Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome bac...Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome background. Transcriptomic analysis based on high-throughput RNA sequencing has been shown to be an efficient and powerful method for the discovery of relevant genes in non-model and genome reference-free organisms. Here, we constructed two c DNA libraries(control and Cd exposure groups) from the digestive gland of C. farreri and compared the transcriptomic data between them. A total of 227 673 transcripts were assembled into 105 071 unigenes, most of which shared high similarity with sequences in the NCBI non-redundant protein database. For functional classification, 24 493 unigenes were assigned to Gene Ontology terms. Additionally, Eu Karyotic Ortholog Groups and Kyoto Encyclopedia of Genes and Genomes analyses assigned 12 028 unigenes to 26 categories and 7 849 unigenes to five pathways, respectively. Comparative transcriptomics analysis identified 3 800 unigenes that were differentially expressed in the Cd-treated group compared with the control group. Among them, genes associated with heavy metal accumulation were screened, including metallothionein, divalent metal transporter, and metal tolerance protein. The functional genes and predicted pathways identified in our study will contribute to a better understanding of the metabolic and immune system in the digestive gland of C. farreri. In addition, the transcriptomic data will provide a comprehensive resource that may contribute to the understanding of molecular mechanisms that respond to marine pollutants in bivalves.展开更多
The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the...The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.展开更多
Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explor...Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explored the adaptation mechanisms through comparative transcriptome sequencing and analysis of different tissues between seep mussels and vent mussels.We performed the comparative transcriptome sequencing and analysis for three tissue types(gill,mantle,and adductor muscle)of Bathymodiolus mussels collected from a cold seeping site Station S 11 and the 50-km away hydrothermal field Minami-Ensei Knoll in the Okinawa Trough.Results show that gene expression patterns had distinct tissue specificity.Compared with the non-endosymbiotic tissues(mantle and adductor muscle),the significantly strengthened gene functions in endosymbiotic gill included microbial recognition(fibrinogen C domain-containing protein 1-B-like(fibcd),fibrinogen-related protein 8(frp),peptidoglycan recognition proteins(pgrp),and C-type lectin(clec)),cell apoptosis and immunity(interferon regulatory factor 1/2-like 1(ir f),cathepsin D(ctsd),caspase 2(casp 2)),and antioxidant capacity(copper/zinc superoxide dismutase(czsod),glutathione peroxidase(gpx),selenoprotein(sel)),in both seep and vent individuals.Consistent with metal accumulation,high expression levels of genes related to heavy metal detoxification(cytochrome P 450(cyp),ferritin-like(ftl),metallothionein(mt),glutathione S-transferase(gst))were also observed in gill.Moreover,to adapt to high hydrostatic pressure in the deep sea,the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways associated with cellular community were significantly enriched in all three tissues,suggesting the regulation of cell structure and cell adhesion at transcriptional level.This study obtained gene expression profiles of deep-sea mussels subsisting at cold seep and hydrothermal vent sites,which could lay foundations for comprehensive investigations of molecular basis in adaptation of deep-sea mussels to the two extreme ecosystems.展开更多
Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we in...Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we investigated the transcriptional differences of eight c DNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line,W14, using next generation sequencing system. A total of41302 assembled transcripts were obtained and from these,25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and3584 transcripts were found to be differentially expressed in leaf, stem and storage root(150 d after planting),respectively, between Arg7 and W14 and ascribed to 103,93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I(PSA) and photosystem II(PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes(PFK, PGK and PK, GAPDH)coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation(INVs), amylose synthesis(GBSS) and hydrolysis(RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation(ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed therelationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.展开更多
Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize...Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.展开更多
Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as...Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.展开更多
Large yellow croaker(Larimichthys crocea)is an economically important fish,with the annual production ranking second among maricultured fish in China.Outbreaks of visceral white nodules disease caused by Pseudomonas p...Large yellow croaker(Larimichthys crocea)is an economically important fish,with the annual production ranking second among maricultured fish in China.Outbreaks of visceral white nodules disease caused by Pseudomonas plecoglossicida have led to substantial economic losses for the L.crocea aquaculture industry.However,L.crocea defense strategies against P.plecoglossicida infection,especially the role of microRNAs(miRNAs)in the defense against P.plecoglossicida,are poorly understood.Here,we analyzed changes in the mRNA and miRNA expression profiles in the spleen of L.crocea at 96 h post-infection and explored its defensive strategies.Principal component analysis(PCA)showed that P.plecoglossicida infection brought about a profound remodeling of both the miRNA and mRNA profiles.Enrichment analysis showed that the inflammatory response(IL-17 signaling pathway,chemokines and chemokine receptor pathway),ATP synthesis(TCA cycle and oxidative phosphorylation),apoptosis and necroptosis(TNF signaling pathway),and proteolysis(proteasome pathway)were enriched and upregulated by P.plecoglossicida.Thus,P.plecoglossicida infection activated the inflammatory response,stimulated ATP synthesis,and accelerated apoptosis and necroptosis,and promoted proteasome-mediated protein degradation.Additionally,integrated analysis identified 568 miRNA-mRNA pairs.KEGG enrichment analysis of the miRNA targets showed that the enriched pathways included cytokine-cytokine receptor interaction,the chemokine signaling pathway,the C-type lectin receptor signaling pathway,and apoptosis.Integrated analysis identified 14 miRNAs which targeted 44 immune-related genes.Altogether,our results revealed not only the role of the inflammatory response,energy metabolism,apoptosis and necroptosis,and the proteasome pathway in L.crocea defense against P.plecoglossicida infection,but also the regulatory networks of miRNAs associated with host defense against P.plecoglossicida.展开更多
Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agricultur...Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.展开更多
Brassica napus L. (B. napus), recognized as a significant cash and oil crop, faces challenges in popularization and application in northern China due to its limited cold resistance. Clarifying the mechanism of cold st...Brassica napus L. (B. napus), recognized as a significant cash and oil crop, faces challenges in popularization and application in northern China due to its limited cold resistance. Clarifying the mechanism of cold stress on gene regulation and signal transduction in B. napus is crucial. To address these issues, we conducted transcriptome sequencing and gene expression analysis, along with gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway profiling under natural (25℃) and cold (4℃) conditions in cold tolerant 16VHNTS309 and weak cold-resistant Tianyou 2238 B. napus seedlings. Enhanced genomic annotation was achieved through additional sequencing. A total of 6127 and 8531 differentially expressed genes (DEG) were identified in 16VHNTS309 and Tianyou 2238, respectively. The expression patterns of 23 DEGs were validated by quantitative real-time PCR (qRT-PCR), confirming the RNA-Seq results. Under cold stress, 58 pathways in 16VHNTS309 demonstrated significant changes (q-Value < 0.05), compared to 9 pathways in Tianyou 2238 (q-Value < 0.05), highlighting B. napus’ sophisticated regulatory network which aids in managing growth and development challenges. After 48 h of cold stress treatment, genes associated with reactive oxygen species (ROS) clearance, such as those involved in antioxidant VB6, sulfur metabolism, peroxisomes, and phagosomes, were notably up-regulated in 16VHNTS309, indicating its robust ROS clearance capability. Significant gene expressions within Ca^(2+), MAPK, and transcription factor pathways related to ROS suggest that varieties with strong cold resistance possess a complex signal regulation mechanism. Comprehensive analyses of stomatal cells, physiological parameters of ROS, ABA, and H2S, along with transcriptomic data, revealed that optimal ROS levels interact with ABA and H2S to regulate stomatal closure in B. napus 16VHNTS309 under the influence of antioxidant enzymes.展开更多
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
Rosa sterilis S.D.Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value.Many of R.sterills’organs are covered with different types of trichomes or prickles that dir...Rosa sterilis S.D.Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value.Many of R.sterills’organs are covered with different types of trichomes or prickles that directly affect fruit appearance and plant management.This study used RNA sequencing technology to analyze the transcriptomes of two parts of the inflorescence branch,namely inflorescence stems with flagellated trichomes and pedicels with both flagellated and glandular trichomes.Comparative transcriptomic analysis showed that many transcription factors(TFs)are potentially involved in the formation and development of trichomes.The accumulation of RsETC1,a TF of the R3-MYB family,was significantly higher in inflorescence stems than in pedicels;quantitative reverse transcription PCR(qRTPCR)verified that its expression was significantly higher in inflorescence stems than in pedicels during the first three development stages,indicating its inhibitory action on the initiation of glandular trichomes in R.sterilis.The mRNA level of RsETC1 accumulated to significantly higher levels in trichomeless tissues than in tissues with trichromes,suggesting that this gene may inhibit the formation of trichomes in R.sterilis.Over-expression of RsETC1 in Arabidopsis resulted in glabrous phenotypes,and the expression of trichome-related endogenous genes,except for TTG1,was markedly reduced.In addition,the contents of the phytohormones jasmonic acid(JA),gibberellin A3(GA_(3)),and cytokinins(CKs)in pedicels were significantly higher than those in inflorescence stems,and the expression patterns of the genes related to hormone biosynthesis and signal transduction presented consistent responses,suggesting that the transduction of these hormones might be crucial for trichome initiation and development.These data provide a new perspective for revealing the molecular mechanism of trichome formation in R.sterilis.展开更多
The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skir...The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skirt width.Studies focused on these sex disparities have largely neglected potential sex differences in growth.Here,we performed RNA sequencing of muscle tissue components from 1-year-old specimens to reveal gene expression patterns in P.sinensis.In our male and female cohorts,our analysis revealed,respectively,388 and 526 upregulated differentially expressed genes(DEGs)and 1129 and 635 downregulated DEGs.Through weighted coexpression network analysis(WGCNA)and integration with phenotype data,we established two main gene modules:a light yellow module encompassing 191 genes(e.g.,ACACB,CTH,HADHA,and CTNNB)that demonstrated a positive correlation with population traits,and a black module comprising 298 genes(e.g.,CAV3,PIK3CD,SMAD3,and VEGFA)that demonstrated a negative correlation with population traits.We also performed a DEG evaluation and gene set enrichment analysis across individuals of different sizes and noted that pathways such as protein digestion and assimilation(ko04974),were substantially augmented in larger specimens.In these pathways,the collagen(COL)and solute carrier(SLC)gene families were noted to be crucial for sustaining body structure and facilitating nutrient and metabolite transportation.In conclusion,we elucidated the essential modules,pivotal genes,and pathways involved in gene expression differences among various P.sinensis size groupings.Our results provide novel insights for future studies on growth discrepancies in P.sinensis.展开更多
With staggering progress on genetic manipulation strategies,Saccharomyces cerevisiae is becoming an ideal cell factory for the de novo biosynthesis of lipid compounds.However,due to their hydrophobicity,lipids tend to...With staggering progress on genetic manipulation strategies,Saccharomyces cerevisiae is becoming an ideal cell factory for the de novo biosynthesis of lipid compounds.However,due to their hydrophobicity,lipids tend to be accumulated within intracellular spaces and cause a high burden on cell activity and induce product inhibition effect,which ultimately restricted the lipids biomanufacturing for industrial application.Herein,an oleic acid stress(OAS)model was applied for the long-time domestication of BY4741 cells,and a subclone of A-22 was obtained through a series of acclimation(0.1%glucose and 0.2%oleic acid),showing increased accumulation of both biomass and intracellular lipid droplets compared to WT.Comparative transcriptome analysis indicated that compared to fatty acid metabolism,most transcripts enriched in the pathways of glucose catabolism(glycolysis and citrate cycle)and lipid synthesis(phospholipid and sterol)were down-regulated under OAS.While interestingly,most the above transcripts tended to be‘restored’in adapted strain A-22.In addition,for physical adaptation,significant increase of phosphatidylcholines was identified by lipidomic analysis,which probably caused the subsequent subcellular expansion of peroxisomes and lipid droplets as observed in the adapted strain,since phosphatidylcholines are the major constituent of their membranes.The present study systematically investigated both the phenotype change and molecular mechanism on adaptation of S.cerevisiae towards oily environment.Detailed informa-tion on functional transcripts may provide novel rational modification targets to reinforce the hydrophobic lipids biosynthesis within S.cerevisiae engineered cell factory.展开更多
Both activated carbon and magnetite have been reported to promote the syntrophic growth of Geobacter metallireducens and Geobacter sulfurreducens co-cultures, the first model to show direct interspecies electron trans...Both activated carbon and magnetite have been reported to promote the syntrophic growth of Geobacter metallireducens and Geobacter sulfurreducens co-cultures, the first model to show direct interspecies electron transfer (DIET); however, differential transcriptomics of the promotion on co-cultures with these two conductive materials are unknown. Here, the comparative transcriptomic analysis of G. metallireducens and G. sulfurreducens co-cultures with granular activated carbon (GAC) and magnetite was reported. More than 2.6-fold reduced transcript abundances were determined for the uptake hydrogenase genes of G. sulfurreducens as well as other hydrogenases in those co-cultures to which conductive materials had been added. This is consistent with electron transfer in G. metallireducens-G. sulfurreducens co-cultures as evinced by direct interspecies electron transfer (DIET). Transcript abundance for the structural component of electrically conductive pili (e-pili), PilA, was 2.2-fold higher in G. metallireducens, and, in contrast, was 14.9-fold lower in G. sulfurreducens in co-cultures with GAC than in Geobacters co-cultures without GAC. However, it was 9.3-fold higher in G. sulfurreducens in co-cultures with magnetite than in Geobacters co-cultures. Mutation results showed that GAC can be substituted for the e-pili of both strains but magnetite can only compensate for that of G. sulfurreducens, indicating that the e-pili is a more important electron acceptor for the electron donor strain of G. metallireducens than for G. sulfurreducens. Transcript abundance for G. metallireducens c-type cytochrome gene GMET_RS14535, a homologue to c-type cytochrome gene omcE of G. sulfurreducens was 9.8-fold lower in co-cultures with GAC addition, while that for OmcS of G. sulfurreducens was 25.1-fold higher in co-cultures with magnetite, than in that without magnetite. Gene deletion studies showed that neither GAC nor magnetite can completely substitute the cytochrome (OmcE homologous) of G. metallireducens but compensate for the cytochrome (OmcS) of G. sulfurreducens. Moreover, some genes associated with central metabolism were up-regulated in the presence of both GAC and magnetite; however, tricarboxylic acid cycle gene transcripts in G. sulfurreducens were not highly-expressed in each of these amended co-cultures, suggesting that there was considerable redundancy in the pathways utilised by G. sulfurreducens for electron transfer to reduce fumarate with the amendment of GAC or magnetite. These results support the DIET model of G. metallireducens and G. sulfurreducens and suggest that e-pili and cytochromes of the electron donor strain are more important than that of the electron acceptor strain, indicating that comparative transcriptomics may be a promising route by which to reveal different responses of electron donor and acceptor during DIET in co-cultures.展开更多
Nitrogen(N)is essential for rice growth;however,the transcriptional regulation of the primary nitrogen response(PNR),characterized by the rapid upregulation of N uptake and assimilation genes upon N resup-ply,remains ...Nitrogen(N)is essential for rice growth;however,the transcriptional regulation of the primary nitrogen response(PNR),characterized by the rapid upregulation of N uptake and assimilation genes upon N resup-ply,remains poorly understood.This study investigated the dynamics of the PNR in the roots of two rice cultivars(Zhenshan 97 and Nipponbare)via time-series Assay for Transposase-Accessible Chromatin us-ing sequencing and RNA sequencing analyses within 2 h of ammonium nitrate resupply.Regulatory regions responsive to N induction were precisely identified.Coordinated and cascading changes in chromatin accessibility and gene expression were observed,with chromatin state frequently preceding transcrip-tional changes.Integrative analysis of expression–chromatin accessibility associations revealed a redun-dant N-responsive regulatory network.OsLBD38 and OsLBD39,identified as early-response regulators,transcriptionally suppress nitrate reductases while enhancing nitrite reductases;they may function as metabolic safeguarders to prevent nitrite accumulation.OsbZIP23 was identified as a novel regulator directly binding to the promoters of N uptake and metabolism genes,regulating genes in patterns opposite to LBD-regulated genes,suggesting a complex regulatory interplay.Cross-species comparisons with Ara-bidopsis highlighted the conserved N-responsive regulatory roles of these hub regulators and their targets.Comparative analyses between cultivars revealed expression divergence and genetic differentiation in N-responsive genes,implying indica/japonica-specific adaptations.Furthermore,deep learning predic-tions of chromatin accessibility between cultivars indicated that expression variation in N uptake and meta-bolism genes is primarily influenced by trans-acting regulatory factors.These findings provide a compre-hensive view of the dynamic regulatory landscape governing the PNR in rice.展开更多
Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at leas...Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.展开更多
As an important seedling source,monospores closely associate with yields in nori farming.However,the molecular mechanism underlying differences in monospore production for different strains remains unknown.Comparative...As an important seedling source,monospores closely associate with yields in nori farming.However,the molecular mechanism underlying differences in monospore production for different strains remains unknown.Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain(WT)and spore deficient mutant(Y1)of Pyropia chauhanii.The WT strain that produces monospores in abundance exhibited more differentially expressed genes(DEGs)in both number and higher fold-changes than the Y1 strain incapable of producing monospores,indicating that the specific regulation of genes is involved in monospore production.Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram:one expressed only in WT strain,another expressed only in Y1 strain,and the third shared in both strains.DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website.Gene regulatory networks of WT were functionally enriched in the processing,proteolysis,and transport of proteins,especially within the small GTPase protein family,which might be account for the monospore production ability,whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy,which might be account for the rapid growth of blades.We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits.These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities,which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production.展开更多
The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:rumi...The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.展开更多
Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed ...Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.展开更多
There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plan...There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.展开更多
基金Supported by the Shandong Provincial Post-Doctoral Special Fund Innovative Project(No.S43201403)the Post-Doctoral Applied Research Project of Qingdao City(No.Q51201413)the Shandong Provincial Natural Science Foundation,China(No.ZR2015PD004)
文摘Chlamys farreri is an economically important mollusk that can accumulate excessive amounts of cadmium(Cd). Studying the molecular mechanism of Cd accumulation in bivalves is difficult because of the lack of genome background. Transcriptomic analysis based on high-throughput RNA sequencing has been shown to be an efficient and powerful method for the discovery of relevant genes in non-model and genome reference-free organisms. Here, we constructed two c DNA libraries(control and Cd exposure groups) from the digestive gland of C. farreri and compared the transcriptomic data between them. A total of 227 673 transcripts were assembled into 105 071 unigenes, most of which shared high similarity with sequences in the NCBI non-redundant protein database. For functional classification, 24 493 unigenes were assigned to Gene Ontology terms. Additionally, Eu Karyotic Ortholog Groups and Kyoto Encyclopedia of Genes and Genomes analyses assigned 12 028 unigenes to 26 categories and 7 849 unigenes to five pathways, respectively. Comparative transcriptomics analysis identified 3 800 unigenes that were differentially expressed in the Cd-treated group compared with the control group. Among them, genes associated with heavy metal accumulation were screened, including metallothionein, divalent metal transporter, and metal tolerance protein. The functional genes and predicted pathways identified in our study will contribute to a better understanding of the metabolic and immune system in the digestive gland of C. farreri. In addition, the transcriptomic data will provide a comprehensive resource that may contribute to the understanding of molecular mechanisms that respond to marine pollutants in bivalves.
基金supported by the National Key Research and Development Program (2022YEF0203200)National Science and Technology Innovation 2030 Major Program (STI2030-2021ZD0200100)National Key Research and Development Program (2018YFA0801400,2021YFA0805100)。
文摘The amniote pallium,a vital component of the forebrain,exhibits considerable evolutionary divergence across species and mediates diverse functions,including sensory processing,memory formation,and learning.However,the relationships among pallial subregions in different species remain poorly characterized,particularly regarding the identification of homologous neurons and their transcriptional signatures.In this study,we utilized singlenucleus RNA sequencing to examine over 130?000 nuclei from the macaque(Macaca fascicularis)neocortex,complemented by datasets from humans(Homo sapiens),mice(Mus musculus),zebra finches(Taeniopygia guttata),turtles(Chrysemys picta bellii),and lizards(Pogona vitticeps),enablingcomprehensivecross-species comparison.Results revealed transcriptomic conservation and species-specific distinctions within the amniote pallium.Notable similarities were observed among cell subtypes,particularly within PVALB+inhibitory neurons,which exhibited species-preferred subtypes.Furthermore,correlations between pallial subregions and several transcription factor candidates were identified,including RARB,DLX2,STAT6,NR3C1,and THRB,with potential regulatory roles in gene expression in mammalian pallial neurons compared to their avian and reptilian counterparts.These results highlight the conserved nature of inhibitory neurons,remarkable regional divergence of excitatory neurons,and species-specific gene expression and regulation in amniote pallial neurons.Collectively,these findings provide valuable insights into the evolutionary dynamics of the amniote pallium.
基金Supported by the National Natural Science Foundation of China(Nos.91858208,92358301)the Laoshan Laboratory(No.LSKJ 202203500),the China Postdoctoral Science Foundation of China(No.2019M663209)the Fundamental Research Funds for the Central Universities in China(No.19lGPY100)。
文摘Bathymodiolus mussels distribute in both deep-sea cold seep and hydrothermal vent environments,whose endosymbiotic gill tissue is a prominent character for the adaptation of extreme habitats.However,few studies explored the adaptation mechanisms through comparative transcriptome sequencing and analysis of different tissues between seep mussels and vent mussels.We performed the comparative transcriptome sequencing and analysis for three tissue types(gill,mantle,and adductor muscle)of Bathymodiolus mussels collected from a cold seeping site Station S 11 and the 50-km away hydrothermal field Minami-Ensei Knoll in the Okinawa Trough.Results show that gene expression patterns had distinct tissue specificity.Compared with the non-endosymbiotic tissues(mantle and adductor muscle),the significantly strengthened gene functions in endosymbiotic gill included microbial recognition(fibrinogen C domain-containing protein 1-B-like(fibcd),fibrinogen-related protein 8(frp),peptidoglycan recognition proteins(pgrp),and C-type lectin(clec)),cell apoptosis and immunity(interferon regulatory factor 1/2-like 1(ir f),cathepsin D(ctsd),caspase 2(casp 2)),and antioxidant capacity(copper/zinc superoxide dismutase(czsod),glutathione peroxidase(gpx),selenoprotein(sel)),in both seep and vent individuals.Consistent with metal accumulation,high expression levels of genes related to heavy metal detoxification(cytochrome P 450(cyp),ferritin-like(ftl),metallothionein(mt),glutathione S-transferase(gst))were also observed in gill.Moreover,to adapt to high hydrostatic pressure in the deep sea,the Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways associated with cellular community were significantly enriched in all three tissues,suggesting the regulation of cell structure and cell adhesion at transcriptional level.This study obtained gene expression profiles of deep-sea mussels subsisting at cold seep and hydrothermal vent sites,which could lay foundations for comprehensive investigations of molecular basis in adaptation of deep-sea mussels to the two extreme ecosystems.
基金supported by the National Natural Science Foundation of China (31261140363, 31171230)the National Basic Research and Development Program (2010CB126601)+1 种基金China Agriculture Research System (CARS-12wwq)the Hainan Province Innovative Research Team Foundation (2016CXTD013)
文摘Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics.Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not.Here, we investigated the transcriptional differences of eight c DNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line,W14, using next generation sequencing system. A total of41302 assembled transcripts were obtained and from these,25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and3584 transcripts were found to be differentially expressed in leaf, stem and storage root(150 d after planting),respectively, between Arg7 and W14 and ascribed to 103,93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I(PSA) and photosystem II(PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes(PFK, PGK and PK, GAPDH)coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation(INVs), amylose synthesis(GBSS) and hydrolysis(RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation(ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed therelationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.
基金supported by the Ministerio de Economía, Industriay Competitividad (MEIC, grants BIO2017-83472R, RED2018-102407-T, and Ry C17MESFB)by the Convenio Plurianual between Comunidad de Madrid (CM) and Universidad Politécnica de Madrid (UPM) through the Programa de Apoyo a la Realización de Proyectos de I+D para Jóvenes Investigadores (APOYO-JOVENES-SUR6Q9-22-Y)+4 种基金Ry C grant (Ry C2017-21814) from the MEICPlan Propio from the UPM financed MESMEIC to I.R-D (PRE2018083375)Comunidad de Madrid to G.R-H (PEJD-2019-PRE/ BIO-15882)Programa Propio UPM to A.G。
文摘Plants experience different abiotic/biotic stresses,which trigger their molecular machinery to cope with them. Besides general mechanisms prompted by many stresses, specific mechanisms have been introduced to optimize the response to individual threats. However, these key mechanisms are difficult to identify. Here, we introduce an in-depth species-specific transcriptomic analysis and conduct an extensive meta-analysis of the responses to related species to gain more knowledge about plant responses. The spider mite Tetranychus urticae was used as the individual species, several arthropod herbivores as the related species for meta-analysis, and Arabidopsis thaliana plants as the common host. The analysis of the transcriptomic data showed typical common responses to herbivory, such as jasmonate signaling or glucosinolate biosynthesis. Also, a specific set of genes likely involved in the particularities of the Arabidopsis-spider mite interaction was discovered. The new findings have determined a prominent role in this interaction of the jasmonateinduced pathways leading to the biosynthesis of anthocyanins and tocopherols. Therefore, tandem individual/general transcriptomic profiling has been revealed as an effective method to identify novel relevant processes and specificities in the plant response to environmental stresses.
基金supported by the National Natural Science Foundation of China (82021001 and 31825018 to Q.S., 32370658 to Y.M.,82001372 to X.Y.)National Key Research and Development Program of China (2022YFF0710901)+2 种基金National Science and Technology Innovation2030 Major Program (2021ZD0200900) to Q.S.Shanghai Pujiang Program (22PJ1407300)Shanghai Jiao Tong University 2030 Initiative (WH510363001-7) to Y.M。
文摘Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.
基金The National Key Research and Development Program of China under contract No.2022YFD2401002the National Natural Science Foundation of China under contract No.32102784+1 种基金the Natural Science Foundation of Fujian Province under contract No.2022J01211209the Fund of the Institute of Oceanology of Fuzhou under contract No.2021F02.
文摘Large yellow croaker(Larimichthys crocea)is an economically important fish,with the annual production ranking second among maricultured fish in China.Outbreaks of visceral white nodules disease caused by Pseudomonas plecoglossicida have led to substantial economic losses for the L.crocea aquaculture industry.However,L.crocea defense strategies against P.plecoglossicida infection,especially the role of microRNAs(miRNAs)in the defense against P.plecoglossicida,are poorly understood.Here,we analyzed changes in the mRNA and miRNA expression profiles in the spleen of L.crocea at 96 h post-infection and explored its defensive strategies.Principal component analysis(PCA)showed that P.plecoglossicida infection brought about a profound remodeling of both the miRNA and mRNA profiles.Enrichment analysis showed that the inflammatory response(IL-17 signaling pathway,chemokines and chemokine receptor pathway),ATP synthesis(TCA cycle and oxidative phosphorylation),apoptosis and necroptosis(TNF signaling pathway),and proteolysis(proteasome pathway)were enriched and upregulated by P.plecoglossicida.Thus,P.plecoglossicida infection activated the inflammatory response,stimulated ATP synthesis,and accelerated apoptosis and necroptosis,and promoted proteasome-mediated protein degradation.Additionally,integrated analysis identified 568 miRNA-mRNA pairs.KEGG enrichment analysis of the miRNA targets showed that the enriched pathways included cytokine-cytokine receptor interaction,the chemokine signaling pathway,the C-type lectin receptor signaling pathway,and apoptosis.Integrated analysis identified 14 miRNAs which targeted 44 immune-related genes.Altogether,our results revealed not only the role of the inflammatory response,energy metabolism,apoptosis and necroptosis,and the proteasome pathway in L.crocea defense against P.plecoglossicida infection,but also the regulatory networks of miRNAs associated with host defense against P.plecoglossicida.
基金Guangxi Science and Technology Base and Talent Special Fund,Project No.AD21220130Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain,Project No.20-065-7Guangxi Institute of Botany Fund,Project No.21014.
文摘Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis.
基金supported by the National Nature Science Foundation Regional Fund Project(32360455)QingyangCity Joint Research Fund Project—Major Project(QY-STK-2024A-046)+1 种基金Doctoral Foundation of Longdong University(XYBYZK2107)University Teachers Innovation Fund Project of Gansu Province(2025A-198).
文摘Brassica napus L. (B. napus), recognized as a significant cash and oil crop, faces challenges in popularization and application in northern China due to its limited cold resistance. Clarifying the mechanism of cold stress on gene regulation and signal transduction in B. napus is crucial. To address these issues, we conducted transcriptome sequencing and gene expression analysis, along with gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway profiling under natural (25℃) and cold (4℃) conditions in cold tolerant 16VHNTS309 and weak cold-resistant Tianyou 2238 B. napus seedlings. Enhanced genomic annotation was achieved through additional sequencing. A total of 6127 and 8531 differentially expressed genes (DEG) were identified in 16VHNTS309 and Tianyou 2238, respectively. The expression patterns of 23 DEGs were validated by quantitative real-time PCR (qRT-PCR), confirming the RNA-Seq results. Under cold stress, 58 pathways in 16VHNTS309 demonstrated significant changes (q-Value < 0.05), compared to 9 pathways in Tianyou 2238 (q-Value < 0.05), highlighting B. napus’ sophisticated regulatory network which aids in managing growth and development challenges. After 48 h of cold stress treatment, genes associated with reactive oxygen species (ROS) clearance, such as those involved in antioxidant VB6, sulfur metabolism, peroxisomes, and phagosomes, were notably up-regulated in 16VHNTS309, indicating its robust ROS clearance capability. Significant gene expressions within Ca^(2+), MAPK, and transcription factor pathways related to ROS suggest that varieties with strong cold resistance possess a complex signal regulation mechanism. Comprehensive analyses of stomatal cells, physiological parameters of ROS, ABA, and H2S, along with transcriptomic data, revealed that optimal ROS levels interact with ABA and H2S to regulate stomatal closure in B. napus 16VHNTS309 under the influence of antioxidant enzymes.
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 grants from the Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province,China(U1812401)the Talent Project of Guizhou Province,China(20164016)。
文摘Rosa sterilis S.D.Shi is an important economic tree in China that produces fruits with high nutritional and medicinal value.Many of R.sterills’organs are covered with different types of trichomes or prickles that directly affect fruit appearance and plant management.This study used RNA sequencing technology to analyze the transcriptomes of two parts of the inflorescence branch,namely inflorescence stems with flagellated trichomes and pedicels with both flagellated and glandular trichomes.Comparative transcriptomic analysis showed that many transcription factors(TFs)are potentially involved in the formation and development of trichomes.The accumulation of RsETC1,a TF of the R3-MYB family,was significantly higher in inflorescence stems than in pedicels;quantitative reverse transcription PCR(qRTPCR)verified that its expression was significantly higher in inflorescence stems than in pedicels during the first three development stages,indicating its inhibitory action on the initiation of glandular trichomes in R.sterilis.The mRNA level of RsETC1 accumulated to significantly higher levels in trichomeless tissues than in tissues with trichromes,suggesting that this gene may inhibit the formation of trichomes in R.sterilis.Over-expression of RsETC1 in Arabidopsis resulted in glabrous phenotypes,and the expression of trichome-related endogenous genes,except for TTG1,was markedly reduced.In addition,the contents of the phytohormones jasmonic acid(JA),gibberellin A3(GA_(3)),and cytokinins(CKs)in pedicels were significantly higher than those in inflorescence stems,and the expression patterns of the genes related to hormone biosynthesis and signal transduction presented consistent responses,suggesting that the transduction of these hormones might be crucial for trichome initiation and development.These data provide a new perspective for revealing the molecular mechanism of trichome formation in R.sterilis.
基金supported by the National Natural Science Foundation of China(32302992)the Central Public-Interest Scientific Institution Basal Research Fund+1 种基金CAFS(No.2023TD36 and YFI202406)the National Freshwater Aquatic Germplasm Resource Center(FGRC18537).
文摘The Chinese soft-shelled turtle(Pelodiscus sinensis)exhibits sexual dimorphism.Compared with females,males are considered to have higher economic value due to their accelerated growth,greater body mass,and longer skirt width.Studies focused on these sex disparities have largely neglected potential sex differences in growth.Here,we performed RNA sequencing of muscle tissue components from 1-year-old specimens to reveal gene expression patterns in P.sinensis.In our male and female cohorts,our analysis revealed,respectively,388 and 526 upregulated differentially expressed genes(DEGs)and 1129 and 635 downregulated DEGs.Through weighted coexpression network analysis(WGCNA)and integration with phenotype data,we established two main gene modules:a light yellow module encompassing 191 genes(e.g.,ACACB,CTH,HADHA,and CTNNB)that demonstrated a positive correlation with population traits,and a black module comprising 298 genes(e.g.,CAV3,PIK3CD,SMAD3,and VEGFA)that demonstrated a negative correlation with population traits.We also performed a DEG evaluation and gene set enrichment analysis across individuals of different sizes and noted that pathways such as protein digestion and assimilation(ko04974),were substantially augmented in larger specimens.In these pathways,the collagen(COL)and solute carrier(SLC)gene families were noted to be crucial for sustaining body structure and facilitating nutrient and metabolite transportation.In conclusion,we elucidated the essential modules,pivotal genes,and pathways involved in gene expression differences among various P.sinensis size groupings.Our results provide novel insights for future studies on growth discrepancies in P.sinensis.
基金supported by the National Key Research and Development Project of China(2019YFA0905300).
文摘With staggering progress on genetic manipulation strategies,Saccharomyces cerevisiae is becoming an ideal cell factory for the de novo biosynthesis of lipid compounds.However,due to their hydrophobicity,lipids tend to be accumulated within intracellular spaces and cause a high burden on cell activity and induce product inhibition effect,which ultimately restricted the lipids biomanufacturing for industrial application.Herein,an oleic acid stress(OAS)model was applied for the long-time domestication of BY4741 cells,and a subclone of A-22 was obtained through a series of acclimation(0.1%glucose and 0.2%oleic acid),showing increased accumulation of both biomass and intracellular lipid droplets compared to WT.Comparative transcriptome analysis indicated that compared to fatty acid metabolism,most transcripts enriched in the pathways of glucose catabolism(glycolysis and citrate cycle)and lipid synthesis(phospholipid and sterol)were down-regulated under OAS.While interestingly,most the above transcripts tended to be‘restored’in adapted strain A-22.In addition,for physical adaptation,significant increase of phosphatidylcholines was identified by lipidomic analysis,which probably caused the subsequent subcellular expansion of peroxisomes and lipid droplets as observed in the adapted strain,since phosphatidylcholines are the major constituent of their membranes.The present study systematically investigated both the phenotype change and molecular mechanism on adaptation of S.cerevisiae towards oily environment.Detailed informa-tion on functional transcripts may provide novel rational modification targets to reinforce the hydrophobic lipids biosynthesis within S.cerevisiae engineered cell factory.
基金supported by the Major Research plan(91751112)the General Programme(41371257,41573071)of the National Natural Science Foundation of China+2 种基金Shandong Natural Science Fund for Distinguished Young Scholars(JQ201608)the Young Taishan Scholars Programme of Shandong Province(tsqn20161054)the Key Research Project for Frontier Science of the Chinese Academy of Sciences(QYZDJ-SSW-DQC015)
文摘Both activated carbon and magnetite have been reported to promote the syntrophic growth of Geobacter metallireducens and Geobacter sulfurreducens co-cultures, the first model to show direct interspecies electron transfer (DIET); however, differential transcriptomics of the promotion on co-cultures with these two conductive materials are unknown. Here, the comparative transcriptomic analysis of G. metallireducens and G. sulfurreducens co-cultures with granular activated carbon (GAC) and magnetite was reported. More than 2.6-fold reduced transcript abundances were determined for the uptake hydrogenase genes of G. sulfurreducens as well as other hydrogenases in those co-cultures to which conductive materials had been added. This is consistent with electron transfer in G. metallireducens-G. sulfurreducens co-cultures as evinced by direct interspecies electron transfer (DIET). Transcript abundance for the structural component of electrically conductive pili (e-pili), PilA, was 2.2-fold higher in G. metallireducens, and, in contrast, was 14.9-fold lower in G. sulfurreducens in co-cultures with GAC than in Geobacters co-cultures without GAC. However, it was 9.3-fold higher in G. sulfurreducens in co-cultures with magnetite than in Geobacters co-cultures. Mutation results showed that GAC can be substituted for the e-pili of both strains but magnetite can only compensate for that of G. sulfurreducens, indicating that the e-pili is a more important electron acceptor for the electron donor strain of G. metallireducens than for G. sulfurreducens. Transcript abundance for G. metallireducens c-type cytochrome gene GMET_RS14535, a homologue to c-type cytochrome gene omcE of G. sulfurreducens was 9.8-fold lower in co-cultures with GAC addition, while that for OmcS of G. sulfurreducens was 25.1-fold higher in co-cultures with magnetite, than in that without magnetite. Gene deletion studies showed that neither GAC nor magnetite can completely substitute the cytochrome (OmcE homologous) of G. metallireducens but compensate for the cytochrome (OmcS) of G. sulfurreducens. Moreover, some genes associated with central metabolism were up-regulated in the presence of both GAC and magnetite; however, tricarboxylic acid cycle gene transcripts in G. sulfurreducens were not highly-expressed in each of these amended co-cultures, suggesting that there was considerable redundancy in the pathways utilised by G. sulfurreducens for electron transfer to reduce fumarate with the amendment of GAC or magnetite. These results support the DIET model of G. metallireducens and G. sulfurreducens and suggest that e-pili and cytochromes of the electron donor strain are more important than that of the electron acceptor strain, indicating that comparative transcriptomics may be a promising route by which to reveal different responses of electron donor and acceptor during DIET in co-cultures.
基金supported by grants from the National Key R&D Program of China(2023ZD04073)the National Natural Science Foundation of China(U23A20189 and 32261143466)+2 种基金the Hubei Provincial Natural Science Foundation of China(2023AFA043)the Earmarked Fund for China Agriculture Research System(CARS-01)the Fundamental Research Funds for the Central Universities(2662023PY002).
文摘Nitrogen(N)is essential for rice growth;however,the transcriptional regulation of the primary nitrogen response(PNR),characterized by the rapid upregulation of N uptake and assimilation genes upon N resup-ply,remains poorly understood.This study investigated the dynamics of the PNR in the roots of two rice cultivars(Zhenshan 97 and Nipponbare)via time-series Assay for Transposase-Accessible Chromatin us-ing sequencing and RNA sequencing analyses within 2 h of ammonium nitrate resupply.Regulatory regions responsive to N induction were precisely identified.Coordinated and cascading changes in chromatin accessibility and gene expression were observed,with chromatin state frequently preceding transcrip-tional changes.Integrative analysis of expression–chromatin accessibility associations revealed a redun-dant N-responsive regulatory network.OsLBD38 and OsLBD39,identified as early-response regulators,transcriptionally suppress nitrate reductases while enhancing nitrite reductases;they may function as metabolic safeguarders to prevent nitrite accumulation.OsbZIP23 was identified as a novel regulator directly binding to the promoters of N uptake and metabolism genes,regulating genes in patterns opposite to LBD-regulated genes,suggesting a complex regulatory interplay.Cross-species comparisons with Ara-bidopsis highlighted the conserved N-responsive regulatory roles of these hub regulators and their targets.Comparative analyses between cultivars revealed expression divergence and genetic differentiation in N-responsive genes,implying indica/japonica-specific adaptations.Furthermore,deep learning predic-tions of chromatin accessibility between cultivars indicated that expression variation in N uptake and meta-bolism genes is primarily influenced by trans-acting regulatory factors.These findings provide a compre-hensive view of the dynamic regulatory landscape governing the PNR in rice.
基金supported by the International Science and Technology Cooperation of China(2011DFA32730)
文摘Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.
基金supported by the National Key Research and Development Program of China(2018YFD0900606)National Natural Science Foundation of China(31072208)+2 种基金Major Science and Technology Specific Program of Zhejiang Province,China(2016C02055-6)Science and Technology Planning Project of Jiangsu Province,China(BE2018335)Open Program of Key Laboratory of Cultivation and High-value of Marine Organisms in Fujian Province,China(2017fjscq02).
文摘As an important seedling source,monospores closely associate with yields in nori farming.However,the molecular mechanism underlying differences in monospore production for different strains remains unknown.Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain(WT)and spore deficient mutant(Y1)of Pyropia chauhanii.The WT strain that produces monospores in abundance exhibited more differentially expressed genes(DEGs)in both number and higher fold-changes than the Y1 strain incapable of producing monospores,indicating that the specific regulation of genes is involved in monospore production.Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram:one expressed only in WT strain,another expressed only in Y1 strain,and the third shared in both strains.DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website.Gene regulatory networks of WT were functionally enriched in the processing,proteolysis,and transport of proteins,especially within the small GTPase protein family,which might be account for the monospore production ability,whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy,which might be account for the rapid growth of blades.We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits.These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities,which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production.
基金supported by the National Natural Science Foundation of China(31822052,31572381)the National Thousand Youth Talents Plan to Y.J.+3 种基金National Natural Science Foundation of China(31660644)to S.H.National Natural Science Foundation of China(41422604)to S.L.The Villum Foundation(VKR 023447)the Independent Research Fund Denmark(8049-00098B)。
文摘The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.
基金supported by the National Natural Science Foundation of China(Grant Nos.31771415 and 31801054)the Bureau of Science and Technology of Yunnan Province,China(Grant No.2015FA026)+1 种基金the Youth Innovation Promotion Association,Chinese Academy of Sciencesthe support of the CAS-TWAS President’s Fellowship Program for Doctoral Candidates。
文摘Piao chicken,a rare Chinese native poultry breed,lacks primary tail structures,such as pygostyle,caudal vertebra,uropygial gland,and tail feathers.So far,the molecular mechanisms underlying tail absence in this breed remain unclear.In this study,we comprehensively employed comparative transcriptomic and genomic analyses to unravel potential genetic underpinnings of rumplessness in Piao chicken.Our results reveal many biological factors involved in tail development and several genomic regions under strong positive selection in this breed.These regions contain candidate genes associated with rumplessness,including Irx4,Il18,Hspb2,and Cryab.Retrieval of quantitative trait loci(QTL)and gene functions implies that rumplessness might be consciously or unconsciously selected along with the high-yield traits in Piao chicken.We hypothesize that strong selection pressures on regulatory elements might lead to changes in gene activity in mesenchymal stem cells of the tail bud.The ectopic activity could eventually result in tail truncation by impeding differentiation and proliferation of the stem cells.Our study provides fundamental insights into early initiation and genetic basis of the rumpless phenotype in Piao chicken.
基金supported by a Singapore Ministry of Education tier-two grant(MOE2018-T2-2-053)a Singapore Food Agency grant(SFS_RND_SUFP_001_05).
文摘There are now more than 300000 RNA sequencing samples available,stemming from thousands of exper-iments capturing gene expression in organs,tissues,developmental stages,and experimental treatments for hundreds of plant species.The expression data have great value,as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data.Because gene expression provides essential clues to where and when a gene is active,the data provide powerful tools for predicting gene function,and comparative analyses allow us to study plant evolution from a new perspective.This review describes how we can gain new knowledge from gene expression profiles,expres-sion specificities,co-expression networks,differential gene expression,and experiment correlation.We also introduce and demonstrate databases that provide user-friendly access to these tools.
