The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis...The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.展开更多
Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence sugge...Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.展开更多
RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of wate...RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.展开更多
Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was...Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.展开更多
The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order t...The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.展开更多
We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using t...We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.展开更多
Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjus...Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.展开更多
Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were invest...Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.展开更多
The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In ad...The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.展开更多
Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tande...Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.展开更多
The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencin...The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.展开更多
The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect T...The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.展开更多
The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular...The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.展开更多
Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other...Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.展开更多
Safflower is an important oilseed crop that has been used in traditional Chinese medicine for thousands of years because of the clinically valuable flavonoid glycosides in its flower petals.However,the biosynthesis an...Safflower is an important oilseed crop that has been used in traditional Chinese medicine for thousands of years because of the clinically valuable flavonoid glycosides in its flower petals.However,the biosynthesis and molecular regulation of these compounds are still elusive due to the lack of a high-quality reference genome and scarce identification of key biosynthetic pathway genes in a medicinal safflower variety.Here we leveraged an integrative multi-omics strategy by combining genomic,comparative genomics,and tissue-specific transcriptome profiling with biochemical analysis to identify uridine diphosphate glycosyltransferases(UGTs)for flavonoid glycoside biosynthesis in safflower.We assembled and annotated a high-quality reference genome of a medicinal safflower variety,‘Yunhong3’.A comprehensive comparative genomic analysis indicated that an evolutionary whole-genome triplication event occurring in safflower contributed to gene amplification of the flavonoid biosynthetic pathway.By combining comparative transcriptome profiling with enzymatic reactions,we identified 11 novel UGTs that could catalyze the conversion of naringenin chalcone and phloretin to the corresponding O-glycosides.Moreover,we outlined the molecular pathway of hydroxysafflor yellow A(HSYA)biosynthesis featured by 17 newly identified UGTs with promising catalytic activity,laying the foundation for the synthetic production of HSYA.Our study reports systemic genome and gene expression information for flavonoid glycoside biosynthesis in medicinal safflower and provides insights into mechanisms regulating HSYA biosynthesis,which would facilitate the genetic improvement and synthetic bioengineering design for producing clinically valuable flavonoid glycosides in safflower.展开更多
Advances in skeletal muscle omics has expanded our understanding of exercise-induced adaptations at the molecular level.Over the past 2 decades,transcriptome studies in muscle have detailed acute and chronic responses...Advances in skeletal muscle omics has expanded our understanding of exercise-induced adaptations at the molecular level.Over the past 2 decades,transcriptome studies in muscle have detailed acute and chronic responses to resistance,endurance,and concurrent exercise,focusing on variables such as training status,nutrition,age,sex,and metabolic health profile.Multi-omics approaches,such as the integration of transcriptomic and epigenetic data,along with emerging ribosomal RNA sequencing advancements,have further provided insights into how skeletal muscle adapts to exercise across the lifespan.Downstream of the transcriptome,proteomic and phosphoproteomic studies have identified novel regulators of exercise adaptations,while single-cell/nucleus and spatial sequencing technologies promise to evolve our understanding of cellular specialization and communication in and around skeletal muscle cells.This narrative review highlights(a)the historical foundations of exercise omics in skeletal muscle,(b)current research at 3 layers of the omics cascade(DNA,RNA,and protein),and(c)applications of single-cell omics and spatial sequencing technologies to study skeletal muscle adaptation to exercise.Further elaboration of muscle's global molecular footprint using multi-omics methods will help researchers and practitioners develop more effective and targeted approaches to improve skeletal muscle health as well as athletic performance.展开更多
Anthocyanins are important flavonoid pigments in the coloration of fruits.To identify candidate genes involved in anthocyanin accumulation,metabolic and transcriptome analyses were conducted in‘Nanguo'pear and it...Anthocyanins are important flavonoid pigments in the coloration of fruits.To identify candidate genes involved in anthocyanin accumulation,metabolic and transcriptome analyses were conducted in‘Nanguo'pear and its red sport cultivar‘Nanhong'pear.The results showed that‘Nanhong'pear had significantly higher anthocyanin and flavonol contents.Additionally,transcriptomic analysis showed that there were significant differences in the expression of genes involved in phenylpropanoid and flavonoid biosynthesis pathways between the two cultivars,with PuGSTF12 being the most upregulated gene in the‘Nanhong'cultivar.Further analysis identified a novel MYB transcription factor(PuMYB93),and its silencing repressed PuGSTF12 expression and anthocyanin accumulation,suggesting it plays an essential role in the regulation of anthocyanin biosynthesis.Moreover,yeast one-hybrid analysis,electrophoretic mobility shift assay,andβ-glucuronidase assay indicated that PuMYB93 can directly bind to the PuGSTF12 promoter to positively regulate its expression.Additionally,PuGSTF12 silencing suppressed the coloration of PuMYB93-OE peels,suggesting that PuGSTF12 act downstream of PuMYB93.Overall,the findings of this study show that PuMYB93 promotes anthocyanin transport in pears by regulating PuGSTF12 expression to further enhance anthocyanin accumulation.展开更多
Ischemic stroke remains a leading cause of disability and death,with mesenchymal stem cell-derived exosomes emerging as a promising therapeutic avenue.However,the optimal timing and underlying therapeutic mechanisms o...Ischemic stroke remains a leading cause of disability and death,with mesenchymal stem cell-derived exosomes emerging as a promising therapeutic avenue.However,the optimal timing and underlying therapeutic mechanisms of exosome treatment require further elucidation.In this study,we used a murine model of middle cerebral artery occlusion to investigate the therapeutic efficacy of human umbilical cord mesenchymal stem cell-derived exosomes administered intravenously at an early(6 hours)or delayed(3 days)time point post-ischemia.Compared with delayed treatment,early administration of exosomes resulted in significantly superior efficacy,as evidenced by improved neurological function scores and reduced infarct volumes.Transcriptomic analysis of brain tissues from mice receiving early exosome treatment revealed marked downregulation of inflammation-related genes,including Ccl2,Ccl5,Cxcl10,Il-1β,Il-6,Itgam,Itgax,and Tnf-α.Metabolomic profiling of these brain tissues further identified modulation of key metabolites,including trimethylamine N-oxide,glutathione,1-stearoyl-rac-glycerol,and phosphatidylcholine,suggesting that alteration of metabolic pathways contributes to the therapeutic effect.Integrated transcriptomic and metabolomic analysis pinpointed significant modulation of pathways involving metabolism of eicosapentaenoic acid,lysine,propanoate,and tyrosine.These findings suggest that umbilical cord mesenchymal stem cell-derived exosomes,particularly when administered early post-ischemia,exert their neuroprotective effects by broadly suppressing inflammatory pathways and modulating key metabolic processes in the ischemic brain,highlighting their potential as a therapeutic intervention for ischemic stroke.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
Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses.However,the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplor...Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses.However,the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplored.This study identified a genomic region(q NLQ3.1) for head-splitting resistance on chromosome C03 through the combination of QTLseq and GPS analysis in an F_(2) population derived from hybridizing two cabbage inbred lines,‘Dazhengfu'(ZF,susceptible) and ‘103'(resistant).Traditional genetic linkage analysis narrowed q NLQ3.1 to a 74.6 kb region.Furthermore,comparative analysis of the two parental lines using transcriptomic and metabolic profiling demonstrated the crucial role of hormones in regulating head-splitting resistance.Bol028000,encoding a homologue of Arabidopsis Cytokinin Response Factor 3(CRF3),emerged as a promising candidate for head-splitting resistance and was subsequently validated through Sanger sequencing and quantitative RT-PCR(qRT-PCR).Subcellular localisation analysis revealed that Bol028000 was mainly expressed in the nucleus.Additionally,one kompetitive allele-specific PCR(KASP) marker from Bol028000 was developed and utilized to screen 42 inbred lines.These findings enhance the theoretical understanding of head-splitting resistance and provide valuable insights for the molecular breeding of head-splitting resistant cabbages.展开更多
基金supported by the National Natural Science Foundation of China(31870664)the 948 Program of National Forestry and Grassland Administration(2013-4-47)the National Key Research and Development Program of China(2022YFD2200103)。
文摘The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.
基金supported by the National Natural Science Foundation of China(31972532)the China Agricultural Research System(CARS-40-K05)the Innovation Base Cu。
文摘Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
文摘RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.
基金jointly funded by the National Natural Science Foundation of China (31661143010)the Pilot Project of Breeding of the Seven Major Crops,China (2016YFD0101803)
文摘Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.
基金The National Natural Science Foundation of China under contract No.40976089the State Science&Technology Support Program in the 12th Five Year Plan of China under contract No.2011BAD13B05the National High-tech R&D Program of China(863 Program) under contract No.2012AA10A412
文摘The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.
基金supported by the grants from the Ministry of Science and Technology of China (No.2006AA02Z331 and 2004CB117404)the Key Project of Chinese Academy of Sciences (No.KSCX2-YW-N-020) to Liangbiao ChenNSF OPP 0636696 to C-H CC
文摘We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.
文摘Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.
基金Supported by the Project of China One-Belt-One-Road Foreign Expert Research Collaboration,Ministry of Science and Technology,China (No.DL2021002001L)the Open Project Program of State Key Laboratory of Food Nutrition and Safety,Tianjin University of Science&Technology (No.SKLFNS-KF-202205)。
文摘Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214)the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015)National Science Foundation of China (grant no. 30960027)
文摘The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
文摘Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.
基金supported by the internal fund(5020)of the Temasek Life Sciences Laboratory,Singapore。
文摘The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.
基金supported by AP21PPQS&T00C108 from USDA-APHIS to ELS。
文摘The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.
基金This study was partially supported by grants from the National Natural Science Foundation of China (31490591,31330032,and 61327902)the National Key R&D Program of China (2017YFA 0700500)+1 种基金the Frontier Key Project of the Chinese Academy of Sciences (QYZDJ-SSW-SMCO25)Shanghai Municipal Science and Technology Major Project (2018SHZDZX05).
文摘The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.
文摘Alzheimer’s disease(AD)is the most common form of dementia.In addition to the lack of effective treatments,there are limitations in diagnostic capabilities.The complexity of AD itself,together with a variety of other diseases often observed in a patient’s history in addition to their AD diagnosis,make deciphering the molecular mechanisms that underlie AD,even more important.Large datasets of single-cell RNA sequencing,single-nucleus RNA-sequencing(snRNA-seq),and spatial transcriptomics(ST)have become essential in guiding and supporting new investigations into the cellular and regional susceptibility of AD.However,with unique technology,software,and larger databases emerging;a lack of integration of these data can contribute to ineffective use of valuable knowledge.Importantly,there was no specialized database that concentrates on ST in AD that offers comprehensive differential analyses under various conditions,such as sex-specific,region-specific,and comparisons between AD and control groups until the new Single-cell and Spatial RNA-seq databasE for Alzheimer’s Disease(ssREAD)database(Wang et al.,2024)was introduced to meet the scientific community’s growing demand for comprehensive,integrated,and accessible data analysis.
基金supported by the ability establishment of sustainable use for valuable Chinese medicine resources(Grant No.2060302)the National Key R&D Program of China(Grant No.2018YFA0900603)+1 种基金the National Key R&D Program of China(Grant No.2020YFA0908000)the crosswise task based on DEYUANTANG pharmacy Co.,Ltd.Shanxi,China(Grant No.DYTKY180725).
文摘Safflower is an important oilseed crop that has been used in traditional Chinese medicine for thousands of years because of the clinically valuable flavonoid glycosides in its flower petals.However,the biosynthesis and molecular regulation of these compounds are still elusive due to the lack of a high-quality reference genome and scarce identification of key biosynthetic pathway genes in a medicinal safflower variety.Here we leveraged an integrative multi-omics strategy by combining genomic,comparative genomics,and tissue-specific transcriptome profiling with biochemical analysis to identify uridine diphosphate glycosyltransferases(UGTs)for flavonoid glycoside biosynthesis in safflower.We assembled and annotated a high-quality reference genome of a medicinal safflower variety,‘Yunhong3’.A comprehensive comparative genomic analysis indicated that an evolutionary whole-genome triplication event occurring in safflower contributed to gene amplification of the flavonoid biosynthetic pathway.By combining comparative transcriptome profiling with enzymatic reactions,we identified 11 novel UGTs that could catalyze the conversion of naringenin chalcone and phloretin to the corresponding O-glycosides.Moreover,we outlined the molecular pathway of hydroxysafflor yellow A(HSYA)biosynthesis featured by 17 newly identified UGTs with promising catalytic activity,laying the foundation for the synthetic production of HSYA.Our study reports systemic genome and gene expression information for flavonoid glycoside biosynthesis in medicinal safflower and provides insights into mechanisms regulating HSYA biosynthesis,which would facilitate the genetic improvement and synthetic bioengineering design for producing clinically valuable flavonoid glycosides in safflower.
基金supported by National Institutes of Health(NIH)Grants AG063944 and AG080047 to KAM.
文摘Advances in skeletal muscle omics has expanded our understanding of exercise-induced adaptations at the molecular level.Over the past 2 decades,transcriptome studies in muscle have detailed acute and chronic responses to resistance,endurance,and concurrent exercise,focusing on variables such as training status,nutrition,age,sex,and metabolic health profile.Multi-omics approaches,such as the integration of transcriptomic and epigenetic data,along with emerging ribosomal RNA sequencing advancements,have further provided insights into how skeletal muscle adapts to exercise across the lifespan.Downstream of the transcriptome,proteomic and phosphoproteomic studies have identified novel regulators of exercise adaptations,while single-cell/nucleus and spatial sequencing technologies promise to evolve our understanding of cellular specialization and communication in and around skeletal muscle cells.This narrative review highlights(a)the historical foundations of exercise omics in skeletal muscle,(b)current research at 3 layers of the omics cascade(DNA,RNA,and protein),and(c)applications of single-cell omics and spatial sequencing technologies to study skeletal muscle adaptation to exercise.Further elaboration of muscle's global molecular footprint using multi-omics methods will help researchers and practitioners develop more effective and targeted approaches to improve skeletal muscle health as well as athletic performance.
基金supported by the National Natural Science Foundation of China(32372641)the Shandong Provincial Natural Science Foundation,China(ZR2024QC143)the Liaoning Provincial Natural Science Foundation,China(2022-MS-258)。
文摘Anthocyanins are important flavonoid pigments in the coloration of fruits.To identify candidate genes involved in anthocyanin accumulation,metabolic and transcriptome analyses were conducted in‘Nanguo'pear and its red sport cultivar‘Nanhong'pear.The results showed that‘Nanhong'pear had significantly higher anthocyanin and flavonol contents.Additionally,transcriptomic analysis showed that there were significant differences in the expression of genes involved in phenylpropanoid and flavonoid biosynthesis pathways between the two cultivars,with PuGSTF12 being the most upregulated gene in the‘Nanhong'cultivar.Further analysis identified a novel MYB transcription factor(PuMYB93),and its silencing repressed PuGSTF12 expression and anthocyanin accumulation,suggesting it plays an essential role in the regulation of anthocyanin biosynthesis.Moreover,yeast one-hybrid analysis,electrophoretic mobility shift assay,andβ-glucuronidase assay indicated that PuMYB93 can directly bind to the PuGSTF12 promoter to positively regulate its expression.Additionally,PuGSTF12 silencing suppressed the coloration of PuMYB93-OE peels,suggesting that PuGSTF12 act downstream of PuMYB93.Overall,the findings of this study show that PuMYB93 promotes anthocyanin transport in pears by regulating PuGSTF12 expression to further enhance anthocyanin accumulation.
基金supported by the National Key R&D Program of China,Nos.2021YFA1101703/2021YFA1101700(to YD).
文摘Ischemic stroke remains a leading cause of disability and death,with mesenchymal stem cell-derived exosomes emerging as a promising therapeutic avenue.However,the optimal timing and underlying therapeutic mechanisms of exosome treatment require further elucidation.In this study,we used a murine model of middle cerebral artery occlusion to investigate the therapeutic efficacy of human umbilical cord mesenchymal stem cell-derived exosomes administered intravenously at an early(6 hours)or delayed(3 days)time point post-ischemia.Compared with delayed treatment,early administration of exosomes resulted in significantly superior efficacy,as evidenced by improved neurological function scores and reduced infarct volumes.Transcriptomic analysis of brain tissues from mice receiving early exosome treatment revealed marked downregulation of inflammation-related genes,including Ccl2,Ccl5,Cxcl10,Il-1β,Il-6,Itgam,Itgax,and Tnf-α.Metabolomic profiling of these brain tissues further identified modulation of key metabolites,including trimethylamine N-oxide,glutathione,1-stearoyl-rac-glycerol,and phosphatidylcholine,suggesting that alteration of metabolic pathways contributes to the therapeutic effect.Integrated transcriptomic and metabolomic analysis pinpointed significant modulation of pathways involving metabolism of eicosapentaenoic acid,lysine,propanoate,and tyrosine.These findings suggest that umbilical cord mesenchymal stem cell-derived exosomes,particularly when administered early post-ischemia,exert their neuroprotective effects by broadly suppressing inflammatory pathways and modulating key metabolic processes in the ischemic brain,highlighting their potential as a therapeutic intervention for ischemic stroke.
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funded by the Agricultural Development Program through Science and Technology of Shanghai,China (2022-02-08-00-12-F01099)the National Key R&D Program of China (2023YFD1201501)+1 种基金the Science and Technology Commission of Shanghai Municipality,China (22DX1900100)the Excellent Team Project of Shanghai Academy of Agricultural Sciences,China (2022(007))。
文摘Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses.However,the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplored.This study identified a genomic region(q NLQ3.1) for head-splitting resistance on chromosome C03 through the combination of QTLseq and GPS analysis in an F_(2) population derived from hybridizing two cabbage inbred lines,‘Dazhengfu'(ZF,susceptible) and ‘103'(resistant).Traditional genetic linkage analysis narrowed q NLQ3.1 to a 74.6 kb region.Furthermore,comparative analysis of the two parental lines using transcriptomic and metabolic profiling demonstrated the crucial role of hormones in regulating head-splitting resistance.Bol028000,encoding a homologue of Arabidopsis Cytokinin Response Factor 3(CRF3),emerged as a promising candidate for head-splitting resistance and was subsequently validated through Sanger sequencing and quantitative RT-PCR(qRT-PCR).Subcellular localisation analysis revealed that Bol028000 was mainly expressed in the nucleus.Additionally,one kompetitive allele-specific PCR(KASP) marker from Bol028000 was developed and utilized to screen 42 inbred lines.These findings enhance the theoretical understanding of head-splitting resistance and provide valuable insights for the molecular breeding of head-splitting resistant cabbages.
