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Pan-genome-wide identification and co-expression analysis of rapeseed SBT genes reveals that BnaSBT1.4 negatively regulates the salt-stress response 认领 引用
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作者 Shengting Li Xiaodong Li +8 位作者 Boyu Meng Daifei Song Yuanyi Mao Lin Liu Wei Chang Yonghai Fan Mingchao Qian Shahid Ullah Khan Kun Lu 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第5期1245-1249,共5页
Subtilases(SBTs)play important roles in plant development and resistance to environmental stresses.However,a systematic pan-genome characterization and functional analysis of the SBT family in polyploid crops had not ... Subtilases(SBTs)play important roles in plant development and resistance to environmental stresses.However,a systematic pan-genome characterization and functional analysis of the SBT family in polyploid crops had not been performed.In this study,we performed a pan-genome analysis of 17 rapeseed genomes and identified 1844 SBT family members,which were divided into 82 orthologous gene groups(OGGs)and classified into six subfamilies.Analysis of gene duplication analysis and gene expression patterns reveled that SBT subfamily 1A contains many core OGGs.The expression levels of the subfamily 1 OGG member Bna SBT.CR04 increased under salt-stress treatment. 展开更多
关键词 gene duplication analysis rapeseed genomes rapeseed sbt genes salt stress response gene expression patterns co expression analysis pan genome analysis orthologous gene groups oggs
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Morphological changes and gibberellin-related gene expression patterns during fruit growth and development of Amomum villosum 认领 引用 被引量：1
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作者 LÜ Bingding ZHANG Yuyi +5 位作者 TANG Liyun HU Jiajia SU Jing XU Jie HE Zhuohang HE Guozhen 《中山大学学报（自然科学版）（中英文）》 CAS CSCD 北大核心 2026年第3期19-32,共14页
The fruit of Amomum villosum is highly valued for its medicinal and edible properties.However,the fruit abscission rate is exceptionally high,resulting in low unit yield.To better understand the fruit growth and devel... The fruit of Amomum villosum is highly valued for its medicinal and edible properties.However,the fruit abscission rate is exceptionally high,resulting in low unit yield.To better understand the fruit growth and development,this study investigated the characteristic changes of fruits and the expression patterns of GA-related genes in both fruits and fruit stalks.Results revealed that it takes approximately 90 days for the ovary of A.villosum to reach maturity.Fruit growth pattern exhibited a slow-fast-slow trend,with the peak of fruit weight accumulation occurring between the 14 and 25 days after artificial pollination(DAP).Before the 27 DAP,significant changes were observed in the ovary,fruit color,pericarp thickness,and fruit thorn length.Additionally,ten candidate GA-related genes,including 1 GA13ox,1 GA20ox,1 GA3ox,2 GA2oxs,4 GID1cs,and 1 DELLA,were analyzed using bioinformatics tools.The GA-related genes in fruit and fruit stalk exhibited significant correlations with fruit growth/development and fruit dropping.Overall,the fruit growth and development law,and the expression patterns of GA-related genes provided a theoretical foundation for further functional study and the screening of candidate genes for potential applications in A.villosum. 展开更多
关键词 Amomum villosum gibberellin fruit development gene expression pattern bioinformatic
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Recombinant expression of a novel Mytilus defensin in Pichia pastoris 认领 引用 被引量：1
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作者 XIAO Wenhui SONG Fang +4 位作者 CHEN Chuanyue HUANG Fangfang YANG Qiaomei ZHANG Xiaolin LIAO Zhi 《生物工程学报》 EI CAS CSCD 北大核心 2026年第2期852-864,共13页
Mytilus contain abundant antimicrobial peptides(AMPs)that play a key role in the innate immunity.However,heterologous production of these AMPs remains challenging due to their short sequences,multiple disulfide bonds,... Mytilus contain abundant antimicrobial peptides(AMPs)that play a key role in the innate immunity.However,heterologous production of these AMPs remains challenging due to their short sequences,multiple disulfide bonds,and high content of cationic amino acids,which hinder functional expression in prokaryotic systems such as Escherichia coli.To establish a eukaryotic recombinant expression system for the AMPs of mussel and obtain recombinant mussel AMPs for subsequent studies,we reported the successful recombinant expression of myticofensin B1,a novel defensin-like AMP identified previously in Mytiluscoruscus,using the eukaryotic host Pichia pastoris.The codon-optimized gene encoding the mature myticofensin-B1(composed of 65 amino acid residues,including 6 conserved cysteine residues)was cloned into a pPICZαA vector and expressed in P.pastoris GS115.Structural fidelity of the recombinant peptide was confirmed by liquid chromatography-tandem mass spectrometry(LC-MS/MS),showing a molecular weight of 8849.9 Da,which was consistent with the theoretical prediction.Functional assays demonstrated a broad-spectrum antimicrobial activity of the recombinant myticofensin-B1,with stronger inhibition against Gram-negative bacteria.Scanning electron microscopy revealed different effects of the recombinant myticofensin-B1 against different bacteria.In addition,the recombinant myticofensin-B1 exhibited a very low hemolytic activity against sheep red blood cells and weak cytotoxicity against human A549 lung cancer cells.This study establishes P.pastoris as a powerful platform to produce functional mussel AMP and highlights the potential of the recombinant myticofensin-B1 as a therapeutic agent for aquaculture pathogens and infections. 展开更多
关键词 Mytilus coruscus myticofensin recombinant expression antimicrobial peptide Pichia pastoris
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Population-level analyses reveal contrasting landscapes of gene expression divergence and evolution between male and female transcriptome lineages in the house mouse 认领 引用
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作者 Kaizong Wei Chen Xie +6 位作者 Xianghui Zhang Aftab Ahmad Lei Duan Mingji Chu Yuanxiao Gao Diethard Tautz Wenyu Zhang 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第3期470-484,共15页
While sex-biased gene expression and its evolutionary dynamics across taxa have been extensively investigated,systematic separate characterization of the evolutionary patterns in transcriptome divergence between male ... While sex-biased gene expression and its evolutionary dynamics across taxa have been extensively investigated,systematic separate characterization of the evolutionary patterns in transcriptome divergence between male and female lineages remains underexplored.Here,we analyze a comprehensive RNA-seq data set from the house mouse complex,spanning multiple organs across subspecies and species,to delineate the evolutionary trajectories of gene expression in males and females in intra-and inter-species contrasts.For both sexes,we find specific gene expression divergence patterns across the surveyed organs,with a particularly high divergence rate at early evolutionary stages of separation.Comparative analysis between sexes demonstrates male reproductive organs,particularly the testis,displaying accelerated evolutionary rates of expression divergence.Strikingly,testicular long non-coding RNA genes show the most pronounced acceleration,with differences emerging already after a few thousand years of population separation.In contrast,somatic organs and female reproductive auxiliary tissues show no major sex-specific evolutionary dynamics.Genes with sex-biased expression substantially contribute to differentially expressed genes across evolutionary transitions,though without predominant directional bias toward either sex.Notably,these differentially expressed genes display significant over-representation on autosomes.A general functional divergence process is found between male and female transcriptomes across organs mainly driven by sex-specific differentially expressed genes.Collectively,our findings establish a new evolutionary framework for sex-specific expression divergence and provide novel insights into the role of reproductive constraints in shaping transcriptome evolution in mammals. 展开更多
关键词 house mouse complex population transcriptomics sex-biased gene expression sex-specific gene expression evolution transcriptome divergence
Characterizing breed-shared and breed-specific genetic regulatory effects of gene expression across three pig breeds 认领 引用
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作者 Xiaojing Li Xiaodian Cai +5 位作者 Jiajian Chen Xiangchun Pan Wentao Gong Zhanming Zhong Jinyan Teng Zhe Zhang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2026年第3期1284-1296,共13页
Background Differences across breeds in adaptation to various environments and in performance on complex traits such as growth rate are very common in livestock.These differences have been attributed to various factor... Background Differences across breeds in adaptation to various environments and in performance on complex traits such as growth rate are very common in livestock.These differences have been attributed to various factors,including genetic variation,selection,and environmental influences.Gene expression regulation,serving as a critical intermediary mechanism that bridges genotypes and phenotypes,may play a pivotal role in driving these differences across breeds.Hence,we characterized the breed-shared and breed-specific pattern in genetic regulatory effects on gene expression via expression quantitative trait locus(eQTL)mapping in three pig breeds(Duroc,Landrace,and Yorkshire),aiming to gain a deeper understanding of the molecular basis underlying complex trait differences across breeds.Results We observed breed differentiation at both the single-nucleotide polymorphism(SNP)and gene expression levels.By eQTL mapping,within each tissue,an average of 71.1% of the eGenes identified in each breed were breed-shared,while the remaining 28.9% were breed-specific.We found that some regulatory effects are relevant to either the difference in average gene expression or expression variance among populations.Breed-shared eGenes were more abundant,showed larger effect sizes and lower evolutionary conservation,and vice versa.Enrichment analysis showed that the genome-wide association studies(GWAS)loci were significantly enriched in the cis-eQTLs of eGenes for an average of 12 of 19 complex traits per breed.These loci exhibited higher enrichment for breedspecific eGenes than for breed-shared eGenes.Through colocalization analyses with GWAS loci,we observed 220 colocalization events(PP.H4>0.8)with breed-specific eGenes and 758 events with breed-shared eGenes.Conclusions Our study reveals breed-shared and breed-specific effects and characteristics of genetic regulation on gene expression in three pig breeds.Both breed-shared and breed-specific eGenes contribute to the regulatory variation in complex traits,with breed-specific eGenes capturing additional regulatory signals not explained by breeshared eGenes.Together,these findings demonstrate that both shared and breed-specific regulatory variation play important roles in shaping gene expression and suggest their potential contribution to complex traits. 展开更多
关键词 Breed-stratified analysis Cis-eQTL mapping Complex traits Gene expression Regulatory architecture
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The evolution of sexually dimorphic expression in Salicaceae with repeated sex chromosome turnovers 认领 引用
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作者 Deyan Wang Lanxing Shan +3 位作者 Yiling Li Jiale Zhao Matthew S.Olson Tao Ma 《Journal of Systematics and Evolution》 SCIE CSCD 2026年第3期437-453,共17页
Sexual dimorphism in dioecious plants is common in reproductive tissues.Genes expressed in these tissues often show sex bias and differ between sexes in their protein evolutionary rates.At the same time,sex-linked gen... Sexual dimorphism in dioecious plants is common in reproductive tissues.Genes expressed in these tissues often show sex bias and differ between sexes in their protein evolutionary rates.At the same time,sex-linked genes often balance their expression levels between sexes through dosage compensation.We compared gene expression between males and females in floral and leaf tissues of eight dioecious Salicaceae species whose sex chromosomes are young to understand the level of conservation and diversity of genes with sex-biased expression.Our results revealed that sexually dimorphic gene expression showed large numbers of differences among these species,with only 6%of the genes remaining conserved,showing a consistent sex-biased direction in at least seven species.Protein evolutionary rates depended on their degree of conservation and the direction of sex bias in expression.Non-core sex-biased genes showed elevated evolutionary rates and core male-biased genes showed higher nonsynonymous and synonymous substitutions than unbiased genes.Detailed studies in three willow species revealed that the expression dosage of most sex-linked genes was partially(0.51)compensated through reducing gene expression in the homogametic sex.Our results provide novel insights into how sexually dimorphic gene expression evolves during repeated turnovers of sex chromosomes in plants and confirm that dosage compensation mechanisms evolve relatively early in the development of sex chromosomes. 展开更多
关键词 Dosage compensation evolution salicaceae sex-biased expression sexual dimorphism.
Tissue-specific epigenetic regulation of fat metabolism in pigs through integrated analysis of DNA methylation and gene expression networks 认领 引用
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作者 Do-Young Kim Byeonghwi Lim +3 位作者 Rajesh Kumar Pathak Woncheoul Park Jong-Eun Park Jun-Mo Kim 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2026年第3期1328-1344,共17页
Background Fat metabolism in pigs is controlled by tissue-specific molecular mechanisms that ultimately affect growth performance and meat quality.Understanding how epigenetic modifications interact with gene expressi... Background Fat metabolism in pigs is controlled by tissue-specific molecular mechanisms that ultimately affect growth performance and meat quality.Understanding how epigenetic modifications interact with gene expression across key metabolic and fat-depositing tissues is essential for identifying regulatory processes and potential biomarkers to improve pork quality traits.Therefore,this study aimed to elucidate tissue specific epigenetic regulation of fat metabolism by integrating DNA methylation and gene expression profiles from liver,backfat,and loin(longissimus dorsi)tissues at two physiologically developmental stages(10 and 26 weeks),representing the early post-weaning growth phase and near-market weight,respectively.By explicitly comparing these ages and tissues,the study was designed to capture the transition from muscle-dominated growth to increased lipid deposition and to identify tissue-and stage-specific regulatory signatures that may serve as biomarkers for pork quality.Results Genome-wide DNA methylation exhibited weak clustering by tissue,whereas gene expression showed clear tissue separation.The liver harbored fewer genes with differential methylation across stage and tissue but a greater number of genes with differential expression than backfat and loin,suggesting distinct regulatory modes.Integrative analysis of the overlap genes between methylation and expression signals highlighted epigenetically mediated regulation of extracellular matrix organization,lipid metabolism,and muscle development pathways.Furthermore,weighted gene co-expression network analysis revealed distinct tissue-specific correlations between co-methylated and co-expressed modules,with enrichment in cholesterol biosynthesis,muscle contractility,and extracellular matrix remodeling.Together,these findings suggest that methylation changes are more subtle than transcriptional shifts,yet they are aligned with key functional pathways,consistent with a role for methylation as a fine-tuning mechanism that shapes tissue-specific transcriptional networks during growth.Conclusions Across liver,backfat,and loin,DNA methylation modulates transcriptional programs in a tissue-dependent manner,prioritizing pathways central to lipid handling,extracellular matrix remodeling,and muscle function.This integrated multi-omics framework highlights candidate epigenetic markers and regulatory modules with potential utility for improving pork quality traits through selection or management strategies. 展开更多
关键词 DNA methylation Epigenetic Gene expression Multi-omics integration analysis Porcine
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Dynamic Facial Expression Recognition of Learners via Adaptive Global Attention and Differential Temporal Transformer 认领 引用
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作者 Wei Liu Lujia Li +4 位作者 Chun Yan Yulin Zhang Xiaochun Cheng Xinyan Zhao Mingshi Liu 《CAAI Transactions on Intelligence Technology》 SCIE EI CSCD 2026年第2期514-528,共15页
Analysing learners'facial expressions during learning and exploring their learning processes and emotional changes are of great significance for assisting teachers'teaching and promoting smart education.In com... Analysing learners'facial expressions during learning and exploring their learning processes and emotional changes are of great significance for assisting teachers'teaching and promoting smart education.In complex learning environments,static facial expression recognition fails to capture the dynamic changes of learners'expressions losing the continuous features in the learning process,and its recognition effect is easily interfered with by factors such as occlusion and lighting variations during learning.To address the above issues,a network model based on adaptive global attention and temporal difference is proposed to recognise learners'dynamic expression sequences.Firstly,we have designed an Adaptive Global Attention(AGA)block,which adaptively models inter-channel relationships to dynamically enhance key channels that are highly correlated with learners'states while suppressing redundant information,thereby improving the model's feature representation capability under noisy environments.Secondly,we have designed a Differential Temporal Transformer(DTFormer)to extract differential information between consecutive frames,increasing the model's sensitivity to learners'facial expression dynamics and improving recognition performance.The two components complement each other in terms of spatial feature enhancement and temporal dynamic modelling effectively improving the model's overall capability for representing learners'dynamic facial expressions.Experiments were conducted on public datasets DFEW,FERV39k and the learner E-learning emotional state data set DAiSEE,and comparisons were made with classical methods using objective indicators.The results demonstrate that the proposed method outperforms the comparison methods in multiple performance indicators,thereby verifying its effectiveness. 展开更多
关键词 face analysis facial expression recognition spatial-temporal feature transformer
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Expression level and spatial distribution of opsin gene in Oratosquilla oratoria compound eye 认领 引用
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作者 Fangrui LOU Xiaowen DUAN +2 位作者 Jiaoli ZHOU Yue DING Zhiqiang HAN 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2026年第1期340-356,共17页
Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)a... Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species. 展开更多
关键词 Oratosquilla oratoria opsin gene expression pattern single-cell RNA sequencing in-situ hybridization
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A machine learning-based depression recognition model integrating spiritexpression features from traditional Chinese medicine 认领 引用
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作者 Minghui Yao Rongrong Zhu +4 位作者 Peng Qian Huilin Liu Xirong Sun Limin Gao Fufeng Li 《Digital Chinese Medicine》 CAS CSCD 2026年第1期68-79,共12页
Objective To develop a depression recognition model by integrating the spirit-expression diagnostic framework of traditional Chinese medicine(TCM)with machine learning algorithms.The proposed model seeks to establish ... Objective To develop a depression recognition model by integrating the spirit-expression diagnostic framework of traditional Chinese medicine(TCM)with machine learning algorithms.The proposed model seeks to establish a TCM-informed tool for early depression screening,thereby bridging traditional diagnostic principles with modern computational approaches.Methods The study included patients with depression who visited the Shanghai Pudong New Area Mental Health Center from October 1,2022 to October 1,2023,as well as students and teachers from Shanghai University of Traditional Chinese Medicine during the same period as the healthy control group.Videos of 3–10 s were captured using a Xiaomi Pad 5,and the TCM spirit and expressions were determined by TCM experts(at least 3 out of 5 experts agreed to determine the category of TCM spirit and expressions).Basic information,facial images,and interview information were collected through a portable TCM intelligent analysis and diagnosis device,and facial diagnosis features were extracted using the Open CV computer vision library technology.Statistical analysis methods such as parametric and non-parametric tests were used to analyze the baseline data,TCM spirit and expression features,and facial diagnosis feature parameters of the two groups,to compare the differences in TCM spirit and expression and facial features.Five machine learning algorithms,including extreme gradient boosting(XGBoost),decision tree(DT),Bernoulli naive Bayes(BernoulliNB),support vector machine(SVM),and k-nearest neighbor(KNN)classification,were used to construct a depression recognition model based on the fusion of TCM spirit and expression features.The performance of the model was evaluated using metrics such as accuracy,precision,and the area under the receiver operating characteristic(ROC)curve(AUC).The model results were explained using the Shapley Additive exPlanations(SHAP).Results A total of 93 depression patients and 87 healthy individuals were ultimately included in this study.There was no statistically significant difference in the baseline characteristics between the two groups(P>0.05).The differences in the characteristics of the spirit and expressions in TCM and facial features between the two groups were shown as follows.(i)Quantispirit facial analysis revealed that depression patients exhibited significantly reduced facial spirit and luminance compared with healthy controls(P<0.05),with characteristic features such as sad expressions,facial erythema,and changes in the lip color ranging from erythematous to cyanotic.(ii)Depressed patients exhibited significantly lower values in facial complexion L,lip L,and a values,and gloss index,but higher values in facial complexion a and b,lip b,low gloss index,and matte index(all P<0.05).(iii)The results of multiple models show that the XGBoost-based depression recognition model,integrating the TCM“spirit-expression”diagnostic framework,achieved an accuracy of 98.61%and significantly outperformed four benchmark algorithms—DT,BernoulliNB,SVM,and KNN(P<0.01).(iv)The SHAP visualization results show that in the recognition model constructed by the XGBoost algorithm,the complexion b value,categories of facial spirit,high gloss index,low gloss index,categories of facial expression and texture features have significant contribution to the model.Conclusion This study demonstrates that integrating TCM spirit-expression diagnostic features with machine learning enables the construction of a high-precision depression detection model,offering a novel paradigm for objective depression diagnosis. 展开更多
关键词 Traditional Chinese medicine Spirit Expression Feature fusion Depression Recognition model
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Genome-wide identification and expression profiles of flavonoid O-methyltransferase gene family in Scutellaria baicalensis 认领 引用
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作者 Cheng-Hao Fei Yi-Bo He +3 位作者 Peng Chen Bin Chen Kai Qian Pei-Na Zhou 《Traditional Medicine Research》 2026年第8期43-52,共10页
Background:Scutellaria baicalensis Georgi is a medicinal plant prized for its bioactive flavonoid derivatives.Flavonoid O-methyltransferases(OMTs)in this species play a vital role in enhancing these compounds’pharmac... Background:Scutellaria baicalensis Georgi is a medicinal plant prized for its bioactive flavonoid derivatives.Flavonoid O-methyltransferases(OMTs)in this species play a vital role in enhancing these compounds’pharmacological activities,including their antioxidant,anti-inflammatory,and anticancer effects.However,a comprehensive genomic overview of the OMT gene family in S.baicalensis is lacking.Methods:This study conducted a genome-wide identification of the OMT gene family in S.baicalensis using bioinformatics approaches.The identified genes were characterized through phylogenetic,physicochemical,and structural analyses.Furthermore,the response of methoxylated flavonoids and key SbOMT genes to drought stress was investigated.Results:A total of 54 SbOMTs were identified and classified into 9 CCoAOMT and 45 COMT subfamily members.These proteins,with lengths from 129 to 695 amino acids and molecular weights from 14.42 to 76.94 kDa,were predominantly acidic.Subcellular localization predicted 43% to be cytoplasmic.Structurally,the CCoAOMT subfamily was more conserved than the COMT subfamily.Promoter analysis revealed hormone-and stress-responsive cis-elements.Under drought stress,the root content of methoxylated flavonoids(wogonin,wogonoside,and oroxylin A)decreased initially and then increased.The expression of SbOMT06,SbOMT41,SbOMT27,and SbOMT29 was positively correlated with this accumulation,suggesting their involvement in biosynthesis.Conclusion:This study provides foundational insights into the SbOMT gene family,revealing key candidates likely involved in methoxyflavonoid biosynthesis.The findings advance our understanding of the molecular mechanisms in S.baicalensis and offer valuable resources for future metabolic engineering and pathway optimization efforts. 展开更多
关键词 Scutellaria baicalensis flavonoids O-methyltransferase bioinformatics expression analysis
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Unveiling cell-type-specific mode of evolution in comparative single-cell expression data 认领 引用
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作者 Tian Qin Hongju Zhang Zhengting Zou 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第1期28-42,共15页
While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an an... While methodology for determining the mode of evolution in coding sequences has been well established,evaluation of adaptation events in emerging types of phenotype data needs further development.Here,we propose an analysis framework(expression variance decomposition,EVaDe)for comparative single-cell expression data based on phenotypic evolution theory.After decomposing the gene expression variance into separate components,we use two strategies to identify genes exhibiting large between-taxon expression divergence and small within-cell-type expression noise in certain cell types,attributing this pattern to putative adaptive evolution.In a dataset of primate prefrontal cortex,we find that such humanspecific key genes enrich with neurodevelopment-related functions,while most other genes exhibit neutral evolution patterns.Specific neuron types are found to harbor more of these key genes than other cell types,thus likely to have experienced more extensive adaptation.Reassuringly,at the molecular sequence level,the key genes are significantly associated with the rapidly evolving conserved non-coding elements.An additional case analysis comparing the naked mole-rat(NMR)with the mouse suggests that innateimmunity-related genes and cell types have undergone putative expression adaptation in NMR.Overall,the EVaDe framework may effectively probe adaptive evolution mode in single-cell expression data. 展开更多
关键词 Single-cell transcriptomics Gene expression Adaptive evolution Cell type Phenotypic evolution Prefrontal cortex Naked mole-rat
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A novel and efficient Agrobacterium-mediated transient gene expression in citrus epicotyls and mature stem tissues 认领 引用 被引量：1
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作者 Yanjun Li Wei Hu +4 位作者 Showkat Ahmad Ganie Zongrang Liu Baoping Cheng Hui Duan Yi Li 《Fruit Research》 2025年第1期501-509,共9页
Agrobacterium-mediated transient gene expression is a powerful technique for rapidly evaluating gene expression in higher plants.This study aimed to improve transient expression levels of T-DNA genes in citrus by inve... Agrobacterium-mediated transient gene expression is a powerful technique for rapidly evaluating gene expression in higher plants.This study aimed to improve transient expression levels of T-DNA genes in citrus by investigating the effects of various factors,including seedling age,tissue treatments,Agrobacterium incubation medium and duration,hormone combinations,methylation inhibitors,antioxidants,and more.These parameters were optimized and tested,and significant increases in transient gene expression in juvenile epicotyls of Carrizo citrange and mature stem tissues of Pineapple sweet orange,Valencia orange,and Washington navel orange were observed.The present results demonstrated up to a six-fold increase in transient GUS gene expression,highlighting the effectiveness of these simple and inexpensive treatments.The juvenile and mature citrus explants used in this study displayed high levels of transient expression,which may provide a valuable tool for studying phloem-associated diseases such as Huanglongbing(HLB),facilitating rapid analysis of gene expression involved in Candidatus Liberibacter asiacticus(CLas)pathogenicity.This optimized method may also offer a promising tool for advancing genetic studies and improving the efficiency of Agrobacterium-mediated transgene-free editing in citrus and other economically significant perennial crops. 展开更多
关键词 Juvenile epicotyls Agrobacterium mediated transient gene expression Citrus evaluating gene expression Mature stem tissues Transient gene expression optimization transient gene expression investigating effects
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CpMYB114-like enhances CpNADP-ME2 expression to induce malate reduction and sugar accumulation during papaya ripening 认领 引用 被引量：2
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作者 Chenping Zhou Ruibin Kuang +5 位作者 Xiaming Wu Ze Xu Han He Chuanhe Liu Yuerong Wei Min Yang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第8期1810-1826,共17页
Sugars and organic acids form the core fundamental flavor foundation of ripe papaya fruit.Although R2R3-type v-myb myeloblastosis viral oncogene homolog transcription factors(R2R3-MYB TFs)have been reported to play im... Sugars and organic acids form the core fundamental flavor foundation of ripe papaya fruit.Although R2R3-type v-myb myeloblastosis viral oncogene homolog transcription factors(R2R3-MYB TFs)have been reported to play important roles in regulating the primary and secondary metabolism in fruits.However,the functions and underlying regulatory mechanisms of R2R3-MYB TFs in the metabolism of sugars and organic acids during papaya ripening remain unclear.In this study,through RNA sequencing(RNA-seq)coupled with quantitative real-time polymerase chain reaction(qRT-PCR)validation,a novel ethylene-responsive R2R3-MYB TF gene,CpMYB114-like(CpMYB114L),was identified.Transcriptome analysis and ethylene induction assays highlighted CpMYB114L as the key MYB gene activated during papaya ripening.Subcellular localization experiments confirmed that CpMYB114L was localized in the nucleus.Analyses of transgenic papaya fruits and calli,demonstrated that CpMYB114L promoted the accumulation of glucose,fructose,and sucrose,while simultaneously accelerating malate degradation.DNA Affinity Purification sequencing(DAP-seq)combined with yeast one-hybrid(Y1H)assays identified that CpMYB114L directly bound to the promoters of two sugar/organic acid metabolism-related genes,Isocitrate dehydrogenase 5(CpIDH5)and NADP-dependent malic enzyme 2(CpNADP-ME2).Electrophoretic mobility shift(EMSA),dual-luciferase reporter(Dual-LUC)and chromatin immunoprecipitation-quantitative PCR(ChIP-qPCR)assays further confirmed that CpMYB114L positively activated the expression of CpIDH5 and CpNADP-ME2 by directly binding to the specific regions of their promoters.Notably,transient overexpression of CpNADP-ME2 in papaya fruits and calli recapitulated decreased malate levels and increased sugar content,whereas CpIDH5 overexpression did not exhibit any functional relevance.This study elucidates a regulatory module,CpMYB114L-CpNADP-ME2,linking malate catabolism and sugar accumulation,offering valuable insights into flavor improvement strategies for papaya. 展开更多
关键词 Carica papaya Differentially expressed genes Ethylene Fruit quality Malic enzyme MYB transcription factor
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Effects of Acute Hypoxia and Reoxygenation on Hematological Parameters,Antioxidant Activity,and Hypoxia-Related Genes Expressions in Rainbow Trout and Steelhead 认领 引用
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作者 CHEN Xiaoqun ZHOU Yangen +5 位作者 JIA Kuntong FENG Zhanxian XU Tao GAO Qinfeng DONG Yunwei DONG Shuanglin 《Journal of Ocean University of China》 SCIE CAS CSCD 2026年第2期599-610,I0009-I0012,共12页
Global warming and water eutrophication are expanding oceanic anoxic zones and increasingly exposing offshore salmonid aquaculture to hypoxia during summer time.To evaluate the potential hypoxic tolerance difference b... Global warming and water eutrophication are expanding oceanic anoxic zones and increasingly exposing offshore salmonid aquaculture to hypoxia during summer time.To evaluate the potential hypoxic tolerance difference between landlocked rainbow trout(Oncorhynchus mykiss)and anadromous steelhead(O.mykiss)in physiological responses,hematological parameters,liver antioxidant activities,and gene expression were measured before stress,after 12 and 24 h of hypoxia,and after 24 h of reoxygenation.Serum alanine aminotransferase(ALT),alkaline phosphatase(ALP),and lactate dehydrogenase(LDH)activities initially increased significantly in both fishes,then declined during extended hypoxia and reoxygenation.Peak values occurred at 12 h in steelhead and 24 h in rainbow trout,indicating a superior metabolic adjustment in steelhead.In rainbow trout liver,hypoxia significantly elevated catalase(CAT)activity but reduced superoxide dismutase(SOD)activity and lipid peroxidation(LPO)content.Conversely,steelhead showed increased SOD activity and decreased CAT activity,malondialdehyde(MDA)and LPO contents.Total antioxidative capacity(T-AOC)was significantly higher in steelhead than in rainbow trout under hypoxic stress.The Integrated Biomarker Response Version 2(IBRv2)index was higher in rainbow trout,reflecting greater physiological stress.Both fishes exhibited significant upregulation of liver erythropoietin(epo)expression after 12 h of hypoxia,suggesting an adaptive enhancement of erythropoiesis.Overall,rainbow trout is more sensitive to hypoxia than steelhead. 展开更多
关键词 hypoxia gene expression rainbow trout reoxygenation steelhead oxidative stress
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Genome-wide characterization and expression analysis of the cultivated peanut AhPR10 gene family mediating resistance to Aspergillus flavus 认领 引用
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作者 Qi Zhao Mengjie Cui +11 位作者 Tengda Guo Lei Shi Feiyan Qi Ziqi Sun Pei Du Hua Liu Yu Zhang Zheng Zheng Bingyan Huang Wenzhao Dong Suoyi Han Xinyou Zhang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第1期56-67,共12页
The pathogenesis-related protein PR10 plays a vital role in plant growth,development,and stress responses.This study systematically identified and analyzed PR10 genes in cultivated peanut(Arachis hypogaea L.),examinin... The pathogenesis-related protein PR10 plays a vital role in plant growth,development,and stress responses.This study systematically identified and analyzed PR10 genes in cultivated peanut(Arachis hypogaea L.),examining their phylogenetic relationships,conserved motifs,gene structures,and syntenic relationships.The analysis identified 54 Ah PR10 genes,which were classified into eight groups based on phylogenetic relationships,supported by gene structure and conserved motif characterization.Analysis of chromosomal distribution and synteny demonstrated that segmental duplications played a crucial role in the expansion of the Ah PR10 gene family.The identified Ah PR10 genes exhibited both constitutive and inducible expression patterns.Significantly,Ah PR10-7,Ah PR10-33,and Ah PR10-41 demonstrated potential importance in peanut resistance to Aspergillus flavus.In vitro fungistatic experiments demonstrated that recombinant Ah PR10-33 effectively inhibited A.flavus mycelial growth.These findings provide valuable insights for future investigations into Ah PR10 functions in protecting peanut from A.flavus infection. 展开更多
关键词 cultivated peanut PR10 phylogenetic analysis expression pattern Aspergillus avus
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Low temperature mitigates mango quality deterioration by improving antioxidant ability and gene expression levels 认领 引用
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作者 Jinhe Li Yuanhui Gao +5 位作者 Xin Wang Shaobin Zeng Dexin Ma Yan Gong Yuanzhi Shao Wen Li 《Tropical Plants》 CSCD 2026年第1期139-148,共10页
Mango(Mangifera indica)is a tropical,climacteric fruit with unique flavor and rich nutrition,but its postharvest shelf life is limited due to softening,rotting,and cold damage susceptibility.Recent research indicates ... Mango(Mangifera indica)is a tropical,climacteric fruit with unique flavor and rich nutrition,but its postharvest shelf life is limited due to softening,rotting,and cold damage susceptibility.Recent research indicates that storage at 12℃ can preserve mango fruit well,but the underlying preservation mechanism remains poorly understood.In this study,postharvest quality changes and antioxidant mechanism of‘Tainong No.1'mango stored at 12 and 30℃ with 90%±5%RH for 24 d were explored.The results showed that,compared with storage at 30℃,storage at 12℃ significantly maintained fruit firmness,while reducing weight loss rate and malondialdehyde(MDA)content.Better cell morphology and delayed starch degradation were found at 12℃ through microscopic analysis.Moreover,the mango fruit stored at 12℃ showed significantly enhanced activities of antioxidant enzymes,including peroxidase(POD),superoxide dismutase(SOD),phenylalanine ammonia lyase(PAL),and ascorbate peroxidase(APX).Induced expressions of enzyme genes supported the corresponding enhanced enzyme activities.Furthermore,correlation analysis demonstrated that SOD,total phenols,and flavonoids might have a greater contribution to balancing the ROS homeostasis of postharvest mangoes.These findings suggest that storage at 12℃ might maintain mango quality and prolong the storage period by regulating fruit antioxidant capacity. 展开更多
关键词 storage temperature postharvest quality preservation mechanism firmness antioxidant mechanism antioxidant ability mango gene expression
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Gap-free,haplotype-resolved genome assembly reveals allele-specific expression and fruit color regulation in coconut 认领 引用
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作者 Min Chen Jing Li +6 位作者 Ziqi Ye Xiwei Sun Xiaomei Liu Hao Ding Lixia Zhou Xingtan Zhang Yaodong Yang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第1期217-220,共4页
Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin... Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce. 展开更多
关键词 allele specific expression Cocos nucifera haplotype resolved fruit color Asia Pacific region coconut phenotypic trai oil fruit crop
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Ectopic expression of structurally similar major royal jelly proteins reveals their distinct functions in Drosophila 认领 引用
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作者 Lingqi YU Danfeng WANG +7 位作者 Xuanhao CHEN Jiayu XIE Dongjing WEN Yi ZHANG Lirong SHEN Wenfeng CHEN Zhenxing LIU Yufeng YANG 《Journal of Zhejiang University-SCIENCE B》 SCIE CAS CSCD 2026年第3期295-309,共15页
Royal jelly(RJ),secreted by the hypopharyngeal and mandibular glands of young worker bees,is rich in proteins,80%-90%of which are major royal jelly proteins(MRJPs).While MRJPs from RJ have been shown to exhibit specif... Royal jelly(RJ),secreted by the hypopharyngeal and mandibular glands of young worker bees,is rich in proteins,80%-90%of which are major royal jelly proteins(MRJPs).While MRJPs from RJ have been shown to exhibit specific biological functions and are also expressed in neuronal cells,their roles in vivo remain poorly understood.The aim of this study was to elucidate the functional roles of individual MRJPs(MRJP1-9)in vivo by ectopically expressing them in Drosophila neurons in a binary expression system using fluorescent proteins as controls.Transcriptome sequencing revealed that although MRJP1-9 share similar tertiary structures,their overexpression affects distinct gene sets.MRJP1,MRJP2,MRJP3,MRJP5,and MRJP7 induced more differentially expressed genes(DEGs),while MRJP4,MRJP6,MRJP8,and MRJP9 induced fewer such genes.Weighted gene co-expression network analysis(WGCNA)and gene set enrichment analysis(GSEA)revealed that MRJP1,MRJP2,MRJP3,MRJP5,and MRJP7 regulated overlapping gene sets,including an estradiol-responsive set,and activated cell proliferation pathways.MRJP6 lacked any significant gene set enrichment,while MRJP8 and MRJP9 modulated similar sets.Notably,the neuron-specific overexpression of MRJP1,MRJP2,MRJP3,and MRJP5 in Drosophila showed activated cell proliferation-related pathways and increased body sizes,highlighting their functional diversity and context-dependent effects.These findings expand our understanding of the functional roles of MRJPs and provide a foundation for further exploring their biological significance in honeybees and beyond. 展开更多
关键词 Drosophila melanogaster Major royal jelly protein(MRJP) Ectopic expression
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SQSNet: Hybrid CNN-Transformer Fusion with Spatial Quad-Similarity for Robust Facial Expression Recognition 认领 引用
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作者 Mohammed AAhmed Jian Dong +3 位作者 Ronghua Shi Ammar Nassr Hani Almaqtari Ala AAlsanabani 《Computers, Materials & Continua》 SCIE EI 2026年第6期1781-1800,共20页
Facial Expression Recognition(FER)is an essential endeavor in computer vision,applicable in human-computer interaction,emotion assessment,and mental health surveillance.Although Convolutional Neural Networks(CNNs)have... Facial Expression Recognition(FER)is an essential endeavor in computer vision,applicable in human-computer interaction,emotion assessment,and mental health surveillance.Although Convolutional Neural Networks(CNNs)have proven effective in Facial Emotion Recognition,they encounter difficulties in capturing long-range connections and global context.To address these constraints,we propose Spatial Quad-Similarity Network(SQSNet),an innovative hybrid framework that integrates the local feature extraction capabilities of CNNs with the global contextual modeling efficacy of Swin Transformers via a cohesive fusion technique.SQSNet introduces the Spatial Quad-Similarity(SQS)module,a feature refinement approach that amplifies discriminative characteristics and mitigates redundancy.Unlike conventional metric learning approaches that operate on global feature representations,SQS computes fine-grained spatial-level similarity across multiple instances,enforcing H×W independent constraints that preserve spatial correspondence between expression-relevant facial regions.This spatial-level formulation is particularly effective for FER,where expressions manifest as localized muscle movements that are lost in global pooling operations.Moreover,SQSNet employs sophisticated regularization methods,including Mixup augmentation,label smoothing,and adaptive learning rate scheduling,to enhance generalization.Experimental findings on three benchmark datasets,RAF-DB,FERPlus,and AffectNet,indicate that SQSNet surpasses current FER methodologies,attaining state-of-the-art accuracies of 91.90%,91.11%,and 67.15%,respectively.These findings underscore the efficacy of integrating CNNs,Swin Transformers,and spatial similarity-driven feature refining for facial emotion identification,facilitating the development of more dependable emotion recognition systems. 展开更多
关键词 Facial expression recognition convolutional neural networks swin transformers cross attention adaptive learning
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