss,dysregulation of lipid metabolism in blood and liver,and oxidative stress in the liver,but CTs treatment dramatically reversed these negative effects.Hematoxylin and eosin(H&E)staining and frozen section observation manifested that CTs treatment could effectively reduce the deposition of liver cholesterol and tissue necrosis caused by high cholesterol intake.CTs alleviated liver injury mainly by regulating the expression of related genes in cholesterol metabolism pathway and AMPK phosphorylation.Our results confirmed that CTs have remarkable cholesterol lowering and anti-liver injury effects in vivo.
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.
基金financially supported by the National Science and Technology Program of China during the 12th Five-Year Plan Period(No.2013AA102704)the National Natural Science Foundation of China(NO:31200510)
文摘MADS-box transcription factors show highly diverse regulatory functions in a wide variety of organisms. In this study, we characterized a MADS-box gene （BpMADS12） from the white birch （Betula platyphylla Suk）. This gene is a member of the suppressor of overexpression of CO 1/tomato MADS 3 class of MADS-box genes. We generated lines overexpressing BpMADS12 and found that these had higher levels of lignin compared to that observed in nontransgenic lines. Transcriptome anal- ysis revealed numerous changes in gene expression patterns. In total, 8794 differentially expressed genes were identified, including 5006 upregulated unigenes and 3788 downregulated unigenes in BpMADS-overexpression lines. Differentially expressed genes involved in the pathways for lignin and brassinosteroid biosynthesis were significantly enriched and may have contributed to phenotypic changes. The results from a quantitative RT-PCR analysis were consistent those obtained with the transcriptome analysis.Our transcriptome analysis, in combination with measure- ment of lignin level, indicated that BpMADS12 promotes lignin synthesis through regulation of key enzymes in response to brassinosteroid signaling. These results suggest that this MADS-box protein is crucial to all subsequent structural events and provide a good foundation for studies aiming to elucidate the developmental mechanisms underlying formation of wood.
基金supported by grants from the National Natural Science Foundation of China,Youth Science Foundation Project(Grant Number 32002031)the Basic Scientific Research Operating Expenses of Provincial College in Heilongjiang Province,China(Grant Numbers 2020-KYYWF-1026,2020-KYYWF-1027)the Heilongjiang Provincial Natural Science Foundation of China(Grant Number LH2020C090).
文摘The phenotype of a common bean plant is often closely related to its yield,and the yield of plants with reduced height or poor stem development during growth is low.Mutants serve as an essential gene resource for common bean breeding genetic research.Although model plants and crops are studied to comprehend the molecular mechanisms and genetic basis of plant phenotypes,the molecular mechanism of phenotypic variation in common beans remains underexplored.We here used the mutant‘nts’as material for transcriptome sequencing analysis.This mutant was obtained through 60Co-γirradiation from the common bean variety‘A18’.Differentially expressed genes were mainly enriched in GO functional entries such as cell wall organization,auxin response and transcription factor activity.Metabolic pathways significantly enriched in KEGG analysis included plant hormone signal transduction pathways,phenylpropanoid biosynthesis pathways,and fructose and mannose metabolic pathways.AUX1(Phvul.001G241500),the gene responsible for auxin transport,may be the key gene for auxin content inhibition.In the plant hormone signal transduction pathway,AUX1 expression was downregulated and auxin transport across the membrane was blocked,resulting in stunted growth of the mutant‘nts’.The results provide important clues for revealing the molecular mechanism of‘nts’phenotype regulation in bean mutants and offer basic materials for breeding beneficial phenotypes of bean varieties.
基金supported by the National Key R&D Program(No.2018YFD0900301-03)the MNR Key Laboratory of Marine Eco-Environmental Science and Technology,China(No.MEEST-2021-04).
文摘Perfluorooctanoic acid(PFOA)is a widespread synthetic persistent organic pollutant that may enrich along the food chain and affect the growth,development,reproduction,and lipid metabolism of aquatic organisms,particularly the benthic organisms.How-ever,the toxic effects of PFOA on the half-smooth tongue sole Cynoglossus semilaevis,a commercial benthic fish in China,have rarely been reported.Because juvenile fish are sensitive to environmental pollutants,in the present study,histological assessment and tran-scriptome sequencing were performed to determine the short-term impact of PFOA on juvenile half-smooth tongue soles.Histologi-cal analysis showed that PFOA exposure caused hepatocyte rupture,intestinal villi breakage,increased goblet cell count,and brain ab-normal.Transcriptome results showed that some interesting signaling pathways,such as glycolysis/gluconeogenesis,PPAR signaling pathway and GABAergic synapse signaling pathway,were enriched after PFOA exposure.In addition,some metabolic,immune and neural genes were differentially expressed,which including ependymin,hbb1-like and gad 1,and they were up-regulated after 14 days of exposure.Transcriptome results also indicated that half-smooth tongue sole might improve energy metabolism in response to PFOA toxicity after 7 days of exposure.These findings provide a basis for studying the ecological effects of PFOA on marine benthic fishes.
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 by the National Natural Science Foundation of China,No.31700926the Priority Academic Program Development of Jiangsu Higher Education Institutions of China
文摘The neural regeneration process is driven by a wide range of molecules and pathways. Adherens junctions are critical cellular junctions for the integrity of peripheral nerves. However, few studies have systematically characterized the transcript changes in the adherens junction pathway following injury. In this study, a rat model of sciatic nerve crush injury was established by forceps. Deep sequencing data were analyzed using comprehensive transcriptome analysis at 0, 1, 4, 7, and 14 days after injury. Results showed that most individual molecules in the adherens junctions were either upregulated or downregulated after nerve injury. The m RNA expression of ARPC1 B, ARPC3, TUBA8, TUBA1 C, CTNNA2, ACTN3, MET, HGF, NME1 and ARF6, which are involved in the adherens junction pathway and in remodeling of adherens junctions, was analyzed using quantitative real-time polymerase chain reaction. Most of these genes were upregulated in the sciatic nerve stump following peripheral nerve injury, except for CTNNA2, which was downregulated. Our findings reveal the dynamic changes of key molecules in adherens junctions and in remodeling of adherens junctions. These key genes provide a reference for the selection of clinical therapeutic targets for peripheral nerve injury.
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 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Research in the J.X.laboratory is supported by the Institute for Water and Wetland Research,Radboud Universityby the Department of Biological Sciences,National University of Singaporeby the Joint Center for Single Cell Biology,Radboud University/Shanghai Jiao Tong University/Shandong Agricultural University.
文摘The rapid and enthusiastic adoption of single-cell RNA sequencing(scRNA-seq)has demonstrated that this technology is far more than just another way to perform transcriptome analysis.It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell.With this disruptive technology,it is now possible to mine heterogeneity between tissue types and within cells like never before.This enables more rapid identification of rare and novel cell types,simultaneous characterization of multiple different cell types and states,more accurate and integrated understanding of their roles in life processes,and more.However,we are only at the beginning of unlocking the full potential of scRNA-seq applications.This is particularly true for plant sciences,where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome.In this review,we compare and evaluate recent pioneering studies using the A rabidopsis root model,which has established new paradigms for scRNA-seq studies in plants.We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale.In addition,we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.
文摘High-temperature stress, like any abiotic stress, impairs the physiology and development of plants, including the stages of seed setting and ripening. We used the Affymetrix 22K Barley1 GeneChip microarray to investigate the response of developing barley （Hordeum vulgare） seeds, termed caryopses, after 0.5, 3, and 6 h of heat stress exposure; 958 induced and 1122 repressed genes exhibited spatial and temporal expression patterns that provide a detailed insight into the caryopses＇ early heat stress responses. Down-regulation of genes related to storage compound biosynthesis and cell growth provides evidence for a rapid impairment of the caryopsis＇ development. Increased levels of sugars and amino acids were indicative for both production of compatible solutes and feedback-induced accumulation of substrates for storage compound biosynthesis. Metadata analysis identified embryo and endosperm as primary locations of heat stress responses, indicating a strong impact of short-term heat stress on central developmental functions of the caryopsis. A comparison with heat stress responses in Arabidopsis shoots and drought stress responses in barley caryopses identified both conserved and presumably heat- and caryopsis-specific stress-responsive genes. Summarized, our data provide an important basis for further investigation of gene functions in order to aid an improved heat tolerance and reduced losses of yield in barley as a model for cereal crops.
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 that β-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 the β-carotene content,while the β-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(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support of the "Cooperative Research Program for Agriculture Science & Technology Development (Project No. 200908FHT020609001)" Rural Development Administration (RDA),Republic of Korea
文摘Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.
基金funded by the Hebei Provincial High-level Talents (A201901058)the Education Department of Hebei Province (QN2018138),China。
文摘Objectives:Peach(Prunus persica L.)is an ancient fruit tree that originated from China.It is the climacteric fruit belonging to genus Prunus in family Rosaceae.Ethylene,which is produced during ripening,accelerates fruit softening,and therefore peaches cannot be stored for a long time.Materials and Methods:To study the mechanism of fruit late ripening,transcriptome analysis of the fruit of a late-ripening mutant of'Jinghong'peach was performed to identify genes and pathways involved in fruit late ripening.Results:A total of 1805,1511,and 2309 genes were found to be differentially expressed in W2_vs_M1,W3_vs_M2,and W3_vs_M3,respectively.Functional enrichment analysis of the differentially expressed genes showed they were related to carotenoid biosynthesis,starch and sucrose metabolism plant hormone signal transduction,flavonoid biosynthesis,and photosynthesis.The expression trends of ripening-related genes that encode transcription factors and plant hormone signal transduction-related genes that encode enzymes were similar.Conclusions:It will help to elucidate the transcriptional regulatory network of fruit development in the spontaneous late-ripening mutant of‘Jinghong’peach and provide a theoretical basis for understanding the molecular regulatory mechanism of fruit ripening.
