The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis...The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.展开更多
Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence sugge...Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.展开更多
RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of wate...RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.展开更多
Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was...Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.展开更多
The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order t...The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.展开更多
We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using t...We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.展开更多
Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjus...Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.展开更多
Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were invest...Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.展开更多
The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In ad...The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.展开更多
Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tande...Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.展开更多
The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencin...The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.展开更多
The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect T...The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.展开更多
The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,lar...The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,larval,pupal,and adult stages.During postembryonic life,the larval brain transforms into a mature adult version after metamorphosis.The silkworm,Bombyx mori,is a lepidopteran model insect.Here,we characterized the brain cell repertoire of larval and adult B.mori by obtaining 50708 single-cell transcriptomes.Seventeen and 12 cell clusters from larval and adult brains were assigned based on marker genes,respectively.Identified cell types include Kenyon cells,optic lobe cells,monoaminergic neurons,surface glia,and astrocyte glia.We further assessed the cell type compositions of larval and adult brains.We found that the transition from larva to adult resulted in great expansion of glial cells.The glial cell accounted for 49.8%of adult midbrain cells.Compared to flies and ants,the mushroom body kenyon cell is insufficient in B.mori,which accounts for 5.4%and 3.6%in larval and adult brains,respectively.Analysis of neuropeptide expression showed that the abundance and specificity of expression varied among individual neuropeptides.Intriguingly,we found that ion transport peptide was specifically expressed in glial cells of larval and adult brains.The cell atlas dataset provides an important resource to explore cell diversity,neural circuits and genetic profiles.展开更多
Drought-induced osmotic stress severely affects the growth and yield of maize.However,the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear.To gain a systemat...Drought-induced osmotic stress severely affects the growth and yield of maize.However,the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear.To gain a systematic understanding of age-related stress responses,we compared osmotic-stress-induced changes in maize leaves of different ages using multi-omics approaches.After short-term osmotic stress,old leaves suffered more severe water deficits than young leaves.The adjustments of transcriptomes,proteomes,and hormones in response to osmotic stress were more dynamic in old leaves.Metabolic activities,stress signaling pathways,and hormones(especially abscisic acid)responded to osmotic stress in an age-dependent manner.We identified multiple functional clusters of genes and proteins with potential roles in stress adaptation.Old leaves significantly accumulated stress proteins such as dehydrin,aquaporin,and chaperones to cope with osmotic stress,accompanied by senescence-like cellular events,whereas young leaves exhibited an effective water conservation strategy mainly by hydrolyzing transitory starch and increasing proline production.The stress responses of individual leaves are primarily determined by their intracellular water status,resulting in differential transcriptomes,proteomes,and hormones.This study extends our understanding of the mechanisms underlying plant responses to osmotic stress.展开更多
Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hem...Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hemisphere forests,and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations.Here we used a newly sequenced genome of Quercus gilva,an evergreen oak species from East Asia,with 18 published Fagales genomes to determine how Fagaceae genomes have evolved,identify genomic footprints of ecological adaptability in oaks in general,as well as between evergreen and deciduous oaks.We found that oak species exhibited a higher degree of genomic conservation and stability,as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events.In addition,we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense(e.g.,cuticle biosynthesis and oxidosqualene cyclase genes),which may represent the foundation for the ecological adaptation of oak species.Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks.This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic,genome evolutionary,and functional genomic analyses.展开更多
The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular...The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.展开更多
Artificial intelligence(AI)is significantly advancing precision medicine,particularly in the fields of immunogenomics,radiomics,and pathomics.In immunogenomics,AI can process vast amounts of genomic and multi-omic dat...Artificial intelligence(AI)is significantly advancing precision medicine,particularly in the fields of immunogenomics,radiomics,and pathomics.In immunogenomics,AI can process vast amounts of genomic and multi-omic data to identify biomarkers associated with immunotherapy responses and disease prognosis,thus providing strong support for personalized treatments.In radiomics,AI can analyze high-dimensional features from computed tomography(CT),magnetic resonance imaging(MRI),and positron emission tomography/computed tomography(PET/CT)images to discover imaging biomarkers associated with tumor heterogeneity,treatment response,and disease progression,thereby enabling non-invasive,real-time assessments for personalized therapy.Pathomics leverages AI for deep analysis of digital pathology images,and can uncover subtle changes in tissue microenvironments,cellular characteristics,and morphological features,and offer unique insights into immunotherapy response prediction and biomarker discovery.These AI-driven technologies not only enhance the speed,accuracy,and robustness of biomarker discovery but also significantly improve the precision,personalization,and effectiveness of clinical treatments,and are driving a shift from empirical to precision medicine.Despite challenges such as data quality,model interpretability,integration of multi-modal data,and privacy protection,the ongoing advancements in AI,coupled with interdisciplinary collaboration,are poised to further enhance AI’s roles in biomarker discovery and immunotherapy response prediction.These improvements are expected to lead to more accurate,personalized treatment strategies and ultimately better patient outcomes,marking a significant step forward in the evolution of precision medicine.展开更多
Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conve...Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.展开更多
Melon fruit flavor is a key quality characteristic that influences consumer preference.Grafting is an effective technique to enhance fruit quality but yields divergent outcomes in terms of fruit flavor.To address this...Melon fruit flavor is a key quality characteristic that influences consumer preference.Grafting is an effective technique to enhance fruit quality but yields divergent outcomes in terms of fruit flavor.To address this problem,we analyzed parallel changes in flavor-related metabolite accumulation and gene expression in two pumpkin rootstock grafted melons during four fruit developmental stages.We identified 26061 expressed genes and 840 metabolites from 21 different compound classes,including carbohydrates,amino acids,and lipids.We also detected 50 aroma volatile compounds in the grafted melons.Results showed that genes and metabolites associated with metabolic pathways(carbohydrate,amino acid,lipid,and phenylpropanoid)play a key role in flavor formation.Compared with‘Sizhuang 12’,‘Tianzhen 1’rootstock improved melon fruit flavor by upregulating sugar-related genes(HK,MPI,MIOX,and STP)and inducing metabolite accumulation(d-ribose-5-phosphate,d-galactose,and trehalose 6-phosphate),whereas decreasing bitterness-related amino acids(l-arginine,l-asparagine,and l-tyrosine)and associated genes(thrC,ACS,and GLUL)expression at ripening stage.Furthermore,‘Tianzhen 1’exhibited higher expression levels of enzyme-coding genes(4CL,CSE,and COMT)responsible for aroma volatile synthesis than‘Sizhuang 12’rootstock.Taken together,our results decipher the basis of the molecular mechanism underlying fruit flavor in grafted melons and provide valuable information for the melons genetic improvement.展开更多
基金supported by the National Natural Science Foundation of China(31870664)the 948 Program of National Forestry and Grassland Administration(2013-4-47)the National Key Research and Development Program of China(2022YFD2200103)。
文摘The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.
基金supported by the National Natural Science Foundation of China(31972532)the China Agricultural Research System(CARS-40-K05)the Innovation Base Cu。
文摘Background:Tibetan chickens,a unique native breed in the Qinghai-Tibet Plateau of China,possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment.Increasing evidence suggests that long non-coding RNAs(lncRNAs)and microRNAs(miRNAs)play roles in the hypoxic adaptation of high-altitude animals,although their exact involvement remains unclear.Results:This study aimed to elucidate the global landscape of mRNAs,lncRNAs,and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs(ceRNAs)and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos.In total,354 differentially expressed genes(DE genes),389 differentially expressed lncRNAs(DE lncRNAs),and 73 differentially expressed miRNAs(DE miRNAs)were identified between Tibetan chickens(TC)and control Chahua chickens(CH).GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis(including blood vessel development and blood circulation)and energy metabolism(including glucose,carbohydrate,and lipid metabolism).The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions,which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens.Conclusions:Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism.These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.
文摘RNA sequencing of the sensitive GH01 variety of Brassica napus L. seedling roots under 12 h of waterlogging was compared with previously published data of the ZS9 tolerant variety to unravel genetic mechanisms of waterlogging tolerance beyond natural variation. A total of 2 977 genes with similar expression patterns and 17 genes with opposite expression patterns were identiifed in the transcription proifles of ZS9 and GH01. An additional 1 438 genes in ZS9 and 1 861 genes in GH01 showed strain speciifc regulation. Analysis of the overlapped genes between ZS9 and GH01 revealed that waterlogging tolerance is determined by ability to regulate genes with similar expression patterns. Moreover, differences in both gene expression proifles and abscisic acid (ABA) contents between the two varieties suggest that ABA may play some role in waterlogging tolerance. This study identiifes a subset of candidate genes for further functional analysis.
基金jointly funded by the National Natural Science Foundation of China (31661143010)the Pilot Project of Breeding of the Seven Major Crops,China (2016YFD0101803)
文摘Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered （control） and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ＇RNA transcript＇ and ＇mRNA surveillance＇ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.
基金The National Natural Science Foundation of China under contract No.40976089the State Science&Technology Support Program in the 12th Five Year Plan of China under contract No.2011BAD13B05the National High-tech R&D Program of China(863 Program) under contract No.2012AA10A412
文摘The sea cucumberApostichopus japonicus is an important economic species in China. Its dorsal body wall color is commonly tawny, whereas its ventral surface is fawn. Albino sea cucumbers are rarely observed. In order to profile gene expression and screen albinism-related genes, we compared the transcriptome of albino samples with a control by 454 cDNA sequencing. We found that 6 539 identified genes on the basis of sequence similarity to known genes were expressed in the albino A. japonicus. The gene ontology analysis indicated that the transcription of genes associated with the terms of biological regulation and pigmenta-tion was non-abundant in the albino library compared to the control. Based on an analysis using the Kyoto Encyclopedia of Genes and Genomics （KEGG） database, we identified 14 important genes that were in-volved in major intercellular signaling pathways related to melanin synthesis, such as tyrosine metabolism, the mitogen-activated protein kinase （MAPK） pathway, and melanogenesis. The expressions of fibroblast growth factor receptor 4 （FGFR4）, protein kinase C （PKC）, protein kinase A （PKA）, and Ras genes were sig-nificantly down-regulated in the albino transcriptome compared with the control, while the expressions of homogentisate 1, 2-dioxygenase gene （HGO）, cAMP-responsive element binding protein （CREB）, transcrip-tion factor AP-1（c-jun）, and calmodulin （CaM） were significantly up-regulated （Fisher＇s exact test,p 〈 0.05）. These differentially expressed genes could be candidate genes for revealing the mechanism of albinism and investigating regulation of melanin synthesis inA. japonicus.
基金supported by the grants from the Ministry of Science and Technology of China (No.2006AA02Z331 and 2004CB117404)the Key Project of Chinese Academy of Sciences (No.KSCX2-YW-N-020) to Liangbiao ChenNSF OPP 0636696 to C-H CC
文摘We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to im- plement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus maw- soni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data （available at： http：//www.fishgenome.org/ polarbank/） from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the com- parison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diffprogram and operation manual can be downloaded from： http：//www.fishgenome.org/download/Prodiff.rar.
文摘Lactation in dairy cattle is coupled with increased nutrient requirements for milk synthesis. Therefore, dairy cattle metabolism has to adapt to meet lactation-associated challenges and requires major functional adjustments of the rumen and whole digestive system. This report describes the use of next-generation sequencing technology for assembly and profiling of the transcriptome of cattle rumen epithelial tissues from cattle in both dry and lactation periods. Transcriptomics profiling and comparison revealed extensive changes in gene expression related to metabolism in rumen epithelial tissue due to the adaptation to lactation. Ruminal epithelial adaptation to the challenges of metabolism and high nutrient requirements during lactation is presumably the primary triggers for these alterations in gene expression. Principal component analysis (PCA) indicated that the gene expression profiles of the rumen epithelia from dry and lactating cattle fall into two very distinct clusters. Gene Ontology (GO) enrichment analysis revealed that the most GO terms were related to various metabolic processes in lactating cattle. The most significantly (false discovery rate (FDR) p-value < 0.05) enriched GO term in biological processes was “carbohydrate derivative metabolic process”, followed by “nucleoside metabolic process”. Up-stream regulators, such as PPARA (Peroxisome proliferator-activated receptor alpha) gene, and up-regulated genes of molecular transporters are the focal points of this report.
基金Supported by the Project of China One-Belt-One-Road Foreign Expert Research Collaboration,Ministry of Science and Technology,China (No.DL2021002001L)the Open Project Program of State Key Laboratory of Food Nutrition and Safety,Tianjin University of Science&Technology (No.SKLFNS-KF-202205)。
文摘Oxidative stress induced by factors such as ammonia nitrogen has become a major issue in shrimp farming.The effects of carotenoids on the growth and antioxidant capability of Litopenaeus vannamei juveniles were investigated in this study using dietary archaeal carotenoids supplementation.For four weeks,shrimp were given diets containing 0 mg/kg(Ctrl)and 55.98 mg/kg(Car)archaeal carotenoids.Dietary archaeal carotenoids significantly enhanced the astaxanthin content in shrimp muscles and carapaces,as well as the superoxide dismutase(SOD)and glutathione peroxidase(GSH-Px)activity(P<0.05).The malonaldehyde(MDA)content in Car group significantly decreased(P<0.05).The transcriptome analysis was conducted to determine the molecular processes in response to archaeal carotenoids supplementation.A total of 1536 differentially expressed genes(DEGs)were detected,including 538 upregulated DEGs and 998 downregulated DEGs.GO functional enrichment analysis between Ctrl and Car indicated that 26 GO terms including extracellular region,metabolic process,and proteolysis were enriched.The KEGG pathway enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism,cysteine and methionine metabolism,glycine serine and threonine metabolism,and amino acid biosynthesis were enriched.Archaeal carotenoids influenced the expression of several important genes involved in reactive oxygen species(ROS)generation,Nrf2 signaling,and antioxidant enzymes.Seven DEGs were chosen to confirm the RNA-Seq data using qRT-PCR.The genes and pathways discovered in this work assist to elucidate the molecular processes through which archaeal carotenoid enhances L.vannamei antioxidative system.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31370241, 31570214)the International Cooperation and Exchange of the National Natural Science Foundation of China (Grant Nos. 31511140095, 31561143015)National Science Foundation of China (grant no. 30960027)
文摘The genus Croomia(Stemonaceae) is an excellent model for studying the evolution of the Eastern Asia(EA)-Eastern North America(ENA) floristic disjunction and the genetic mechanisms of floral zygomorphy formation. In addition to the presence of both actinomorphic and zygomorphic flowers within the genus, species are disjunctively distributed between EA and ENA. However, due to the limited availability of genomic resources, few studies of Croomia have examined these questions. In this study,we sequenced the floral and leaf transcriptomes of the zygomorphic flowered Croomia heterosepala and the actinomorphic flowered Croomia japonica, and used comparative genomic approaches to investigate the transcriptome evolution of the two closely related species. The sequencing and de novo assembly of transcriptomes from flowers of C. heterosepala(ChFlower), flowers of C. japonica(CjFlower), and leaves of C. japonica(CjLeaf) yielded 57,193, 62,131 and 64,448 unigenes, respectively. In addition, estimation of Ka/Ks ratios for 11,566 potential orthologous groups between ChFlower and CjFlower revealed that only six pairs had Ka/Ks ratios significantly greater than 1 and are likely under positive selection. A total of 429 single copy nuclear genes(SCNGs) and 21,460 expression sequence tags-simple sequence repeats(ESTSSRs) were identified in this study. Specifically, we identified seven CYC/TB1-like genes from Stemonaceae. Phylogenetic and molecular evolution analyses indicated that these CYC/TB1-like genes formed a monophyletic clade(SteTBL1) and were subject to strong purifying selection. The shifts of floral symmetry in Stemonaceae do not appear to be correlated with TBL copy number.
文摘Characterization of occurrence, density and motif sequence of tandem repeats in the transcribed regions is helpful in understanding the functional significance of these repeats in the modern genomes. We analyzed tandem repeats present in expressed sequences of thirteen species belonging to genera Capsicum, Nicotiana, Petunia and Solanum of family Solanaceae and the genus Coffea of Rubiaceae to investigate the propagation and evolutionary sustenance of these repeats. Tandem repeat containing sequences constituted 1.58% to 7.46% of sequences analyzed. Tandem repetitions of size 2, 15, 18 and 21 bp motifs were more frequent. Repeats with unit sizes 21 and 22 bp were also abundant in genomic sequences of potato and tomato. While mutations occurring in these repeats may alter the repeat number, genomes adjust to these changes by keeping the translated products unaffected. Surprisingly, in majority of the species under study, tandem repeat motif length did not exceed 228 bp. Conserved tandem repeat motifs of sizes 180, 192 and 204 bp were also abundant in the genomic sequences. Our observations lead us to propose that these tandem repeats are actually remnants of ancestral megasatellite repeats, which have split into multiple repeats due to frequent insertions over the course of evolution.
基金supported by the internal fund(5020)of the Temasek Life Sciences Laboratory,Singapore。
文摘The pmel17 gene plays a crucial role in melanin pigmentation.Our previous studies showed that in Mozambique tilapia,a transposon inserted into the 3'untranslated region(3'UTR)of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments(golden mutant phenotype).Additionally,the transposon insertion caused reduced growth performance and increased locomotion.In this study,to investigate the mechanisms underlying these phenotypic changes,we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias.A total of 51 and 141 differentially expressed genes(DEGs)were identified in the skin and muscle transcriptomes,respectively.DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways.Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates,14 DEGs were also observed to be related to melanogenesis.In muscle transcriptomes,there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes.Specifically,DEGs related to growth factor binding exhibited a down-regulation,while those related to lipid metabolism showed an up-regulation in mutant genotypes.These findings agree with observed phenotypic changes.Furthermore,several DEGs associated with muscle function and mobility were up-regulated.Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks.The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.
基金supported by AP21PPQS&T00C108 from USDA-APHIS to ELS。
文摘The Mexican fruit fly,Anastrepha ludens,is a polyphagous pest that is a constant threat to US agriculture because of its proximity to citrus production in border region of the United States and Mexico.Sterile Insect Technique has been used to manage and eradicate of the Mexican Fruit Fly.SIT,however,requires millions of sterile male flies to be released each week from mass-rearing facilities.The mass-reared colonies must deal with microbial infections that reduce survivorship,fecundity and male-male competition.Meta-transcriptomics joins culturing and next generation DNA sequencing techniques to understand these changing microbial communities.This study uses advances in microbial meta-transcriptome sequencing to analyze the microbial communities from the four major developmental stages of A.ludens.The composition of the microbial communities was analyzed and revealed the large transcriptional presence of the phyla Microsporidia,a known animal pathogen.Clustering and ordination analyses revealed groupings based on developmental phase for egg,larvae and pupa.Adult samples had little clustering;a not unexpected result given the known turn-over in microbial community that occurs in the first 5 d after pupation.The transcriptional activity of three known pathogens of A.ludens between developmental phases were investigated.Two of the three pathogens had significant transcriptional differences between the phases with the larvae phase having the most activity.This increase in transcriptional activity agrees with culture-based surveillance and current mitigation strategies employed in the mass-rearing facility.This result reinforces the utility of transcriptomics in combating microbial threats.
基金supported by the National Science Foundation of China(32000339,32000336 and 31925007)the Natural Science Foundation of Jiangsu Province(BK20231249,BK20221292 and BK20210880)。
文摘The diversity of cell types in the brain and how these change during different developmental stages,remains largely unknown.The life cycle of insects is short and goes through 4 distinct stages including embryonic,larval,pupal,and adult stages.During postembryonic life,the larval brain transforms into a mature adult version after metamorphosis.The silkworm,Bombyx mori,is a lepidopteran model insect.Here,we characterized the brain cell repertoire of larval and adult B.mori by obtaining 50708 single-cell transcriptomes.Seventeen and 12 cell clusters from larval and adult brains were assigned based on marker genes,respectively.Identified cell types include Kenyon cells,optic lobe cells,monoaminergic neurons,surface glia,and astrocyte glia.We further assessed the cell type compositions of larval and adult brains.We found that the transition from larva to adult resulted in great expansion of glial cells.The glial cell accounted for 49.8%of adult midbrain cells.Compared to flies and ants,the mushroom body kenyon cell is insufficient in B.mori,which accounts for 5.4%and 3.6%in larval and adult brains,respectively.Analysis of neuropeptide expression showed that the abundance and specificity of expression varied among individual neuropeptides.Intriguingly,we found that ion transport peptide was specifically expressed in glial cells of larval and adult brains.The cell atlas dataset provides an important resource to explore cell diversity,neural circuits and genetic profiles.
基金supported by the National Natural Science Foundation of China(32272026 and U1904107 to W.W.)the National Key Laboratory of Wheat and Maize Crop Science,Henan agricultural University,China(39990101 to W.W.).
文摘Drought-induced osmotic stress severely affects the growth and yield of maize.However,the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear.To gain a systematic understanding of age-related stress responses,we compared osmotic-stress-induced changes in maize leaves of different ages using multi-omics approaches.After short-term osmotic stress,old leaves suffered more severe water deficits than young leaves.The adjustments of transcriptomes,proteomes,and hormones in response to osmotic stress were more dynamic in old leaves.Metabolic activities,stress signaling pathways,and hormones(especially abscisic acid)responded to osmotic stress in an age-dependent manner.We identified multiple functional clusters of genes and proteins with potential roles in stress adaptation.Old leaves significantly accumulated stress proteins such as dehydrin,aquaporin,and chaperones to cope with osmotic stress,accompanied by senescence-like cellular events,whereas young leaves exhibited an effective water conservation strategy mainly by hydrolyzing transitory starch and increasing proline production.The stress responses of individual leaves are primarily determined by their intracellular water status,resulting in differential transcriptomes,proteomes,and hormones.This study extends our understanding of the mechanisms underlying plant responses to osmotic stress.
基金supported by the National Natural Science Foundation of China(No.31901217)the Special Fund for Scientific Research of Shanghai Landscaping and City Appearance Administrative Bureau(grant numbers G192422,G242414,and G242416).
文摘Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change.Quercus is a keystone genus in Northern Hemisphere forests,and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations.Here we used a newly sequenced genome of Quercus gilva,an evergreen oak species from East Asia,with 18 published Fagales genomes to determine how Fagaceae genomes have evolved,identify genomic footprints of ecological adaptability in oaks in general,as well as between evergreen and deciduous oaks.We found that oak species exhibited a higher degree of genomic conservation and stability,as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events.In addition,we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense(e.g.,cuticle biosynthesis and oxidosqualene cyclase genes),which may represent the foundation for the ecological adaptation of oak species.Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks.This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic,genome evolutionary,and functional genomic analyses.
基金This study was partially supported by grants from the National Natural Science Foundation of China (31490591,31330032,and 61327902)the National Key R&D Program of China (2017YFA 0700500)+1 种基金the Frontier Key Project of the Chinese Academy of Sciences (QYZDJ-SSW-SMCO25)Shanghai Municipal Science and Technology Major Project (2018SHZDZX05).
文摘The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammalsThe molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigationHere, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortexFurthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulationThus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.
基金supported by grants from the National Natural Science Foundation of China(Grant No.82272008)The Science&Technology Development Fund of Tianjin Education Commission for Higher Education(Grant No.2021KJ194)Tianjin Key Medical Discipline(Specialty)Construction Project(Grant No.TJYXZDXK-009A).
文摘Artificial intelligence(AI)is significantly advancing precision medicine,particularly in the fields of immunogenomics,radiomics,and pathomics.In immunogenomics,AI can process vast amounts of genomic and multi-omic data to identify biomarkers associated with immunotherapy responses and disease prognosis,thus providing strong support for personalized treatments.In radiomics,AI can analyze high-dimensional features from computed tomography(CT),magnetic resonance imaging(MRI),and positron emission tomography/computed tomography(PET/CT)images to discover imaging biomarkers associated with tumor heterogeneity,treatment response,and disease progression,thereby enabling non-invasive,real-time assessments for personalized therapy.Pathomics leverages AI for deep analysis of digital pathology images,and can uncover subtle changes in tissue microenvironments,cellular characteristics,and morphological features,and offer unique insights into immunotherapy response prediction and biomarker discovery.These AI-driven technologies not only enhance the speed,accuracy,and robustness of biomarker discovery but also significantly improve the precision,personalization,and effectiveness of clinical treatments,and are driving a shift from empirical to precision medicine.Despite challenges such as data quality,model interpretability,integration of multi-modal data,and privacy protection,the ongoing advancements in AI,coupled with interdisciplinary collaboration,are poised to further enhance AI’s roles in biomarker discovery and immunotherapy response prediction.These improvements are expected to lead to more accurate,personalized treatment strategies and ultimately better patient outcomes,marking a significant step forward in the evolution of precision medicine.
基金supported by the National Natural Science Fund of China(Grant Nos.31872066 and 32272663)the Science and Technology Planning Project of Guangzhou(Grant No.2023B01J2002)+1 种基金the Key Research and Development Program of Hainan(Grant No.ZDYF2023XDNY052)the Seed Industry Engineering Project of Ministry of Agriculture and Rural Affairs of Guangdong(Grant Nos.2022-NPY-00-004 and 2022-NBH-00-001)。
文摘Litchi chinensis Sonn.is an important economic fruit tree in tropical and subtropical regions.Regrettably,the efficiency of plant regeneration via somatic embryogenesis in litchi is typically low due to the poor conversion of embryos to plants.The purpose of this study was to establish a regeneration system via somatic embryogenesis from immature embryos explants in‘Heiye'cultivar of litchi.Our results demonstrated that MS medium supplemented with 2.0 mg L^(-1)2,4-D was optimal for callus induction.For somatic embryo(SE)induction,MS medium containing0.5 g L^(-1) activated charcoal(AC)was the most effective,while the use of zeatin(ZT)and thidiazuron(TDZ)resulted in abnormal somatic embryos.The rooting and regeneration rate of 2.15%and 17.5%,respectively,were achieved using MS medium supplemented with 0.5 g L^(-1) AC.Furthermore,transcriptome analysis was performed on embryogenic callus(EC),globular embryo(GE),and heart embryo(HE)to explore the molecular mechanisms of early somatic embryogenesis.2,587 common differentially expressed genes(DEGs)between EC_vs_GE and EC_vs_HE were identified,and the expression patterns of these common DEGs were separated into twelve major clusters.GO annotation and KEGG pathway analysis revealed that these common DEGs were implicated in plant hormone signal transduction,auxin-activated signaling pathway,and other biological processes.Additionally,differentially expressed transcription factors were identified,and the function of LcBBM2 which is specifically highly expressed during early somatic embryogenesis was verified.Overexpression of LcBBM2 in tomato promotes callus and shoot formation.Therefore,this study can provide a theoretical basis and technical support for genetic breeding improvement of litchi.
基金supported by the National Natural Science Foundation of China(31972435)to Jintao Cheng,and Agriculture Research System of MOF and MORA(CARS-25)Natural Science Foundation of Hubei Province(2019CFA017)Ningbo Scientific and Technological Project(2021Z006)to Zhilong Bie.
文摘Melon fruit flavor is a key quality characteristic that influences consumer preference.Grafting is an effective technique to enhance fruit quality but yields divergent outcomes in terms of fruit flavor.To address this problem,we analyzed parallel changes in flavor-related metabolite accumulation and gene expression in two pumpkin rootstock grafted melons during four fruit developmental stages.We identified 26061 expressed genes and 840 metabolites from 21 different compound classes,including carbohydrates,amino acids,and lipids.We also detected 50 aroma volatile compounds in the grafted melons.Results showed that genes and metabolites associated with metabolic pathways(carbohydrate,amino acid,lipid,and phenylpropanoid)play a key role in flavor formation.Compared with‘Sizhuang 12’,‘Tianzhen 1’rootstock improved melon fruit flavor by upregulating sugar-related genes(HK,MPI,MIOX,and STP)and inducing metabolite accumulation(d-ribose-5-phosphate,d-galactose,and trehalose 6-phosphate),whereas decreasing bitterness-related amino acids(l-arginine,l-asparagine,and l-tyrosine)and associated genes(thrC,ACS,and GLUL)expression at ripening stage.Furthermore,‘Tianzhen 1’exhibited higher expression levels of enzyme-coding genes(4CL,CSE,and COMT)responsible for aroma volatile synthesis than‘Sizhuang 12’rootstock.Taken together,our results decipher the basis of the molecular mechanism underlying fruit flavor in grafted melons and provide valuable information for the melons genetic improvement.
