The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic an...The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.展开更多
In addition to the negative consequences of climate change,sucking pest complexes severely limited cotton yields in the recent past.Although the damage caused by bollworms was much reduced by utilizing Bt cotton,the e...In addition to the negative consequences of climate change,sucking pest complexes severely limited cotton yields in the recent past.Although the damage caused by bollworms was much reduced by utilizing Bt cotton,the emergence of sucking pests(such as aphids,thrips,and whiteflies)poses a serious threat to cotton production,as they reduce lint yield by 40%–60%finally.Additionally,these pests also caused yield losses by spreading viral diseases.Promoting innovative and thorough control methods is necessary to counter the threat posed by these sucking pests.Such initiatives necessitate a multifaceted strategy that combines next-generation breeding technology and pest management techniques to produce novel cotton cultivars that are resistant to sucking pests.The discovery of novel genes and regulatory factors linked to cotton’s resistance to sucking pests will be possible by the combination of next-generation breeding technologies and omics approaches and employing those tools on special resistant donors.Continuous research aimed at understanding the genetic basis of insect resistance and improving integrated pest management(IPM)techniques is crucial to the sustainability and resilience of cotton cropping systems.To this end,a sustainable and viable strategy to protect cotton fields from sucking pests is outlined.展开更多
【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response...【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response mecha‐nisms.The findings would provide theoretical references for understanding the molecular mechanisms of taro’s drought regulation and for breeding different drought tolerant taro varieties in the future.【Method】Using Lipu taro as the experi‐mental material,leaf samples were collected after consecutive 7 d of drought treatment as the treatment group,while leaf samples from plants watered daily served as the control group.Transcriptome sequencing was performed to identify dif‐ferentially expressed genes,which were then subjected to GO functional annotation and KEGG pathway enrichment analysis.【Result】Under drought stress,there were 1613 differentially expressed genes(DEGs),including 1043 upregulated and 570 down-regulated genes.GO functional annotation analysis revealed that the DEGs were categorized into three major functional groups:molecular function,cellular component,and biological process.In the molecular function category,DEGs were annotated to binding and catalytic activity.In the cellular component category,DEGs were anno‐tated to cellular anatomical entities and protein-containing complexes.In the biological process category,DEGs were an‐notated to cellular processes and metabolic processes.KEGG signaling pathway enrichment analysis showed that 85.00%of the DEGs were enriched in metabolic pathway.Among these,the DEGs were primarily enriched in the glutathione me‐tabolism pathway and the starch and sucrose metabolism pathway,with 11 and 19 DEGs identified in each pathway re‐spectively.Under drought stress,a total of 112 differentially expressed transcription factors(TFs)were identified,mainly including members of the bHLH,ERF,WRKY and NAC families.Among all differentially expressed TFs,82.14%showed up-regulated transcription levels under drought conditions.Plant hormone signal transduction,carotenoid biosynthesis,and the MAPK signaling pathway-plant were identified as key abscisic acid-responsive pathways involved in drought response,influencing stomatal closure in taro leaves and seed dormancy to cope with drought stress.The reliability of the transcriptome data was confirmed by quantitative real-time PCR analysis.【Conclusion】Under drought stress,the gene expression in the glutathione metabolism pathway,the starch and sucrose metabolism pathway,and transcription factors in taro leaves is affected.Most TFs are positively involved in regulating taro plant’s drought response.展开更多
The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton product...The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton production worldwide.Due to the complex genetic structure of drought tolerance,the development of a tolerant cultivar is cumbersome via conventional breeding.Multiple omics techniques have appeared as successful tool for cotton improvement in drought tolerance.Advanced omics-based biotechniques have paved the way for generation of omics data like transcriptomics,genomics,metabolomics and proteomics,which greatly expand the knowledge of cotton response to drought stress.Omics methodologies and have provided ways for the identification of quantitative trait loci(QTLs),gene regulatory networks,and other regulatory pathways against drought stress in cotton.These resources could speed up the discovery and incorporation of drought tolerant traits in the elite genotypes.The genome wide association study(GWAS),gene-editing system CRISPER/Cas9,gene silencing through RNAi are efficient tools to explore the molecular mechanism of drought tolerance and facilitate the identification of mechanisms and candidate genes for the improvement of drought tolerance in cotton.展开更多
Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their ...Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their physical and mental health.The uterosacral ligament is a critical pelvic support structure.This study aims to investigate the molecular pathological changes in the uterosacral ligament of postmenopausal women with recurrent POP using transcriptomic analysis.Methods:Transcriptomic data of uterosacral ligament tissues were obtained from the public dataset GSE28660,which includes samples from 4 postmenopausal women with recurrent POP,4 with primary POP,and 4 without POP.Differentially expressed genes(DEGs)were identified between recurrent POP and both primary and non-POP groups.Further analysis included intersection analysis of DEGs,gene ontology enrichment,protein protein interaction(PPI)network construction,gene set enrichment analysis(GSEA),single-sample GSEA,and xCell immune cell infiltration analysis to explore molecular pathological changes in recurrent POP.Additionally,histological and molecular differences in the uterosacral ligament were compared between simulated vaginal delivery(SVD)rat models with and without ovariectomy.Results:Compared with primary POP and non-POP groups,recurrent POP exhibited activation of adipogenesis and inflammation-related pathways,while pathways related to muscle proliferation and contraction were downregulated in the uterosacral ligament.Nine key DEGs(ADIPOQ,FABP4,IL-6,LIPE,LPL,PCK1,PLIN1,PPARG,and CD36)were identified,with most enriched in the peroxisome proliferator-activated receptor(PPAR)signaling pathway.These genes were significantly correlated with lipid accumulation,monocyte infiltration,and neutrophil infiltration in the uterosacral ligament.Urodynamic testing revealed that the bladder leak point pressure was significantly higher in ovariectomized SVD rats,both of which had higher values than the sham group.Masson staining showed pronounced adipogenesis in the uterosacral ligament of ovariectomized SVD rats,along with reduced collagen and muscle fibers compared to the sham and non ovariectomized SVD groups.Furthermore,real-time RT-PCR confirmed significantly elevated expression of key DEGs,including ADIPOQ,IL-6,PCK1,and PLIN1,in the uterosacral ligaments of ovariectomized SVD rats.Conclusion:Adipogenesis and inflammation in the uterosacral ligament may contribute to its reduced supportive function,potentially leading to recurrence POP in postmenopausal women.展开更多
Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Sinc...Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.展开更多
Background Aphis gossypii(Hemiptera:Aphididae)is a worldwide polyphagous phloem-feeding agricultural pest,and it can produce offspring by sexual or asexual reproduction.Compared with dozens of generations by parthenog...Background Aphis gossypii(Hemiptera:Aphididae)is a worldwide polyphagous phloem-feeding agricultural pest,and it can produce offspring by sexual or asexual reproduction.Compared with dozens of generations by parthenogenesis,sexual reproduction is performed in only one generation within one year,and little is known about the sexual reproduction of A.gossypii.In this study,sexual females of A.gossypii were successfully obtained through a previously established induction platform,and the morphological characteristics,developmental dynamics,and temporal gene expression were examined.Subsequently,signaling pathways potentially involved in regulating the growth,development,and reproduction of sexual females were investigated.Results The morphological observation showed that from the 1st instar nymph to adult,sexual females exhibited a gradually deepened body color,an enlarged body size,longer antennae with a blackened end,and obviously protruding cauda(in adulthood).The anatomy found that the ovaries of sexual females developed rapidly from the 2^(nd)instar nymph,and the embedded oocytes matured in adulthood.In addition,time-course transcriptome analysis revealed that gene expression profiles across the development of sexual females fell into 9 clusters with distinct patterns,in which gene expression levels in clusters 1,5,and 8 peaked at the 2^(nd)instar nymphal stage with the largest number of up-regulated genes,suggesting that the 2^(nd)instar nymph was an important ovary development period.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis revealed that a large number of genes in the sexual female adult were enriched in the TGF-beta signaling pathway and Forkhead box O(FoxO)signaling pathway,highlighting their important role in sexual female adult development and reproduction.Conclusion The morphological changes of the sexual female at each developmental stage were revealed for the first time.In addition,time-course transcriptomic analyses suggest genes enriched in the TGF-beta signaling pathway and FoxO signaling pathway probably contribute to regulating the development and oocyte maturation of sexual females.Overall,these findings will facilitate the regulating mechanism research in the growth and development of sexual females by providing candidate genes.展开更多
Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti-...Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti- fibrosis. This study aims to investigate the effective targets and the mechanisms of FZHY on liver fibrosis. Methods The liver tissue samples of normal group, model group and FZHY-treated group were examined by microarray and iTRAQ. Profiles of differentially expressed genes （DEGs） and differentially expressed proteins （DEPs） in CC14-in- duced liver fibrosis model in rat were analyzed. GO and Pathway were analyzed by DAVID, and protein-protein in- teraction （PPI） was analyzed by STRING and cytoscape. The targets of FZHY compounds were predicted by TCM- SP. Results The results showed that 255 genes （ fold change ≥ 1.5, P 〈 0.05） and 507 proteins （ fold change ≥ 1.2 ,P 〈 0.05 ） were differentially expressed between FZHY group and model group. The high-throughput data of transcriptomics and proteomics was analyzed synthetically. DAVID function annotation analysis showed that these DEGS and DEPs both enriched in 15 GO terms, among drug metabolic process, response to extracellular stimulus, response to vitamin, arachidonic acid metabolic process, response to wounding and oxidation reduction may involve in liver fibrosis. KEGG pathway analysis showed that these DEGS and DEPs both enriched in 9 pathways, among arachidonic acid metabolism, retinol metabolism, metabolism of xenobiotics by cytochrome P450 and drug metabo- lism may be related to liver fibrosis. PPI analysis found that 10 overlapped core genes and proteins, among, Ugt2a3, Cyp2bl and Cyp3al8 were of higher degree, which are all enriched in retinol metabolism. Interestedly, Cyp2bl and Cyp3al8 were also predicted with TCMSP as the targets of FZHY compounds. Conclusion The re- sults indicated that the effective mechanism of FZHY against liver fibrosis is involved in the regulation of multiple targets and multiple pathways, among, retinol metabolism pathway by targeting Ugt2a3, Cyp2bl and Cyp3al8 may play an important role in the treatment of liver fibrosis.展开更多
Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
Tomato(Solanum lycopersicum L.)is a thermophilic vegetable crop,but sensitive to high temperature stress,especially under the greenhouse conditions.Due to global climate changes,heat stress has now become a great thre...Tomato(Solanum lycopersicum L.)is a thermophilic vegetable crop,but sensitive to high temperature stress,especially under the greenhouse conditions.Due to global climate changes,heat stress has now become a great threat to tomato production and fruit quality.Many studies have been conducted to determine the functions of genes in tomato responsive to abiotic and biotic stresses,but transcriptomic information on heat stress responses of tomato fruit is still limited.To investigate heat stress associated genes in tomato fruit,a cDNA library was constructed using fruit harvested from tomato cv.P19-9 plants grown under 42℃for 0,1,2 and4 h and the expression profiles of heat stress responsive genes in tomato fruit were analyzed through RNA-seq.A total of 632224558 clean high quality paired-end reads were obtained and then mapped to reference genome for RNA-seq analysis.After quality control analysis,alignment analysis and transcript assembly,a total of 55457 RNA transcripts were obtained with functional annotations.Overall,6869 differentially expressed genes(DEGs)were identified with a significant response to one or more of the three heat stress treatment times.Based on GO enrichment analysis,22 genes potentially involved in tomato thermo-tolerance were selected and validated for their expressions through qPCR.The expression profile of tomato fruit genes obtained in this study could shed light on the mechanism and gene editing breeding projects for tomato thermo-tolerance.These findings could also benefit improvement of harvest and storage of tomato in greenhouse.展开更多
Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of u...Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of upland cotton. To investigate molecular mechanisms underlying acquisition of embryogenic potential during this process, comparation analysis of transcriptome dynamics between two upland cotton cultivars with different somatic embryogenesis abilities was conducted. Results： Differentially expressed genes involved in the transformation from NEC to EC were detected in the two different cultivars. Principal component analysis based on DEGs showed that the NEC tissues of the two cultivars were highly heterogeneous, whereas the derived EC tissues were similar, which suggested the homogeneousness of EC between different lines. In the highly embryogenic cultivar CCRI 24, more of these genes were down-regulated, whereas, in the recalcitrant cultivar CCRI 12, more were up-regulated. Bioinformatics analysis on these DEGs showed that the vast majority of differentially expressed genes were enriched in metabolism and secondary metabolites biosynthesis pathways. Flavonoid biosynthesis and phenylpropanoid biosynthesis pathways were enriched in both cultivars, and the associated genes were down-regulated more in CCRI 24 than in CCRI 12. We deduced that vigorous secondary metabolism in CCRI 12 may hinder primary metabolism, resulting in tardiness of cell differentiation. Interestingly, genes involved in the plant hormone signal transduction pathway were enriched in the recalcitrant cultivar CCRI 12, but not in CCRI 24, suggesting more radical regulation of hormone signal transduction in the recalcitrant cultivar. Signal transduction rather than biosynthesis of plant hormones is more likely to be the determining factor triggering NEC to EC transition in recalcitrant cotton lines. Transcription factor encoding genes showed differential regulation between two cultivars. Conclusions： Our study provides valuable information about the molecular mechanism of conversion from NEC to EC in cotton and allows for identification of novel genes involved. By comparing transcriptome changes in transformation from NEC to EC between the two cultivars, we identified 46 transcripts that may contribute to initiating embryogenic shift.展开更多
Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xin...Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.展开更多
Recently,Wang et al.systematically explored the transcription landscape in diploid cotton Gossypium arboreum.In the study,they integrated four high-throughput sequencing techniques,including Pacbio sequencing,strandsp...Recently,Wang et al.systematically explored the transcription landscape in diploid cotton Gossypium arboreum.In the study,they integrated four high-throughput sequencing techniques,including Pacbio sequencing,strandspecific RNA sequencing(ss RNA-seq),Cap analysis gene expression sequencing(CAGE-seq),and Poly A sequencing(Poly A-seq)to profile the RNA transcriptome of G.arboreum.They developed a pipeline,IGIA to construct accurate gene structure annotation based on the updated genome of G.arboreum and the multi-strategic RNA-seq data.Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants,and also provided valuable resources for further functional genomic research in cotton.展开更多
Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL i...Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.展开更多
OBJECTIVE To identify and characterize a novel neuroprotective ShK peptide and its analogue originated from coral P.caribaeoru.METHODS P.caribaeoru was collected and subjected to transcriptome sequencing at which furt...OBJECTIVE To identify and characterize a novel neuroprotective ShK peptide and its analogue originated from coral P.caribaeoru.METHODS P.caribaeoru was collected and subjected to transcriptome sequencing at which further bioinformatics analysis had identified a unigene encoding a putative ShK protein candidate,named as PcShK1.PcShK1 and its rhodamine derivative(PcShK1-RhoB) were synthesized and tested for the neuroprotective effect in 6-OHDA induced Parkinson disease models in vitro and in vivo.Briefly,zebrafish larvae were co-exposed to 6-OHDA and various doses of the peptides;then,dopaminergic(DA) neurons immunoreactivity and locomotion behavior of the zebrafish larvae were examined.Similarly,PC12 cells were cultured with 6-OHDA in the absence or presence of different concentrations of peptides.Cell viability was determined by MTT assay while calcium flow in the PC12 cells was monitored by Fluo-4 fluorescent dye.RESULTS Compared with control group,6-OHDA treatment could lead to DA neurons loss and locomotion deficits in PD model of zebrafish larvae(P<0.01).Both PcS hK 1(2.5,5.0 and 7.5 μmol·L^(-1)) and PcS hK 1-RhoB(0.50 and 0.75 μmol·L^(-1)) were found to protect and restore dopaminergic neurons from6-OHDA mediated injury and locomotion deficiency in the PD zebrafish respectively(P<0.01).In addition,PcShK1(2.5 to 20.0 μmol·L^(-1)) and PcShK1-RhoB(0.6 to 2.5 μmol·L^(-1)) effectively prevented against 6-OHDA toxicity in PC12 cells(P<0.01).Further study revealed that they might exert their neuroprotective effects through regulating the calcium homeostasis.CONCLUSION PcS hK 1 and PcS hK 1-RhoB show neuroprotective effects on 6-OHDA induced PD models,and the underlying protective mechanisms of these peptides probably involve calcium homeostasis regulation.展开更多
OBJECTIVE To analyze the whole transcriptome of zoanthid Protopalythoa variabilis(P.variabilis),a cnidarian,and discover the potential toxic substances in P.variabilis.METHODS The P.variabilis RNA deep sequencing was ...OBJECTIVE To analyze the whole transcriptome of zoanthid Protopalythoa variabilis(P.variabilis),a cnidarian,and discover the potential toxic substances in P.variabilis.METHODS The P.variabilis RNA deep sequencing was performed using the HiSeq 2500 automatic sequencing platform.All the unigenes generated from the assembly process were functionally annotated based on the similarity with databases.The multiple alignments of translated toxin-related sequences were performed with Clustalw2,and amino acid identity and similarity highlighted by using BoxShade tool.Three different methods including ITASSER,PEP-FOLD and MODELLER were applied to predict tri-dimensional models of toxin-related polypeptides from translated transcript sequences of P.variabilis.The toxicity of one of the putative toxins,namely ShK/Aurelin-like peptide,was evaluated using zebrafish model.RESULTS A total of 67,549,914 pairs of quality-filtered,90-base-pair Illumina reads from an mRNA sample were obtained.The de novo assemblies yielded 276,526 contigs.The sequence comparison of 130,121 unigenes with entries in Toxin database showed that 1542 unigenes were potential peptide toxins at which 11 unigenes were related to Stichodactyla toxin(ShK)domain(Pfam ID:PF01549).ShK is a 35 residues peptide sequence that was firstly discovered from the sea anemone Stichodactyla helianthus.Here,we found out one ShK-like peptide that processed a relatively higher sequence similarity with known ShK(Uniprot ID:P29186)of Bunodosoma granuliferum(red warty sea anemone).The Protopalythoa Shk-like peptide was submitted to Probis server to detect probable binding site and found to match with a protein AURELIN(PDB id:2lg4,UniProt id:Q0MWV8)which possesses structural homology with previously identified antimicrobial peptides and K+-channel-blocking toxins.Our results showed that the ShK/Aurelin-like peptide was lethal to zebrafish embryos at concentrations above 30-μmol·L1,and could induce zebrafish locomotor deficit at 10μmol·L-1.CONCLUSION This study,for the first time,presented the whole transcriptome profile and a potential toxic peptide of P.variabilis.展开更多
OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular in...OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular insufficiency conditions.METHODS RNA sequencing of three different Panax notoginseng tissues was performed using next generation DNA sequencing and differential gene expression was validated by real-time PCR.In order to determine pro-angiogenic and therapeutic effects of FS on myocardial infraction(MI),FS was examined on the endothelial cell migration assay,vascular insufficiency model in zebrafish and MI model in rats.RESULTS After assembling the high quality sequencing reads into 107 340 unigenes,biochemical pathways were predicted and 9 908 unigenes were assigned to 135 KEGG pathways.Among them,270 unigenes were identified to be involved in triterpene saponin biosynthesis as well as 350 and 342unigenes were predicted to encode cytochrome P450 sand glycosyltransferases,respectively.One unigene was annotated as CYP716A53v2,probably participates in the formation of protopanaxatriol from protopanaxadiol and the differential expression of this gene was confirmed by real-time PCR.In addition,the pharmacological evaluation demonstrate that FS significantly promoted vascular endothelial growth factor(VEGF)induced the migration of human umbilical vein endothelial cells(HUVECs)and partially restored defective intersegmental vessels in a chemically induced vascular insufficiency model of zebrafish larva.Moreover,the two week posttreatment of the rat MI model with FS(25-50mg·kg-1·d-1)induced approximately 3-fold upregulation of VEGF mRNA expression,with a concomitant increase in blood vessel density in the peri-infarct area of the heart by 50.7%,compared to 41.4%in the MI group.Furthermore,TUNEL analysis indicates a reduction in the mean apoptotic nuclei per field in peri-infarct myocardium upon FS treatment.CONCLUSION We have established a global transcriptome dataset for Panax notoginseng and provided additional genetic information for further genome-wide research and analyses.Candidate genes involved in ginsenoside biosynthesis,including putative cytochrome P450 sand glycosyltransferases were obtained.The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P.notoginseng.And the significant pro-angiogenic effect of FS in multiple experimental models renders the purified saponin preparation as potential preventive and therapeutic agent for cardiovascular diseases yet to be developed.展开更多
OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine ...OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine animals is the cnidocytes in the body tissues,responsible for toxin production and injection that are used majorly for prey capture and defense.With exception for other anthozoans,the toxin cocktails of zoanthids have been scarcely studied and are poorly known.METHODS Based on the analysis of P.caribaeorum transcriptome,numerous predicted venom-featured polypeptides were identified,including allergens,neuro-toxins,membrane-active and Kunitz-like peptides(PcKuz).The three predicted PcKuz isotoxins(1 to 3) were selected for functional studies.Through computational processing comprising structural phylogenetic analysis,molecular docking,and dynamics simulation,PcKuz3 was shown to be a potential voltage gated potassium-channel inhibitor.RESULTS PcKuz3 fitted well as new functional Kunitz-type toxins with strong anti-locomotor activity as in vivo assessed in zebrafish larvae,with weak inhibitory effect toward proteases,as evaluated in vitro.Notably,PcKuz3 can suppress,at low concentration,the 6-OHDA-induced neurotoxicity on the locomotive behavior of zebrafish,which indicated PcKuz3 may have a neuroprotective effect.CONCLUSION Taken together,PcK uz3 figures as a novel neurotoxin structure which differs from known homologous peptides expressed in sea anemone.Moreover,the novel PcKuz3 provides an insightful hint for bio-drug development for prospective neurodegenerative disease treatment.展开更多
In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequ...In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out.展开更多
The transcriptome-wide gene expression was compared between susceptible and resistant Chinese cabbage cultivars to identify genes that contributed to clubroot resistance. A higher number of differentially expressed ge...The transcriptome-wide gene expression was compared between susceptible and resistant Chinese cabbage cultivars to identify genes that contributed to clubroot resistance. A higher number of differentially expressed genes were detected in susceptible cultivars than in resistant cultivars. Fifty-six genes involved in cell wall modification, hormone signaling, root marphogenesis, nematodes response and cell proliferation were uniquely expressed in the resistant cultivars. Among them, 27 genes were involved in cell wall modification and hormone signaling, indicating that genes in these two types might play a vital role in the defense response to pathogen infection.展开更多
文摘The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection.
基金M/s.RASI Seeds Pvt.Ltd.,Attur,Tamil Nadu,India for their generous financial assistance in setting up a MAS study in cotton for genetic improvement of sucking pest resistance.
文摘In addition to the negative consequences of climate change,sucking pest complexes severely limited cotton yields in the recent past.Although the damage caused by bollworms was much reduced by utilizing Bt cotton,the emergence of sucking pests(such as aphids,thrips,and whiteflies)poses a serious threat to cotton production,as they reduce lint yield by 40%–60%finally.Additionally,these pests also caused yield losses by spreading viral diseases.Promoting innovative and thorough control methods is necessary to counter the threat posed by these sucking pests.Such initiatives necessitate a multifaceted strategy that combines next-generation breeding technology and pest management techniques to produce novel cotton cultivars that are resistant to sucking pests.The discovery of novel genes and regulatory factors linked to cotton’s resistance to sucking pests will be possible by the combination of next-generation breeding technologies and omics approaches and employing those tools on special resistant donors.Continuous research aimed at understanding the genetic basis of insect resistance and improving integrated pest management(IPM)techniques is crucial to the sustainability and resilience of cotton cropping systems.To this end,a sustainable and viable strategy to protect cotton fields from sucking pests is outlined.
基金National Natural Science Foundation of China(32460756)Guangxi Key Research and Development Project(Guike AB20297041)+1 种基金Science and Technology Development Fund of Guangxi Academy of Agricultural Sciences(Gui‐nongke 2022JM58)Guangxi Lipu Taro Experimental Station Projec(tTS202113)。
文摘【Objective】This study aimed to clarify the key pathways and related genes of taro leaves in response to drought stress,analyze the gene expression patterns under drought conditions,and explore the molecular response mecha‐nisms.The findings would provide theoretical references for understanding the molecular mechanisms of taro’s drought regulation and for breeding different drought tolerant taro varieties in the future.【Method】Using Lipu taro as the experi‐mental material,leaf samples were collected after consecutive 7 d of drought treatment as the treatment group,while leaf samples from plants watered daily served as the control group.Transcriptome sequencing was performed to identify dif‐ferentially expressed genes,which were then subjected to GO functional annotation and KEGG pathway enrichment analysis.【Result】Under drought stress,there were 1613 differentially expressed genes(DEGs),including 1043 upregulated and 570 down-regulated genes.GO functional annotation analysis revealed that the DEGs were categorized into three major functional groups:molecular function,cellular component,and biological process.In the molecular function category,DEGs were annotated to binding and catalytic activity.In the cellular component category,DEGs were anno‐tated to cellular anatomical entities and protein-containing complexes.In the biological process category,DEGs were an‐notated to cellular processes and metabolic processes.KEGG signaling pathway enrichment analysis showed that 85.00%of the DEGs were enriched in metabolic pathway.Among these,the DEGs were primarily enriched in the glutathione me‐tabolism pathway and the starch and sucrose metabolism pathway,with 11 and 19 DEGs identified in each pathway re‐spectively.Under drought stress,a total of 112 differentially expressed transcription factors(TFs)were identified,mainly including members of the bHLH,ERF,WRKY and NAC families.Among all differentially expressed TFs,82.14%showed up-regulated transcription levels under drought conditions.Plant hormone signal transduction,carotenoid biosynthesis,and the MAPK signaling pathway-plant were identified as key abscisic acid-responsive pathways involved in drought response,influencing stomatal closure in taro leaves and seed dormancy to cope with drought stress.The reliability of the transcriptome data was confirmed by quantitative real-time PCR analysis.【Conclusion】Under drought stress,the gene expression in the glutathione metabolism pathway,the starch and sucrose metabolism pathway,and transcription factors in taro leaves is affected.Most TFs are positively involved in regulating taro plant’s drought response.
文摘The situation of global warming imparts negative impacts on crop growth and development.Cotton is the most important fiber crop around the globe.However,frequent drought episodes pose serious threats to cotton production worldwide.Due to the complex genetic structure of drought tolerance,the development of a tolerant cultivar is cumbersome via conventional breeding.Multiple omics techniques have appeared as successful tool for cotton improvement in drought tolerance.Advanced omics-based biotechniques have paved the way for generation of omics data like transcriptomics,genomics,metabolomics and proteomics,which greatly expand the knowledge of cotton response to drought stress.Omics methodologies and have provided ways for the identification of quantitative trait loci(QTLs),gene regulatory networks,and other regulatory pathways against drought stress in cotton.These resources could speed up the discovery and incorporation of drought tolerant traits in the elite genotypes.The genome wide association study(GWAS),gene-editing system CRISPER/Cas9,gene silencing through RNAi are efficient tools to explore the molecular mechanism of drought tolerance and facilitate the identification of mechanisms and candidate genes for the improvement of drought tolerance in cotton.
基金supported by the Key Research and Development Program of Hunan Province(2023SK2038)the Natural Science Foundation of Hunan Province(2024JJ8121),China。
文摘Objective:Pelvic organ prolapse(POP)is a common condition in postmenopausal women,with an increasing prevalence due to aging.Some women experience POP recurrence after surgical treatment,significantly affecting their physical and mental health.The uterosacral ligament is a critical pelvic support structure.This study aims to investigate the molecular pathological changes in the uterosacral ligament of postmenopausal women with recurrent POP using transcriptomic analysis.Methods:Transcriptomic data of uterosacral ligament tissues were obtained from the public dataset GSE28660,which includes samples from 4 postmenopausal women with recurrent POP,4 with primary POP,and 4 without POP.Differentially expressed genes(DEGs)were identified between recurrent POP and both primary and non-POP groups.Further analysis included intersection analysis of DEGs,gene ontology enrichment,protein protein interaction(PPI)network construction,gene set enrichment analysis(GSEA),single-sample GSEA,and xCell immune cell infiltration analysis to explore molecular pathological changes in recurrent POP.Additionally,histological and molecular differences in the uterosacral ligament were compared between simulated vaginal delivery(SVD)rat models with and without ovariectomy.Results:Compared with primary POP and non-POP groups,recurrent POP exhibited activation of adipogenesis and inflammation-related pathways,while pathways related to muscle proliferation and contraction were downregulated in the uterosacral ligament.Nine key DEGs(ADIPOQ,FABP4,IL-6,LIPE,LPL,PCK1,PLIN1,PPARG,and CD36)were identified,with most enriched in the peroxisome proliferator-activated receptor(PPAR)signaling pathway.These genes were significantly correlated with lipid accumulation,monocyte infiltration,and neutrophil infiltration in the uterosacral ligament.Urodynamic testing revealed that the bladder leak point pressure was significantly higher in ovariectomized SVD rats,both of which had higher values than the sham group.Masson staining showed pronounced adipogenesis in the uterosacral ligament of ovariectomized SVD rats,along with reduced collagen and muscle fibers compared to the sham and non ovariectomized SVD groups.Furthermore,real-time RT-PCR confirmed significantly elevated expression of key DEGs,including ADIPOQ,IL-6,PCK1,and PLIN1,in the uterosacral ligaments of ovariectomized SVD rats.Conclusion:Adipogenesis and inflammation in the uterosacral ligament may contribute to its reduced supportive function,potentially leading to recurrence POP in postmenopausal women.
文摘Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.
基金funded by National Natural Science Foundation of China(No.32102214)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences+1 种基金China Agriculture Research System(CARS-15-21)National Key R&D Program of China(2022YFD1400300)。
文摘Background Aphis gossypii(Hemiptera:Aphididae)is a worldwide polyphagous phloem-feeding agricultural pest,and it can produce offspring by sexual or asexual reproduction.Compared with dozens of generations by parthenogenesis,sexual reproduction is performed in only one generation within one year,and little is known about the sexual reproduction of A.gossypii.In this study,sexual females of A.gossypii were successfully obtained through a previously established induction platform,and the morphological characteristics,developmental dynamics,and temporal gene expression were examined.Subsequently,signaling pathways potentially involved in regulating the growth,development,and reproduction of sexual females were investigated.Results The morphological observation showed that from the 1st instar nymph to adult,sexual females exhibited a gradually deepened body color,an enlarged body size,longer antennae with a blackened end,and obviously protruding cauda(in adulthood).The anatomy found that the ovaries of sexual females developed rapidly from the 2^(nd)instar nymph,and the embedded oocytes matured in adulthood.In addition,time-course transcriptome analysis revealed that gene expression profiles across the development of sexual females fell into 9 clusters with distinct patterns,in which gene expression levels in clusters 1,5,and 8 peaked at the 2^(nd)instar nymphal stage with the largest number of up-regulated genes,suggesting that the 2^(nd)instar nymph was an important ovary development period.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis revealed that a large number of genes in the sexual female adult were enriched in the TGF-beta signaling pathway and Forkhead box O(FoxO)signaling pathway,highlighting their important role in sexual female adult development and reproduction.Conclusion The morphological changes of the sexual female at each developmental stage were revealed for the first time.In addition,time-course transcriptomic analyses suggest genes enriched in the TGF-beta signaling pathway and FoxO signaling pathway probably contribute to regulating the development and oocyte maturation of sexual females.Overall,these findings will facilitate the regulating mechanism research in the growth and development of sexual females by providing candidate genes.
文摘Aim Liver fibrosis is a consequence of chronic liver disease which can progress into liver cirrhosis evenhepatocarcinoma. FuzhengHuayu （FZHY） , a Chinese herbal formula, had been reported to have the effect of anti- fibrosis. This study aims to investigate the effective targets and the mechanisms of FZHY on liver fibrosis. Methods The liver tissue samples of normal group, model group and FZHY-treated group were examined by microarray and iTRAQ. Profiles of differentially expressed genes （DEGs） and differentially expressed proteins （DEPs） in CC14-in- duced liver fibrosis model in rat were analyzed. GO and Pathway were analyzed by DAVID, and protein-protein in- teraction （PPI） was analyzed by STRING and cytoscape. The targets of FZHY compounds were predicted by TCM- SP. Results The results showed that 255 genes （ fold change ≥ 1.5, P 〈 0.05） and 507 proteins （ fold change ≥ 1.2 ,P 〈 0.05 ） were differentially expressed between FZHY group and model group. The high-throughput data of transcriptomics and proteomics was analyzed synthetically. DAVID function annotation analysis showed that these DEGS and DEPs both enriched in 15 GO terms, among drug metabolic process, response to extracellular stimulus, response to vitamin, arachidonic acid metabolic process, response to wounding and oxidation reduction may involve in liver fibrosis. KEGG pathway analysis showed that these DEGS and DEPs both enriched in 9 pathways, among arachidonic acid metabolism, retinol metabolism, metabolism of xenobiotics by cytochrome P450 and drug metabo- lism may be related to liver fibrosis. PPI analysis found that 10 overlapped core genes and proteins, among, Ugt2a3, Cyp2bl and Cyp3al8 were of higher degree, which are all enriched in retinol metabolism. Interestedly, Cyp2bl and Cyp3al8 were also predicted with TCMSP as the targets of FZHY compounds. Conclusion The re- sults indicated that the effective mechanism of FZHY against liver fibrosis is involved in the regulation of multiple targets and multiple pathways, among, retinol metabolism pathway by targeting Ugt2a3, Cyp2bl and Cyp3al8 may play an important role in the treatment of liver fibrosis.
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
文摘Tomato(Solanum lycopersicum L.)is a thermophilic vegetable crop,but sensitive to high temperature stress,especially under the greenhouse conditions.Due to global climate changes,heat stress has now become a great threat to tomato production and fruit quality.Many studies have been conducted to determine the functions of genes in tomato responsive to abiotic and biotic stresses,but transcriptomic information on heat stress responses of tomato fruit is still limited.To investigate heat stress associated genes in tomato fruit,a cDNA library was constructed using fruit harvested from tomato cv.P19-9 plants grown under 42℃for 0,1,2 and4 h and the expression profiles of heat stress responsive genes in tomato fruit were analyzed through RNA-seq.A total of 632224558 clean high quality paired-end reads were obtained and then mapped to reference genome for RNA-seq analysis.After quality control analysis,alignment analysis and transcript assembly,a total of 55457 RNA transcripts were obtained with functional annotations.Overall,6869 differentially expressed genes(DEGs)were identified with a significant response to one or more of the three heat stress treatment times.Based on GO enrichment analysis,22 genes potentially involved in tomato thermo-tolerance were selected and validated for their expressions through qPCR.The expression profile of tomato fruit genes obtained in this study could shed light on the mechanism and gene editing breeding projects for tomato thermo-tolerance.These findings could also benefit improvement of harvest and storage of tomato in greenhouse.
基金supported by National Science and Technology Major Project(2016ZX08010004),China
文摘Background： The conversion from non-embryogenic callus （NEC） to embryogenic callus （EC） is the key bottleneck step in regeneration of upland cotton （Gossypium hirsutum）, and hinders the transgenic breeding of upland cotton. To investigate molecular mechanisms underlying acquisition of embryogenic potential during this process, comparation analysis of transcriptome dynamics between two upland cotton cultivars with different somatic embryogenesis abilities was conducted. Results： Differentially expressed genes involved in the transformation from NEC to EC were detected in the two different cultivars. Principal component analysis based on DEGs showed that the NEC tissues of the two cultivars were highly heterogeneous, whereas the derived EC tissues were similar, which suggested the homogeneousness of EC between different lines. In the highly embryogenic cultivar CCRI 24, more of these genes were down-regulated, whereas, in the recalcitrant cultivar CCRI 12, more were up-regulated. Bioinformatics analysis on these DEGs showed that the vast majority of differentially expressed genes were enriched in metabolism and secondary metabolites biosynthesis pathways. Flavonoid biosynthesis and phenylpropanoid biosynthesis pathways were enriched in both cultivars, and the associated genes were down-regulated more in CCRI 24 than in CCRI 12. We deduced that vigorous secondary metabolism in CCRI 12 may hinder primary metabolism, resulting in tardiness of cell differentiation. Interestingly, genes involved in the plant hormone signal transduction pathway were enriched in the recalcitrant cultivar CCRI 12, but not in CCRI 24, suggesting more radical regulation of hormone signal transduction in the recalcitrant cultivar. Signal transduction rather than biosynthesis of plant hormones is more likely to be the determining factor triggering NEC to EC transition in recalcitrant cotton lines. Transcription factor encoding genes showed differential regulation between two cultivars. Conclusions： Our study provides valuable information about the molecular mechanism of conversion from NEC to EC in cotton and allows for identification of novel genes involved. By comparing transcriptome changes in transformation from NEC to EC between the two cultivars, we identified 46 transcripts that may contribute to initiating embryogenic shift.
基金This work was supported by National R&D Project of Transgenic Crops of Ministry of Science and Technology of China(2016ZX08005–004-002).
文摘Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.
文摘Recently,Wang et al.systematically explored the transcription landscape in diploid cotton Gossypium arboreum.In the study,they integrated four high-throughput sequencing techniques,including Pacbio sequencing,strandspecific RNA sequencing(ss RNA-seq),Cap analysis gene expression sequencing(CAGE-seq),and Poly A sequencing(Poly A-seq)to profile the RNA transcriptome of G.arboreum.They developed a pipeline,IGIA to construct accurate gene structure annotation based on the updated genome of G.arboreum and the multi-strategic RNA-seq data.Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants,and also provided valuable resources for further functional genomic research in cotton.
基金This work was supported by the National Natural Science Foundation of China(31760402)Public Welfare Research Projects in the Autonomous Region(KY2019002)Special Programs for New Varieties Cultivation of Shihezi University(YZZX201701).
文摘Background:Meta-analysis of quantitative trait locus(QTL)is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies.The combination of meta-QTL intervals,significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.Results:In our study,884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1,as a result,74 meta-QTLs were identified,including 19 meta-QTLs for fiber length;18 meta-QTLs for fiber strength;11 meta-QTLs for fiber uniformity;11 meta-QTLs for fiber elongation;and 15 meta-QTLs for micronaire.Combined with 8589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies,297 candidate genes were identified in the meta-QTL intervals,20 of which showed high expression levels specifically in the developing fibers.According to the function annotations,some of the 20 key candidate genes are associated with the fiber development.Conclusions:This study provides not only stable QTLs used for marker-assisted selection,but also candidate genes to uncover the molecular mechanisms for cotton fiber development.
基金Science and Technology Development Fund(FDCT) of Macao SAR (FDCT / 017 / 2015 / AMJFDCT134/2014/A3).
文摘OBJECTIVE To identify and characterize a novel neuroprotective ShK peptide and its analogue originated from coral P.caribaeoru.METHODS P.caribaeoru was collected and subjected to transcriptome sequencing at which further bioinformatics analysis had identified a unigene encoding a putative ShK protein candidate,named as PcShK1.PcShK1 and its rhodamine derivative(PcShK1-RhoB) were synthesized and tested for the neuroprotective effect in 6-OHDA induced Parkinson disease models in vitro and in vivo.Briefly,zebrafish larvae were co-exposed to 6-OHDA and various doses of the peptides;then,dopaminergic(DA) neurons immunoreactivity and locomotion behavior of the zebrafish larvae were examined.Similarly,PC12 cells were cultured with 6-OHDA in the absence or presence of different concentrations of peptides.Cell viability was determined by MTT assay while calcium flow in the PC12 cells was monitored by Fluo-4 fluorescent dye.RESULTS Compared with control group,6-OHDA treatment could lead to DA neurons loss and locomotion deficits in PD model of zebrafish larvae(P<0.01).Both PcS hK 1(2.5,5.0 and 7.5 μmol·L^(-1)) and PcS hK 1-RhoB(0.50 and 0.75 μmol·L^(-1)) were found to protect and restore dopaminergic neurons from6-OHDA mediated injury and locomotion deficiency in the PD zebrafish respectively(P<0.01).In addition,PcShK1(2.5 to 20.0 μmol·L^(-1)) and PcShK1-RhoB(0.6 to 2.5 μmol·L^(-1)) effectively prevented against 6-OHDA toxicity in PC12 cells(P<0.01).Further study revealed that they might exert their neuroprotective effects through regulating the calcium homeostasis.CONCLUSION PcS hK 1 and PcS hK 1-RhoB show neuroprotective effects on 6-OHDA induced PD models,and the underlying protective mechanisms of these peptides probably involve calcium homeostasis regulation.
基金The project supported by grants from the Science and Technology Development Fund of Macao,China(058/2009and 078/2011/A3)Research Committee,University of Macao〔MYRG138(Y1-Y4)-ICMS12-LMY and MYRG139(Y1-Y4)-ICMS-LMY〕
文摘OBJECTIVE To analyze the whole transcriptome of zoanthid Protopalythoa variabilis(P.variabilis),a cnidarian,and discover the potential toxic substances in P.variabilis.METHODS The P.variabilis RNA deep sequencing was performed using the HiSeq 2500 automatic sequencing platform.All the unigenes generated from the assembly process were functionally annotated based on the similarity with databases.The multiple alignments of translated toxin-related sequences were performed with Clustalw2,and amino acid identity and similarity highlighted by using BoxShade tool.Three different methods including ITASSER,PEP-FOLD and MODELLER were applied to predict tri-dimensional models of toxin-related polypeptides from translated transcript sequences of P.variabilis.The toxicity of one of the putative toxins,namely ShK/Aurelin-like peptide,was evaluated using zebrafish model.RESULTS A total of 67,549,914 pairs of quality-filtered,90-base-pair Illumina reads from an mRNA sample were obtained.The de novo assemblies yielded 276,526 contigs.The sequence comparison of 130,121 unigenes with entries in Toxin database showed that 1542 unigenes were potential peptide toxins at which 11 unigenes were related to Stichodactyla toxin(ShK)domain(Pfam ID:PF01549).ShK is a 35 residues peptide sequence that was firstly discovered from the sea anemone Stichodactyla helianthus.Here,we found out one ShK-like peptide that processed a relatively higher sequence similarity with known ShK(Uniprot ID:P29186)of Bunodosoma granuliferum(red warty sea anemone).The Protopalythoa Shk-like peptide was submitted to Probis server to detect probable binding site and found to match with a protein AURELIN(PDB id:2lg4,UniProt id:Q0MWV8)which possesses structural homology with previously identified antimicrobial peptides and K+-channel-blocking toxins.Our results showed that the ShK/Aurelin-like peptide was lethal to zebrafish embryos at concentrations above 30-μmol·L1,and could induce zebrafish locomotor deficit at 10μmol·L-1.CONCLUSION This study,for the first time,presented the whole transcriptome profile and a potential toxic peptide of P.variabilis.
基金The project supported by the Scheme B funding of the project′Establishment of the Centre for Microbial Genomics and Proteomics′and the Scheme D funding of the project′Enhancing the capabilities and strengthening the research personnel of CUHK in Bioinformatics′of the Focused Investment Scheme of The Chinese University of Hong Kongthe Overseas and Hong Kong,Macao Young Scholars Collaborative Research Fund by the Natural National Science Foundation of China(81328025)+1 种基金Science and Technology Development Fund of Macao SAR(058/2009and 078/2011/A3)Research Committee,University of Macao
文摘OBJECTIVE To investigate the transcriptomic details on the biosynthetic pathways in different parts of the Panax notoginseng and the pharmacological activity of the saponins extracted from the flower(FS)on vascular insufficiency conditions.METHODS RNA sequencing of three different Panax notoginseng tissues was performed using next generation DNA sequencing and differential gene expression was validated by real-time PCR.In order to determine pro-angiogenic and therapeutic effects of FS on myocardial infraction(MI),FS was examined on the endothelial cell migration assay,vascular insufficiency model in zebrafish and MI model in rats.RESULTS After assembling the high quality sequencing reads into 107 340 unigenes,biochemical pathways were predicted and 9 908 unigenes were assigned to 135 KEGG pathways.Among them,270 unigenes were identified to be involved in triterpene saponin biosynthesis as well as 350 and 342unigenes were predicted to encode cytochrome P450 sand glycosyltransferases,respectively.One unigene was annotated as CYP716A53v2,probably participates in the formation of protopanaxatriol from protopanaxadiol and the differential expression of this gene was confirmed by real-time PCR.In addition,the pharmacological evaluation demonstrate that FS significantly promoted vascular endothelial growth factor(VEGF)induced the migration of human umbilical vein endothelial cells(HUVECs)and partially restored defective intersegmental vessels in a chemically induced vascular insufficiency model of zebrafish larva.Moreover,the two week posttreatment of the rat MI model with FS(25-50mg·kg-1·d-1)induced approximately 3-fold upregulation of VEGF mRNA expression,with a concomitant increase in blood vessel density in the peri-infarct area of the heart by 50.7%,compared to 41.4%in the MI group.Furthermore,TUNEL analysis indicates a reduction in the mean apoptotic nuclei per field in peri-infarct myocardium upon FS treatment.CONCLUSION We have established a global transcriptome dataset for Panax notoginseng and provided additional genetic information for further genome-wide research and analyses.Candidate genes involved in ginsenoside biosynthesis,including putative cytochrome P450 sand glycosyltransferases were obtained.The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P.notoginseng.And the significant pro-angiogenic effect of FS in multiple experimental models renders the purified saponin preparation as potential preventive and therapeutic agent for cardiovascular diseases yet to be developed.
基金Macao Science and Technology Development Fund(017/2015/AMJ134/2014/A3).
文摘OBJECTIVE Palythoa caribaeorum(class Anthozoa) is a zoanthid that together jellyfishes,hydra,and sea anemones,which are venomous and predatory,belongs to the Phyllum Cnidaria.The distinguished feature in these marine animals is the cnidocytes in the body tissues,responsible for toxin production and injection that are used majorly for prey capture and defense.With exception for other anthozoans,the toxin cocktails of zoanthids have been scarcely studied and are poorly known.METHODS Based on the analysis of P.caribaeorum transcriptome,numerous predicted venom-featured polypeptides were identified,including allergens,neuro-toxins,membrane-active and Kunitz-like peptides(PcKuz).The three predicted PcKuz isotoxins(1 to 3) were selected for functional studies.Through computational processing comprising structural phylogenetic analysis,molecular docking,and dynamics simulation,PcKuz3 was shown to be a potential voltage gated potassium-channel inhibitor.RESULTS PcKuz3 fitted well as new functional Kunitz-type toxins with strong anti-locomotor activity as in vivo assessed in zebrafish larvae,with weak inhibitory effect toward proteases,as evaluated in vitro.Notably,PcKuz3 can suppress,at low concentration,the 6-OHDA-induced neurotoxicity on the locomotive behavior of zebrafish,which indicated PcKuz3 may have a neuroprotective effect.CONCLUSION Taken together,PcK uz3 figures as a novel neurotoxin structure which differs from known homologous peptides expressed in sea anemone.Moreover,the novel PcKuz3 provides an insightful hint for bio-drug development for prospective neurodegenerative disease treatment.
基金Project(31260476)supported by the National Natural Science Foundation of China
文摘In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out.
基金Supported by the National Key Research and Development Project(2017YFD0101803)
文摘The transcriptome-wide gene expression was compared between susceptible and resistant Chinese cabbage cultivars to identify genes that contributed to clubroot resistance. A higher number of differentially expressed genes were detected in susceptible cultivars than in resistant cultivars. Fifty-six genes involved in cell wall modification, hormone signaling, root marphogenesis, nematodes response and cell proliferation were uniquely expressed in the resistant cultivars. Among them, 27 genes were involved in cell wall modification and hormone signaling, indicating that genes in these two types might play a vital role in the defense response to pathogen infection.
