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Long-read transcriptome sequencing for the in-depth understanding of anthocyanin biosynthesis in Jaboticaba 认领 引用
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作者 Shu-Chen Fan Xuan-Yu Yang +3 位作者 Lu-Yao Chen Cai-Ning Liu Wenping Xu Dan-Dan Liu 《Tropical Plants》 CSCD 2025年第1期155-166,共12页
Jaboticaba(Myrciaria cauliflora)is a grape-shaped fruit characterized by high concentrations of anthocyanins concentrated within its peel,representing a valuable natural source of functional pigments.Here,we report lo... Jaboticaba(Myrciaria cauliflora)is a grape-shaped fruit characterized by high concentrations of anthocyanins concentrated within its peel,representing a valuable natural source of functional pigments.Here,we report long-read transcriptome sequencing in Jaboticaba,and 86,758 unigene sequences,9,732 expressed sequence tag-simple sequence repeats,and 1,127 long non-coding RNA sequences were uncovered.In addition,integrated transcriptomic and metabolomic analysis of pigment accumulation during fruit ripening showed that six anthocyanins accumulated in Jaboticaba fruit,with 47 flavonoid synthesis-related genes,and 12 differentially expressed genes.Compared with green fruits,these candidate genes encoded eight upregulated enzymes particularly expressed in ripening fruits—4CL,PAL,F3H,F3'H,DFR,ANS,LAR,and UFGT—and related to the regulation of phenylpropanoid,flavonoid,and anthocyanin biosynthetic pathways.Furthermore,two R2R3-MYB transcription factors McMYB4-1 and McMYB4-2 might negatively regulate anthocyanin accumulation.The results reveal key regulatory mechanisms governing flavonoid and anthocyanin biosynthetic pathways,thereby offering critical perspectives on plant secondary metabolite production in Jaboticaba. 展开更多
关键词 fruit ripening transcriptomic metabolomic analysis flavonoid synthesis anthocyanin biosynthesis Myrciaria cauliflora jaboticaba long read transcriptome sequencing transcription factors
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Transcriptome sequencing reveals gene expression patterns in non-symbiotic tissues of the cold seep clam Phreagena okutanii 认领 引用
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作者 Yinjun Ye Genmei Lin +3 位作者 Huixin Zhao Xuanguang Liang Junrou Huang Jianguo Lu 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2025年第10期171-183,共13页
Deep-sea cold seeps form a benthic hypoxic biome characterized by low temperatures,methane venting,and metalliferous fluid emissions.This extreme environment was dominated by high-biomass species such as clams.While m... Deep-sea cold seeps form a benthic hypoxic biome characterized by low temperatures,methane venting,and metalliferous fluid emissions.This extreme environment was dominated by high-biomass species such as clams.While most studies have focused on the symbiotic function of cold seep clams,research on the roles of their non-symbiotic functions remains limited.In this study,we conducted transcriptome analysis to examine gene expression pattern in the testis,adductor muscle(hereinafter“muscle”),and foot of Phreagena okutanii,a clam species collected from the S11 site on the western slope of the Okinawa Trough.Principal component analysis and differential expression analysis revealed that the gene expression patterns of the muscle and foot tissues were shared more similar gene expression patterns with each other than with the testis.A total of 564 co-expressed genes with transcripts per million(TPM)>10 were identified as co-expressed genes in the testis,muscle,and foot.The gene expression patterns of hemoglobin Ⅰ and Ⅱ(hb1,hb2),heat shock proteins 70 and 90(hsp70,hsp90),glutathione peroxidase(GPx),thioredoxin-2(Trx2),and ferritin(fer)for oxygen transportation,stress response and antioxidation were identified in the three tissues.In particular,4853 and 6194 differentially expressed genes(DEGs)were identified in the testis compared to the muscle and foot,respectively,significantly exceeding the 854 DEGs observed between the muscle and foot.Furthermore,DEG intersection enabled the identification of shared tissue-specific expression patterns,including genes that were upregulated in the testis relative to both the muscle and foot;those upregulated in the muscle relative to both the testis and foot,and those upregulated in the foot relative to both the testis and muscle.Antioxidant genes inhibited the production of reactive oxygen species and catalyzed their removal.The immune response gene played a key role in pathogen recognition and elimination.Energy metabolism genes enhanced energy production and accumulation,supporting adaptation to the high-sulfur and low-oxygen environments.Our study provides further insights into the gene expression pattern of bivalves in specialized deep-sea cold seep environments. 展开更多
关键词 cold seep clam Phreagena okutanii transcriptome sequencing
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Full-length transcriptome sequencing provides insights into chlorogenic acid biosynthesis in Lonicera japonica 认领 引用
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作者 Peng Zhang Tongyao Duan +5 位作者 Qidong Li Luyao Huang Zhenhua Liu Jia Li Zhilong Bao Fangfang Ma 《Ornamental Plant Research》 2025年第1期133-143,共11页
Lonicera japonica Thunb.is a significant medicinal resource within traditional Chinese medicine,exhibiting a variety of pharmacological properties.Previous studies reported that the major bioactive compound in L.japon... Lonicera japonica Thunb.is a significant medicinal resource within traditional Chinese medicine,exhibiting a variety of pharmacological properties.Previous studies reported that the major bioactive compound in L.japonica was chlorogenic acid(CGA),while the mechanism of CGA biosynthesis remained unknown due to the limited genome information.In the present study,PacBio single molecule real-time(SMRT)sequencing technology was employed to conduct the inaugural full-length transcriptome sequencing of the honeysuckle cultivar'Huajin 6'.A total of 97,588 high-quality transcripts,with an average length of 2,883 base pairs,were generated and annotated using the NR,GO,KOG,and KEGG databases.The coding sequences(CDS),transcription factors,simple sequence repeats(SSR),and long non-coding RNA(lncRNA)transcripts were predicted.The key genes encoding hydroxycinnamoyl-CoA quinate transferase(HQT)in CGA biosynthesis were isolated through the combination analysis of transcriptomic data and CGA content in flowers at different development stages.MYB genes that potentially regulated the transcription of HQT were further identified.Taken together,these results provide valuable genetic resources to assist the molecular study of L.japonica genes,which will facilitate the quality improvement of L.japonica cultivars. 展开更多
关键词 full length transcriptome sequencing Pacbio SMRT sequencing chlorogenic acid biosynthesis chlorogenic acid cga Huajin lonicera japonica bioactive compound hydroxycinnamoyl CoA quinate transferase
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Construction of a standardized analysis method for identifying meat quality-related genes in Ordos fine-wool sheep based on transcriptome sequencing data 认领 引用
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作者 Bilige Li Xiawei +4 位作者 Aoqier Liu Yang Jia Xiangchun Yao Duo Niu Lin 《China Standardization》 2025年第2期60-64,共5页
In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to in... In this paper,a standardized analysis method is established for identifying meat quality-related genes in Ordos finewool sheep using transcriptome sequencing data.A meticulously standardized approach is utilized to investigate the genetic determinants of meat quality in Ordos fine-wool sheep through transcriptome sequencing analysis.Muscle samples from the longissimus dorsi of one-year-old sheep are collected under controlled conditions,and key texture properties—hardness,elasticity,and chewiness—are measured to categorize samples into high-and low-textural-value groups.Genes significantly associated with meat quality traits are identified through standardized RNA extraction,high-throughput sequencing,and differential gene expression analysis.Functional enrichment analysis reveals their involvement in biological processes such as extracellular matrix organization and metabolic pathways.The findings underscore the pivotal role of standardization in meat quality research,laying a solid scientific foundation for future research on meat quality improvement and molecular breeding. 展开更多
关键词 Ordos fine-wool sheep meat quality characteristics transcriptome sequencing genes functional enrichment analysis
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Long-distance control of the scion by the rootstock under drought stress as revealed by transcriptome sequencing and mobile mRNA identification 认领 引用 被引量：9
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作者 Marzieh Davoudi Mengfei Song +2 位作者 Mengru Zhang Jinfeng Chen Qunfeng Lou 《Horticulture Research》 SCIE CSCD 2022年第1期402-421,共20页
Grafting with pumpkin rootstock is commonly used not only to improve the quality of cucumber fruits but also to confer biotic or abiotic stress tolerance.However,the molecular mechanism of the response of grafted cucu... Grafting with pumpkin rootstock is commonly used not only to improve the quality of cucumber fruits but also to confer biotic or abiotic stress tolerance.However,the molecular mechanism of the response of grafted cucumbers to drought stress and the possible roles of mobile mRNAs in improving stress tolerance have remained obscure.Hence,we conducted transcriptome sequencing and combined it with morphophysiological experiments to compare the response of homografts(cucumber as scion and rootstock)and heterografts(cucumber as scion and pumpkin as rootstock)to drought stress.After applying drought stress,homografts and heterografts expressed 2960 and 3088 genes,respectively,in response to the stress.The differentially expressed genes identified in heterografts under drought stress were categorized into different stress-responsive groups,such as carbohydrate metabolism(involved in osmotic adjustment by sugar accumulation),lipid and cell wall metabolism(involved in cell membrane integrity by a reduction in lipid peroxidation),redox homeostasis(increased antioxidant enzyme activities),phytohormone(increased abscisic acid content),protein kinases,and transcription factors,using MapMan software.Earlier and greater H2O2 accumulation in xylem below the graft union was accompanied by leaf abscisic acid accumulation in heterografts in response to drought stress.Greater leaf abscisic acid helped heterografted cucumbers to sense and respond to drought stress earlier than homografts.The timely response of heterografts to drought stress led to the maintenance of higher water content in the leaves even in the late stage of drought stress.The mobile mRNAs identified in heterografts were mostly related to photosynthesis,which would be the possible reason for improved chlorophyll content and maximum photochemical efficiency of photosystem II(Fv/Fm).The existence of some stressresponsive pumpkin(rootstock)mRNAs in cucumber(scion),such as heat shock protein(HSP70,a well-known stress-responsive gene),led to higher proline accumulation than in homografts.Expression of mobile and immobile stress-responsive mRNAs and timely response of heterografts to drought stress could improve drought tolerance in pumpkin-rooted plants. 展开更多
关键词 confer biotic abiotic stress tolerancehoweverthe improving stress tolerance molecular mechanism drought stress transcriptome sequencing grafted cucumbers long distance control morphophysiological experiments
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Use of transcriptome sequencing to explore the effect of CSRP3 on chicken myoblasts 认领 引用 被引量：4
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作者 SHAN Yan-ju JI Gai-ge +5 位作者 ZHANG Ming LIU Yi-fan TU Yun-jie JU Xiao-jun SHU Jing-ting ZOU Jian-min 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2023年第4期1159-1171,共13页
The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure a... The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E. 展开更多
关键词 CSRP3 chicken myofiber type transcriptome sequencing
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Transcriptome sequencing-based study on the mechanism of action of Jintiange capsules(金天格胶囊)in regulating synovial mesenchymal stem cells exosomal miRNA and articular chondrocytes mRNA for the treatment of osteoarthritis 认领 引用 被引量：4
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作者 CHEN Zhongying ZHANG Xue +3 位作者 ZHANG Xiaofei ZOU Junbo YUAN Puwei SHI Yajun 《Journal of Traditional Chinese Medicine》 SCIE CSCD 2024年第6期1153-1167,共15页
OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exo... OBJECTIVE: To corroborate the efficacy of Jintiange capsules(JTGs)( 金天格胶囊) in the treatment of osteoarthritis(OA) by exploring the potential mechanism of action of synovial mesenchymal stem cell exosomes(SMSC-Exos) and articular chondrocytes(ACs) through transcriptome sequencing(RNA-seq). METHODS: Type Ⅱ collagenase was used to induce OA in rats. The efficacy of JTGs was confirmed by macroscopic observation of articular cartilage, micro-CT observation, and safranin fast green staining. After SMSC-Exos and ACs were qualified, RNA-seq was used to screen differentially expressed mi RNAs and m RNAs. The target genes of differentially expressed mi RNAs in Synovial mesenchymal stem cells(SMSCs) were predicted based on the multi Mi R R package. The codifferentially expressed genes of SMSC-Exos and ACs were obtained by venny 2.1.0. The mi RNA-m RNA regulatory network was constructed by Cytoscape software. Based on the Omic Share platform, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis was performed on the m RNA regulated by key mi RNAs. Expression trend analysis was performed for co-differentially expressed genes. Correlation analysis was performed on micro-CT efficacy indicators, co-differentially expressed genes mRNA and miRNA. RESULTS: The efficacy of each administration group of JTGs was significant compared with the model group. SMSC-Exos and ACs were identified by their characteristics. The expression of rno-mi R-23a-3p, rnomi R-342-3p, rno-miR-146b-5p, rno-miR-501-3p, rnomiR-214-3p was down-regulated in OA pathological state, and the expression of rno-mi R-222-3p, rno-mi R-30e-3p, rno-mi R-676, and rno-miR-192-5p expression was upregulated, and the expression of all these mi RNAs was reversed after the intervention with JTGs containing serum. The co-differentially expressed genes were enriched in the interleukin 17 signaling pathway, tumor necrosis factor signaling pathway, transforming growth factor-β signaling pathway, etc. The expression trends of Ccl7, Akap12, Grem2, Egln3, Arhgdib, Ccl20, Mmp12, Pla2g2a, and Nr4a1 were significant. There was a correlation between micro-CT pharmacodynamic index, m RNA, and mi RNA. CONCLUSION: JTGs can improve the degeneration of joint cartilage and achieve the purpose of cartilage protection, which can be used for the treatment of OA. SMSCs-related mi RNA expression profiles were significantly altered after the intervention with JTGs containing serum. The 9 co-differentially expressed genes may be the key targets for the efficacy of JTGs in the treatment of OA rats, which can be used for subsequent validation. 展开更多
关键词 transcriptome sequencing technology osteoarthritis Jintiange capsules synovial mesenchymal stem cells articular chondrocytes
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Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database 认领 引用 被引量：2
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作者 Zhoubin Liu Bozhi Yang +12 位作者 Tianyuan Zhang Hao Sun Lianzhen Mao Sha Yang Xiongze Dai Huan Suo Zhuqing Zhang Wenchao Chen Hu Chen Wangjie Xu Komivi Dossa Xuexiao Zou Lijun Ou 《Horticulture Research》 SCIE CSCD 2024年第9期194-206,共13页
Chili pepper is an important spice and a model plant for fruit development studies.Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as caps... Chili pepper is an important spice and a model plant for fruit development studies.Large-scale omics information on chili pepper plant development continues to be gathered for understanding development as well as capsaicin biosynthesis.In this study,a fullspectrum transcriptome data of eight chili pepper tissues at five growth stages using the Oxford Nanopore long-read sequencing approach was generated.Of the 485351 transcripts,35336 were recorded as reference transcripts(genes),while 450015 were novel including coding,lnc,and other non-coding RNAs.These novel transcripts belonged to unknown/intergenic(347703),those retained introns(26336),and had multi-exons with at least one junction match(20333).In terms of alternative splicing,retained intron had the highest proportion(14795).The number of tissue-specific expressed transcripts ranged from 22925(stem)to 40289(f lower).The expression changes during fruit and placenta development are discussed in detail.Integration of gene expression and capsaicin content quantification throughout the placental development clarifies that capsaicin biosynthesis in pepper is mainly derived from valine,leucin,and isoleucine degradation as well as citrate cycle and/or pyrimidine metabolism pathways.Most importantly,a user-friendly Pepper Full-Length Transcriptome Variation Database(PFTVD 1.0)(http://gffzzdaf3ea000ce84e6bh09pxnuno90966xcn.ffgz.tsg.suse.edu.cn/)has been developed.PFTVD 1.0 provides transcriptomics and genomics information and allows users to analyse the data using various tools implemented.This work highlights the potential of long-read sequencing to discover novel genes and transcripts and their diversity in plant developmental biology. 展开更多
关键词 pepper transcript variation database fruit development studieslarge scale fruit development understanding development fullspectrum transcriptome data chili pepper transcriptome sequencing
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Integrative Analyses of Lung Squamous Cell Carcinoma in Ten Chinese Patients with Transcriptome Sequencing 认领 引用 被引量：2
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作者 Lu-Lu Yang Xu-Chao Zhang +13 位作者 Shao-Kun Chuai Zhi-Hong Chen Zhi Xie Wei-Bang Guo Shi-Liang Chen Yuan-Yuan Lei Long-Hua Guo Lan Ying Gou Hui-Wen Sun Qi Zhang Jin-Ji Yang Hai-Yan Tu Jian Su Yi-Long Wu 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2015年第10期579-587,共9页
Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of th... Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants （SNVs： mean of 12.2 SNVs/Mb）, with C〉T/G〉A and A〉G/T〉C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% （93/132） of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets. 展开更多
关键词 Lung squamous cell carcinoma Transcriptome sequencing Gene fusion
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Screening of morphology-related genes based on predatorinduced transcriptome sequencing and the functional analysis of Dagcut gene in Daphnia galeata 认领 引用 被引量：1
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作者 Ya-Qin Cao Ya-Jie Zhao +4 位作者 Hui-Ying Qi Jin-Fei Huang Fu-Cheng Zhu Wen-Ping Wang Dao-Gui Deng 《Current Zoology》 SCIE CAS CSCD 2024年第4期440-452,共13页
High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(... High fish predation pressure can trigger"induced defense"in Daphnia species,resulting in phenotypic plasticity in morphology,behavior,or life-history traits.The molecular mechanisms of defense morphogenesis(e.g.,the tail spine and helmet)in Daphnia remain unclear.In the pres-ent study,the tail spine,helmet,and body of Daphnia galeata under fish and non-fish kairomones conditions were collected for transcriptome analysis.A total of 24 candidate genes related to the morphological defense of D.galeata were identified,including 2 trypsin,one cuticle protein,1 C1qDC protein,and 2 ferritin genes.The function of the Dagcut gene(D.galeata cuticle protein gene)in relation to tail spine morphology was assessed using RNA interference(RNAi).Compared with the EGFP(Enhanced green fluorescent protein)treatment,after RNAi,the expression levels of the Dagcut gene(D.galeata cuticle protein gene)showed a significant decrease.Correspondingly,the tail spines of the offspring pro-duced by D.galeata after RNAi of the Dagcut gene appeared curved during the experiment.In whole-mount in situ hybridization,a clear signal site was detected on the tail spine of D.galeata before RNAi which disappeared after RNAi.Our results suggest that the Dagcut gene may play an important role in tail spine formation of D.galeata,and will provide a theoretical basis for studying the molecular mechanisms of the morpho-logical plasticityin cladocera inthefuture. 展开更多
关键词 Dagcut Daphnia galeata fish kairomones RNAi tail spine transcriptome sequencing.
Transcriptome sequencing reveals novel biomarkers and immune cell infiltration in esophageal tumorigenesis 认领 引用 被引量：1
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作者 Jian-Rong Sun Dong-Mei Chen +2 位作者 Rong Huang Rui-Tao Wang Li-Qun Jia 《World Journal of Gastrointestinal Oncology》 SCIE 2024年第4期1500-1513,共14页
BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the crit... BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC. 展开更多
关键词 Esophageal squamous cell carcinoma Intraepithelial neoplasia Tumorigenesis Transcriptome sequencing Biomarkers Immune cell infiltration 4-nitroquinoline 1-oxid
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Uncovering Small RNAs in Penicillium digitatum by Transcriptome Sequencing 认领 引用 被引量：1
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作者 Pengcheng Zhang Qinru Yu +2 位作者 Ran Li Yaoyao Liu Tongfei Lai 《American Journal of Plant Sciences》 CAS 2022年第7期1006-1022,共17页
Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, se... Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, sequence, predicted construction, base bias, expression levels and potential targets were determined as well. Through pathway and KEGG enrichment analysis, the miRNA target genes were mostly involved in carbohydrate metabolism, transport and catabolism, translation and amino acid metabolism. The target genes involved in aflatoxin biosynthesis and proteasome had a higher rich factor value. The results will provide a theoretical foundation for understanding the developmental and pathogenic mechanisms of P. digitatum at the transcriptional level. 展开更多
关键词 Penicillium digitatum Transcriptome Sequencing MicroRNA Small Interfering RNA
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Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny 认领 引用
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作者 WU Shuangxiu SUN Jing +7 位作者 CHI Shan WANG Liang WANG Xumin LIU Cui LI Xingang YIN Jinlong LIU Tao YU Jun 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2014年第2期1-12,共12页
Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important res... Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae. 展开更多
关键词 Phaeophyceae brown algae Rhodophyta red algae marine macroalgae transcriptome sequencing secondary generation sequencing
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Characterization of Chiton Ischnochiton hakodadensis Foot Based on Transcriptome Sequencing 认领 引用
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作者 DOU Huaiqian MIAO Yan +7 位作者 LI Yuli LI Yangping DAI Xiaoting ZHANG Xiaokang LIANG Pengyu LIU Weizhi WANG Shi BAO Zhenmin 《Journal of Ocean University of China》 SCIE CAS CSCD 2018年第3期632-640,共9页
Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic stu... Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic studies on the chiton are scarce due in part to insufficient genomic resources available for this species. In this study, we investigated the transcriptome of the chiton foot using Illumina sequencing technology. The reads were assembled and clustered into 256461 unigenes, of which 42247 were divided into diverse functional categories by Gene Ontology(GO) annotation terms, and 17256 mapped onto 365 pathways by KEGG pathway mapping. Meanwhile, a set of differentially expressed genes(DEGs) between distal and proximal muscles were identified as the foot adhesive locomotion associated, thus were useful for our future studies. Moreover, up to 679384 high-quality single nucleotide polymorphisms(SNPs) and 19814 simple sequence repeats(SSRs) were identified in this study, which are valuable for subsequent studies on genetic diversity and variation. The transcriptomic resource obtained in this study should aid to future genetic and genomic studies of chiton. 展开更多
关键词 chiton transcriptome sequencing DEG SNP SSR
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Comparative analysis on transcriptome sequencings of six Sargassum species in China 认领 引用
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作者 WANG Guoliang SUN Jing +8 位作者 LIU Guiming WANG Liang YU Jun LIU Tao CHI Shan LIU Cui GUO Haiyan WANG Xumin WU Shuangxiu 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2014年第2期37-44,共8页
Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were perform... Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucle-otides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups （COG）, gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were also performed for further un-derstanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metab-olism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenet-ic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies. 展开更多
关键词 Sargassum Sargassum fusiforme transcriptome sequencing comparative analysis
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Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing 认领 引用
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作者 Jian-Jing Lin Tong Ning +5 位作者 Shi-Cheng Jia Ke-Jia Li Yong-Can Huang Qiang Liu Jian-Hao Lin Xin-Tao Zhang 《World Journal of Stem Cells》 SCIE 2024年第3期305-323,共19页
BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short du... BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation. 展开更多
关键词 Nanosecond pulsed electric fields Whole transcriptome sequencing Mesenchymal stem cells Genetic response Stem cell engineering
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Transcriptome sequencing analysis of ursolic acid-mediated proliferation suppression on cutaneous T-cell lymphoma cells 认领 引用
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作者 Cheng Wang Peng-Cheng Ma +2 位作者 Bao-Le Cai Hong-Yang Li Ling-Jun Li 《Traditional Medicine Research》 2023年第2期36-44,共9页
Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic... Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid. 展开更多
关键词 ursolic acid cutaneous T-cell lymphoma transcriptome sequencing proliferation apoptosis
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Transcriptome Sequencing and de novo Analysis for Oviductus Ranae of Rana chensinensis Using Illumina RNA-Seq Technology 认领 引用 被引量：7
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作者 Mei Zhang Yuntong Li +3 位作者 Baojin Yao Minying Sun Zhiwu Wang Yu Zhao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2013年第3期137-140,共4页
Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicin... Oviductus Ranae is the dried oviduct of female Rana tem-poraria chensinensis （David）, distributed mainly in North- eastern China. Oviductus Ranae is one of the best-known and highly valued oriental foods and medicines. Traditional Chinese medicine holds that Oviductus Ranae can nourish yin, moisten lung and replenish the kidney essence. Meanwhile, activities of Oviductus Ranae such as anti-aging, anti-lipemic, anti-oxidation and anti-fatigue have also been demonstrated by modern phar-macological studies. Previous studies have shown that Oviductus Ranae is mainly composed of proteins, which are up to 50% or more. 展开更多
关键词 Transcriptome Sequencing and de novo Analysis for Oviductus Ranae of Rana chensinensis Using Illumina RNA-Seq Technology RNA
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Transcriptome sequencing analysis of lncRNA expression in peripheral blood mononuclear cells from patients with COPD 认领 引用
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作者 Quan-Ni Li Jie Zhao +5 位作者 Yi-Xiu Yang Juan Sun Xiao-Man Zhou Jian-Fang Liu Qiong Feng Yi-Peng Ding 《Journal of Hainan Medical University》 CAS 2020年第21期48-52,共5页
Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with COPD.Methods:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mon... Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with COPD.Methods:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mononuclear cells were isolated,RNA was extracted and then transcriptome sequencing was performed.The expression difference between the two groups of samples was calculated based on p1.Plot the difference lncRNA heat map and volcano map.The Lncpro database may predict mRNAs regulated by differential lncRNA,and perform the GO function and KEGG signaling clustering.Results:There were 67 lncRNAs between the COPD group and the control group that met the difference of p1,of which 33 were up-regulated and 34 were down-regulated.Between the two groups.The target genes are mainly enriched in GO functions:regulatory functions of multicellular biological processes,regulatory functions of development processes,structured morphogenesis functions,system development functions,and development process functions.Target genes are mainly enriched in KEGG signaling pathways:multi-species apoptotic pathway,TGF-βsignaling pathway,complement and coagulation cascade pathway,colorectal cancer pathway and apoptosis pathway.Conclusion:Our results provide general information and possible regulatory functions and pathways of lncRNA expression changes in peripheral blood mononuclear cells of COPD,which may help clarify the underlying mechanism of COPD. 展开更多
关键词 COPD Transcriptome sequencing Mononuclear cells LncRNA
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Progress and challenges of cerebrovascular endothelial cells research promoted by single-cell transcriptome sequencing technology 认领 引用
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作者 Yakun Gu Jia Liu Xunming Ji 《Journal of Translational Neuroscience》 2024年第2期32-41,共10页
Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebro... Single-cell transcriptome sequencing has been a rapidly developing and powerful biological tool in recent years,and it plays a vital role in describing tissue development,cell heterogeneity,stress response,etc.Cerebrovascular disease is one of the leading causes affecting human health in the world.Thus,it is important to understand the characteristics of cerebrovascular structure,function,and environmental response.Notably,single-cell transcriptome sequencing provides deeper insights into cerebrovascular research in health and disease states.This article will briefly introduce the basic structure and function of cerebrovascular endothelial cells(ECs),summarize the current research and new findings on cerebrovascular ECs at the single-cell transcriptome level,and discuss the challenges in this field. 展开更多
关键词 blood-brain barrier cerebrovascular endothelial cells single-cell transcriptome sequencing cerebrovascular diseases
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