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Impact of machine learning-driven analysis of blood transcriptomes in multiple sclerosis 认领 引用
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作者 Alessandro Digilio Cinthia Farina 《Neural Regeneration Research》 SCIE CAS CSCD 2026年第8期3557-3558,共2页
Multiple sclerosis(MS)is a chronic disorder of the central nervous system characterized by multifocal lesions where inflammation,demyelination,and neurodegeneration occur(Jakimovski et al.,2024).MS diagnosis primarily... Multiple sclerosis(MS)is a chronic disorder of the central nervous system characterized by multifocal lesions where inflammation,demyelination,and neurodegeneration occur(Jakimovski et al.,2024).MS diagnosis primarily relies on the demonstration of dissemination in time and space of the lesions based on clinical,magnetic resonance imaging(MRI),and cerebrospinal fluid assessments(Jakimovski et al.,2024). 展开更多
关键词 multifocal lesions inflammation cerebrospinal fluid assessments jakimovski blood transcriptomes diagnosis multiple sclerosis ms multiple sclerosis resonance imaging mri
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Comparative transcriptomes reveal the disjunction adaptive strategy of Thuja species in East Asia and North America 认领 引用 被引量：2
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作者 Ermei Chang Xue Liu +3 位作者 Jiahui Chen Jingyi Sun Shaowei Yang Jianfeng Liu 《Journal of Forestry Research》 SCIE CAS CSCD 2023年第6期1963-1974,共12页
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
关键词 Thuja species Comparative transcriptomes East Asia-North America disjunction Specific gene Positively selected gene
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Comparison of transcriptomes undergoing waterlogging at the seedling stage between tolerant and sensitive varieties of Brassica napus L. 认领 引用 被引量：9
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作者 ZOU Xi-ling ZENG Liu +3 位作者 LU Guang-yuan CHENG Yong XU Jin-song ZHANG Xue-kun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2015年第9期1723-1734,共12页
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
关键词 rapeseed(Brassica napus L.) waterlogging digital gene expression(DGE) roots transcriptome comparative analysis
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Transcriptomes of early developing tassels under drought stress reveal differential expression of genes related to drought tolerance in maize 认领 引用 被引量：5
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作者 WANG Nan LI Liang +7 位作者 GAO Wen-wei WU Yong-bo YONG Hong-jun WENG Jian-feng LI Ming-shun ZHANG De-gui HAO Zhuan-fang LI Xin-hai 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2018年第6期1276-1288,共13页
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
关键词 Zea mays L. early developing tassel transcriptome drought tolerance
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Comparative analysis of transcriptomes from albino and control sea cucumbers, Apostichopus japonicus 认领 引用 被引量：3
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作者 MA Deyou YANG Hongsheng +1 位作者 SUN Lina XU Dongxue 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2014年第8期55-61,共7页
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
关键词 454 cDNA sequencing albinism Apostichopus japonicus transcriptome
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A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis 认领 引用 被引量：1
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作者 Zuozhou Chen Hua Ye +2 位作者 Longhai Zhou Chi-Hing C. Cheng Liangbiao Chen 《Journal of Genetics and Genomics》 SCIE CAS 2010年第3期205-218,共14页
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
关键词 transcriptome comparison EST protein family reference gene set
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Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens 认领 引用 被引量：7
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作者 Ying Zhang Woyu Su +3 位作者 Bo Zhang Yao Ling Woo Kyun Kim Hao Zhang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2021年第4期1309-1322,共14页
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
关键词 ceRNA Hypoxic adaptation Non-coding RNA Tibetan chicken Transcriptome
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Generation and classification of transcriptomes in two Croomia species and molecular evolution of CYC/TB1 genes in Stemonaceae 认领 引用
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作者 Ruisen Lu Wuqin Xu +5 位作者 Qixiang Lu Pan Li Jocelyn Losh Faiza Hina Enxiang Li Yingxiong Qiu 《Plant Diversity》 SCIE CAS CSCD 2018年第6期253-264,共12页
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
关键词 Croomia Transcriptome SCNGs EST-SSRs Flower symmetry CYC/TB1
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Transcriptomes of Litopenaeus vannamei reveal modulation of antioxidant system induced by dietary archaeal carotenoids 认领 引用
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作者 Wei XIE Guoru DU +5 位作者 Honggang DENG Yingchao MA Meirong GAO Hu DUAN Sung YIK YEONG Liying SUI 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2023年第5期2010-2019,共10页
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
关键词 archaeal carotenoid Litopenaeus vannamei transcriptome antioxidative mechanism
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Tandem repetitions in transcriptomes of some Solanaceae species 认领 引用
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作者 Atul Grover Prakash C. Sharma 《American Journal of Molecular Biology》 CAS 2012年第2期140-152,共13页
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
关键词 ESTs Solanaceae Tandem Repeats Transcriptome TRF
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Assembly and Analysis of Changes in Transcriptomes of Dairy Cattle Rumen Epithelia during Lactation and Dry Periods 认领 引用
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作者 Cong-Jun Li Robert W. Li Ransom L. Baldwin VI 《Agricultural Sciences》 2018年第5期619-638,共20页
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
关键词 Dairy Cattle Lactation RNA-Sequencing Transcriptome Rumen Epithelium Gene Expression
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Differential Evolution of CDS and UTR Non-canonical RNA G-quadruplex Structures in Eukaryotic Transcriptomes 认领 引用
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作者 Eugene Yui-Ching Chow Jieyu Zhao +1 位作者 Chun Kit Kwok Ting-Fung Chani 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2025年第6期263-281,共19页
RNA G-quadruplexes(rG4s)are non-classical,four-stranded secondary RNA structures that play regulatory roles in various biological processes.Although canonical rG4s have been studied extensively,recent advancements hav... RNA G-quadruplexes(rG4s)are non-classical,four-stranded secondary RNA structures that play regulatory roles in various biological processes.Although canonical rG4s have been studied extensively,recent advancements have underscored the importance of non-canonical rG4s.In this study,we experimentally determined rG4 structures from multiple eukaryotic species.Bioinformatic analysis revealed that across 1 billion years of evolution,rG4s have comprised an integral feature of eukaryotic transcriptomes;additionally,non-canonical rG4s consistently were found to dominate the surveyed rG4omes.Over time,the overall size of the rG4ome has expanded progressively,accompanied by a notable compositional shift such that untranslated region(UTR)rG4s became favored over protein coding sequence(CDS)rG4s.Additionally,we observed distinct evolutionary patterns for CDS and UTR rG4s,which involved differential evolutionary origins and canonicality drift patterns.Our findings suggest that new UTR rG4 sequences emerge rapidly during early mammalian evolution,whereas the more gradual increase in CDS rG4s is linked to changes in selective amino acid residue preferences.This plausible theory accounts for both the prevalence of UTR rG4s and the emergence of canonical motifs in mammalian models.Access to all the rG4 structures identified in this study is available through the rG4-seq Database application at https:/g4s.science/. 展开更多
关键词 RNA G-quadruplex RNA structure Evolutionary and computational biology Transcriptomics Comparative genomics
Transposon insertion in pmel17 rewired skin and muscle transcriptomes in Mozambique tilapia 认领 引用 被引量：1
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作者 Fei Sun Le Wang Gen Hua Yue 《Aquaculture and Fisheries》 CAS CSCD 2025年第3期382-391,共10页
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
关键词 Tilapia pmel17 Transcriptome Regulation Melanin Growth
Meta-transcriptomes of the microbial communities of the different developmental life stages of Anastrepha ludens(Diptera:Tephritidae) 认领 引用 被引量：1
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作者 Erin L.Schuenzel 《Insect Science》 SCIE CAS CSCD 2025年第5期1641-1649,共9页
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
关键词 bacteria mass-rearing microsporidium Sterile Insect Technique Tephritids transcriptomics
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Combined volatile metabolome and transcriptome analysis of 60 peach cultivars provide new insights into the formation of aroma and the identification of associated genes 认领 引用 被引量：3
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作者 Wenyi Duan Zhenyu Yao +7 位作者 Chengkui Qiao Junren Meng Shihang Sun Lei Pan Liang Niu Guochao Cui Zhiqiang Wang Wenfang Zeng 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第5期1025-1038,共14页
Volatile organic compounds(VOCs)are the main chemical compounds that determine the characteristic aroma and flavor of fruit.In this study,we identified a total of 97 VOCs,including 5C6 compounds,12 aldehydes,4 alcohol... Volatile organic compounds(VOCs)are the main chemical compounds that determine the characteristic aroma and flavor of fruit.In this study,we identified a total of 97 VOCs,including 5C6 compounds,12 aldehydes,4 alcohols,10 esters,13 lactones,18 terpenes,8 norisoprenoids,8 ketones,3 hydrocarbons,8 phenylalanine derivates,and 8 other compounds,in 60 peach cultivars using headspace solid-phase microextraction(HS-SPME)combined with gas chromatography-mass spectrophotometry(GC-MS).A wide range of VOCs were detected in these germplasm resources with respect to both quantity and concentration.Correlation analysis with different physiological traits demonstrated that the genetic background exerts a significant influence on the composition and content of VOCs among peach cultivars.For example,the content of norisoprenoid was significantly lower in yellow-fleshed peach than in white-fleshed peach,and lactones were almost undetectable in stony hard peach.Among the 97 VOCs,26 exhibited odor activity values(OAVs)exceeding 1,suggesting that these compounds act as key odorants in the peach VOC composition.Moreover,six structural genes associated with the synthesis of γ-decalactone and(Z)-3-hexenyl acetate and five genes linked to aldehyde and 1-octen-3-one biosynthesis were identified through weighted gene co-expression network analysis(WGCNA).Additionally,15 transcription factors(TFs)were identified as potentially regulating VOC synthesis.Overall,these data provide insight into the factors contributing to the differences in aroma qualities among peach cultivars,which can help to promote the development of peach breeding. 展开更多
关键词 Volatile aroma compounds Peach cultivars OAVs Transcriptome
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Transcriptomic profiling of the floral fragrance biosynthesis of Iris germanica'Harvest of Memories'and functional characterization of the IgTPS14 gene 认领 引用 被引量：3
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作者 Qian Zhao Yuqing Li +3 位作者 Lina Gu Di He Jianrang Luo Yanlong Zhang 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第5期1165-1184,共20页
Iris(Iris germanica)is a very popular ornamental plant and is known for the precious spice irone produced from its roots.Many iris varieties can also release fragrances through their flowers.However,the composition of... Iris(Iris germanica)is a very popular ornamental plant and is known for the precious spice irone produced from its roots.Many iris varieties can also release fragrances through their flowers.However,the composition of iris aroma and the molecular mechanism of its synthesis have not been reported.In this study,we analyzed the volatile floral compounds of I.germanica‘Harvest of Memories'at different stages and in different tissues through headspace solid-phase microextraction gas chromatography-mass spectrometry.A total of 36 volatile compounds were identified,and linalool was the dominant component.Transcriptome analysis showed that 35 differentially expressed genes and 218differentially expressed transcription factors were positively correlated with linalool release.According to the results of q RT-PCR,the expression level of the Ig TPS14 gene was consistent with the release trend of linalool,suggesting that Ig TPS14 may play a certain role in linalool synthesis.Phylogenetic analysis showed that the Ig TPS14 protein belonged to the TPS-g subfamily.An in vitro enzymatic assay of Ig TPS14 and its transient and stable overexpression in tobacco indicated that this gene produced linalool.The transient silencing of Ig TPS14 in petals by virus-induced gene silencing technology revealed a significant reduction in the release of linalool.These results will help explore and reveal the molecular mechanism of monoterpenoid synthesis and provide a certain reference for studying the formation of iris aroma. 展开更多
关键词 Iris germanica Floral fragrance Transcriptome Volatiles Linalool
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Neuroserpin alleviates cerebral ischemia-reperfusion injury by suppressing ischemia-induced endoplasmic reticulum stress 认领 引用 被引量：3
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作者 Yumei Liao Qinghua Zhang +15 位作者 Qiaoyun Shi Peng Liu Peiyun Zhong Lingling Guo Zijian Huang Yinghui Peng Wei Liu Shiqing Zhang István Adorján Yumi Fukuzaki Eri Kawashita Xiao-Qi Zhang Nan Ma Xiaoshen Zhang Zoltán Molnár Lei Shi 《Neural Regeneration Research》 SCIE CAS CSCD 2026年第1期333-345,共13页
Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a na... Neuroserpin,a secreted protein that belongs to the serpin superfamily of serine protease inhibitors,is highly expressed in the central nervous system and plays multiple roles in brain development and pathology.As a natural inhibitor of recombinant tissue plasminogen activator,neuroserpin inhibits the increased activity of tissue plasminogen activator in ischemic conditions and extends the therapeutic windows of tissue plasminogen activator for brain ischemia.However,the neuroprotective mechanism of neuroserpin against ischemic stroke remains unclear.In this study,we used a mouse model of middle cerebral artery occlusion and oxygen-glucose deprivationeperfusion-injured cortical neurons as in vivo and in vitro ischemia-reperfusion models,respectively.The models were used to investigate the neuroprotective effects of neuroserpin.Our findings revealed that endoplasmic reticulum stress was promptly triggered following ischemia,initially manifesting as the acute activation of endoplasmic reticulum stress transmembrane sensors and the suppression of protein synthesis,which was followed by a later apoptotic response.Notably,ischemic stroke markedly downregulated the expression of neuroserpin in cortical neurons.Exogenous neuroserpin reversed the activation of multiple endoplasmic reticulum stress signaling molecules,the reduction in protein synthesis,and the upregulation of apoptotic transcription factors.This led to a reduction in neuronal death induced by oxygen/glucose deprivation and reperfusion,as well as decreased cerebral infarction and neurological dysfunction in mice with middle cerebral artery occlusion.However,the neuroprotective effects of neuroserpin were markedly inhibited by endoplasmic reticulum stress activators thapsigargin and tunicamycin.Our findings demonstrate that neuroserpin exerts neuroprotective effects on ischemic stroke by suppressing endoplasmic reticulum stress. 展开更多
关键词 endoplasmic reticulum stress ischemia-reperfusion injury neuron neuronal apoptosis neuroprotection neuroserpin protein synthesis secretory protein stroke transcriptomic analysis
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Transcriptional and epigenetic changes associated with lead exposure in spermatozoa 认领 引用
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作者 Xu Zhang Xiao-Rong Shen +3 位作者 Bin Wu Xue-Mei Wang Hui-Juan Shi Tian-Cheng Zhang 《Asian Journal of Andrology》 SCIE CAS CSCD 2026年第3期297-303,共7页
Lead(Pb)exposure is a risk factor of male infertility,while the transcriptional and epigenetic changes associated with lead exposure in spermatozoa are poorly understood.Our previous findings revealed significant chan... Lead(Pb)exposure is a risk factor of male infertility,while the transcriptional and epigenetic changes associated with lead exposure in spermatozoa are poorly understood.Our previous findings revealed significant changes in DNA methylation of the calcium(Ca)homeostasis pathway of human spermatozoa in men with a blood Pb level over 5µg dl−1,which was associated with decreased sperm motility.In this study,we explored the effects of Pb exposure on expression of differentially methylated genes(DMGs)by analyzing semen samples from six healthy,non-smoking,and non-drinking men(aged 20–40 years).Using methylated DNA immunoprecipitation sequencing(MeDIP-seq)and RNA sequencing(RNA-seq),we compared DNA methylation and RNA abundance patterns between two groups:three men with blood Pb level 0–2.5µg dl−1 and three men with blood Pb level 5–10µg dl−1.Additionally,we experimentally validated the regulatory function of the differentially methylated regions associated with 11 hub genes using dual-luciferase reporter assays.We revealed differences in promoter activity between methylated and unmethylated promoter regions of seven cloned genes,namely calcium voltage-gated channel subunit alpha1 H(CACNA1H),calcium voltage-gated channel subunit alpha1 G(CACNA1G),calcium voltage-gated channel subunit alpha1 I(CACNA1I),calcium/calmodulin dependent protein kinase II gamma(CAMK2G),ATPase sarcoplasmic/endoplasmic reticulum Ca²+transporting 3(ATP2A3),solute carrier family 8 member A2(SLC8A2),and glutamate ionotropic receptor NMDA type subunit 2D(GRIN2D).Our results of Pb exposure-induced expression changes of essential genes associated with the calcium signaling pathway,particularly CACNA1H,SLC8A2,and GRIN2D,in spermatozoa,may be a potential cause of low sperm quality. 展开更多
关键词 calcium homeostasis pathway DNA methylomes lead exposure sperm motility transcriptomes
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Histological,transcriptomic,and gene functional analyses of bulbil initiation and development of Lilium lancifolium 认领 引用 被引量：1
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作者 Xuemin Zhang Jiahui Liang +7 位作者 Mingfang Zhang Wenqiang Pan Mengdi Wang Zhiyi Yue Zhixuan Zhang Jian Wu Xiuhai Zhang Yunpeng Du 《Horticultural Plant Journal》 SCIE CAS CSCD 2026年第6期1433-1449,共17页
The bulbil,originating in the leaf axil of Lilium lancifolium,functions as a vital reproductive organ for bulbous propagation.The mechanism of bulbil formation,however,is still unclear.In this study,we conducted histo... The bulbil,originating in the leaf axil of Lilium lancifolium,functions as a vital reproductive organ for bulbous propagation.The mechanism of bulbil formation,however,is still unclear.In this study,we conducted histological,transcriptomic,and gene function analyses on leaf axil samples throughout bulbil formation.Histological analysis revealed that the bulbils arose from the axillary meristem and bulbil formation undergoes a two-step process:initiation and development.During the bulbil initiation stage,RNA-seq analysis revealed that the differentially expressed genes(DEGs) were primarily enriched in phytohormone-related pathways,especially auxin.Through virus-induced gene silencing(VIGS),the individual silencing phenotypes of nine genes derived from four hormones imply that decreased auxin and ethylene signaling,paired with increased cytokinin and gibberellin,may contribute to bulbil initiation.Among the numerous differentially expressed transcription factors,LIMYB119 may play a role as a candidate gene in auxin-regulated bulbil initiation,as confirmed by quantitative real-time PCR(qRT-PCR)and VIGS.During bulbil development,DEGs showed significant enrichment in carbohydrate metabolism,as well as phytohormone signal transduction.Silencing seven specific genes involved in auxin and ethylene signaling,cytokinin and gibberellin biosynthesis,as well as carbohydrate metabolism,resulted in inhibition of axillary organ development.In summary,this study offers a rich pool of candidate genes,enhancing our understanding of the regulatory mechanism underlying bulbil initiation and development,and holding significant commercial potential for the advancement of new reproductive organs in L.lancifolium. 展开更多
关键词 Lilium lancifolium Bulbil formation Histological Transcriptome analysis Hormone
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Candidate gene analysis of cabbage head-splitting resistance based on QTL mapping and omics profiling 认领 引用 被引量：1
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作者 Xiaowei Zhu Min Wang +4 位作者 Xiang Tai Panling Lu Hang Gui Jinxiu Chen Tianyue Bo 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第2期709-720,共12页
Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses.However,the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplor... Head-splitting is a prevalent physiological disorder in cabbage that causes substantial economic losses.However,the genetic factors and molecular mechanisms underlying head-splitting resistance remain largely unexplored.This study identified a genomic region(q NLQ3.1) for head-splitting resistance on chromosome C03 through the combination of QTLseq and GPS analysis in an F2 population derived from hybridizing two cabbage inbred lines,‘Dazhengfu'(ZF,susceptible) and ‘103'(resistant).Traditional genetic linkage analysis narrowed q NLQ3.1 to a 74.6 kb region.Furthermore,comparative analysis of the two parental lines using transcriptomic and metabolic profiling demonstrated the crucial role of hormones in regulating head-splitting resistance.Bol028000,encoding a homologue of Arabidopsis Cytokinin Response Factor 3(CRF3),emerged as a promising candidate for head-splitting resistance and was subsequently validated through Sanger sequencing and quantitative RT-PCR(qRT-PCR).Subcellular localisation analysis revealed that Bol028000 was mainly expressed in the nucleus.Additionally,one kompetitive allele-specific PCR(KASP) marker from Bol028000 was developed and utilized to screen 42 inbred lines.These findings enhance the theoretical understanding of head-splitting resistance and provide valuable insights for the molecular breeding of head-splitting resistant cabbages. 展开更多
关键词 cabbage head-splitting resistance QTL transcriptomic and metabolic profiling
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