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WheatCENet:A Database for comparative co-expression network Analysis of Allohexaploid Wheat and Its Progenitors

Genomics, Proteomics & Bioinformatics 2023年第2期21卷 324-336页

作者： Zhongqiu Li Yiheng Hu Xuelian Ma Lingling Da Jiajie She Yue Liu Xin Yi Yaxin Cao Wenying Xu Yuannian Jiao Zhen Su State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBejing 100193China StateKey Laboratory of Systematic and Eolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Bejing 100049China

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named *** is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered therein.Functional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid *** is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.

关键词： co-expression network Species comparison Diploid and polyploid wheat Functional annotation

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Transcriptome and morphological analyses of double flower formation in Dianthus chinensis

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Horticultural Plant Journal 2024年第1期10卷 181-193页

作者： Xiaoni Zhang Shengnan Lin Quanshu Wu Qijian Wang Chunmei Shi Manzhu Bao Mohammed Bendahmane Xiaopeng Fu Zhiqiang Wu Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Key Laboratory of Horticultural Plant Biology College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubei 430070China Laboratoire Reproduction et Development des Plantes INRA-CNRS-Lyon1-ENSEcole Normale Superieure de LyonLyon 520074France

The double flower developmental process is regulated via a complex transcriptional regulatory network.To understand this highly dynamic and complex developmental process of Dianthus spp.,we performed a comparative analysis of floral morphology and transcriptome dynamics in simple flowers and double flowers.We found that the primordium of double flowers of‘X’was larger in size compared to that of simple flowers of‘L’in Dianthus chinensis.RNA-seq and Weighted Gene co-expression network Analysis(WGCNA)during flower development,identified stage-specific gene network modules.expression analysis by RNA-seq indicated that a group of genes related to floral meristem identity,primordia position and polarity were highly expressed in double flowers genotypes compared to simple flowers genotypes,suggesting their roles in double-petal formation.A total of 21 DEGs related to petal number were identified between simple and double flowers.The experiments of in situ hybridization revealed that DcaAP2L,DcaLFY and DcaUFO genes were expressed in the intra-sepal boundary and petal boundary.We proposed a potential transcriptional regulatory network for simple and double flower development.This study provides novel insights into the molecular mechanism underlying double flower formation in Dianthus spp.

关键词： Dianthus spp. Petal boundary Floral morphology Double flower co-expression network

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Identification of a TSPY co-expression network associated with DNA hypomethylation and tumor gene expression in somatic cancers

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Journal of Genetics and Genomics 2016年第10期43卷 577-585页

作者： Tatsuo Kido Yun-Fai Chris Lau Division of Cell and Developmental Genetics Department of Medicine Veterans Affairs Medical Center and Institute for Human Genetics University of California

Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas（TCGA） database. A total of 53 genes,including oncogenic lineage protein 28 homolog B（LIN28B） gene and RNA-binding motif protein Y-linked（RBMY） gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network（TCN）. TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma（30%） and lung adenocarcinoma（10%） regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes.

关键词： co-expression network DNA methylation Gene expression signature Cancer subclassification Y chromosome genes TSPY Cancer/testis antigens

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co-expression network analysis of virulence genes exoS and exoU of pseudomonas aeruginosa in lower respiratory tract based on histological data expression profiles

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Discussion of Clinical Cases 2019年第4期6卷 10-16页

作者： Erli Jiao Bo Chen Clinical Laboratory Baogang HospitalBaotouInner MongoliaChina The First Affiliated Hospital of Baotou Medical college Inner Mongolia University of Science and TechnologyBaotouInner MongoliaChina

Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of pseudomonas aeruginosa in the lower respiratory tract from the perspective of molecular biology and identifying its key regulatory genes.Methods:From March 2016 to May 2018,312 patients infected with pseudomonas aeruginosa in the lower respiratory tract who were admitted to Department of Respiratory Medicine of Baogang Hospital and given follow-up treatments in the hospital were selected as subjects by use of cluster sampling.Alveolar lavage fluid and sputum collected from those patients were used as biological specimens.The genes of pseudomonas aeruginosa were detected with the help of oligonucleotide probes to make a pre-processing of chip data.A total of 8 common antibiotics(ceftazidime,gentamicin,piperacillin,amikacin,ciprofloxacin,levofloxacin,doripenem and ticarcillin)against Gram-negative bacteria were selected to determine the drug resistance of biological specimens.McoDE algorithm was used to construct a co-expression network model of the drug-resistance genes focused on exoS/exoU.Results:The expression level of exoS/exoU in the drug-resistance group was significantly higher than that in the non-resistance group(pcorrelation with the expression of exoS and exoU(pcorrelated with the expression of exoS and exoU(pco-expression network contained exoS,exoU,RAC1,ITGB1,ITGB5,CRK,CAMK2D,RHOA,FLNA,IGF1R,TGFBR2 and FOS.Among them,RAC1 had a highest

关键词： Omics data expression profile Lower respiratory tract Pseudomonas aeruginosa exoS exoU co-expression network

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High transcriptome plasticity drives phosphate starvation responses in tomato

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Stress Biology 2022年第1期2卷 458-480页

作者： Viswanathan Satheesh Jieqiong Zhang Jinkai Li Qiuye You Panfeng Zhao Peng Wang Mingguang Lei Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China School of Life Science and Technology Tongji UniversityShanghai 200092China University of Chinese Academy of Sciences Beijing 100049China

Tomato is an important vegetable crop and fluctuating available soil phosphate(Pi)level elicits several morpho-physiological responses driven by underlying molecular responses.Therefore,understanding these molecular responses at the gene and isoform levels has become critical in the quest for developing crops with improved Pi use efficiency.A quantitative time-series RNA-seq analysis was performed to decipher the global transcriptomic changes that accompany Pi starvation in tomato.Apart from changes in the expression levels of genes,there were also alterations in the expression of alternatively-spliced transcripts.Physiological responses such as anthocyanin accumulation,reactive oxygen species generation and cell death are obvious 7 days after Pi deprivation accompanied with the maximum amount of transcriptional change in the genome making it an important stage for in-depth study while studying Pi stress responses(PSR).Our study demonstrates that transcriptomic changes under Pi deficiency are dynamic and complex in tomato.Overall,our study dwells on the dynamism of the transcriptome in eliciting a response to adapt to low Pi stress and lays it bare.Findings from this study will prove to be an invaluable resource for researchers using tomato as a model for understanding nutrient deficiency.

关键词： Tomato Pi starvation Transcriptome Gene expression Alternative splicing co-expression network

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comparative transcriptome analysis of Ts(Resistant genotype)and Ma(Susceptible genotype)marigold(Tagetes erecta L.)leaves in response to Alternaria tagetica

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Horticultural Plant Journal 2023年第2期9卷 321-334页

作者： Xi Cheng Dongliang Chen Chang Luo Hua Liu conglin Huang Institute of Grassland Flowers and EcologyBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China Beijing Engineering Research Center of Functional Floriculture Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China

Marigold black spot caused by Alternaria tagetica is a major disease that can decrease marigold production by 40%,resulting in serious economic losses.In this study,we identified many genes responsive to A.tagetica in the resistant and susceptible marigold genotypes.Analyses of differentially expressed genes,expression trends,and a weighted gene co-expression network revealed a series of hub genes with key roles in different A.tagetica infection stages.Additionally,1216 unigenes encoding transcription factors from eight families were differentially expressed between Ts and Ma.Moreover,R genes fromvarious families(e.g.,N,NL,RLP,and TNL)were differentially expressed in the twomarigold genotypes before and after the inoculation with A.tagetica.Pathway diagrams were used to visualize the leaf transcriptional changes in the two marigold genotypes infected by A.tagetica to clarify the effects of A.tagetica on the expression patterns of genes involved in phosphatidylinositol signaling,plant–pathogen interactions,and plant hormone signal transduction.We identified candidate genes related to disease resistance and generated valuable resources for analyzing the candidate gene functions related to black spot resistance in marigold.The study data may be useful for the molecular marker-assisted screening and breeding of marigold lines with increased disease resistance.

关键词： Tagetes erecta co-expression network Gene expression Black spot resistance Transcriptional modules

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LjaFGD:Lonicera japonica functional genomicsdatabase

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Journal of Integrative Plant Biology 2021年第8期63卷 1422-1436页

作者： Qiaoqiao Xiao Zhongqiu Li Mengmeng Qu Wenying Xu Zhen Su Jiaotong Yang Guizhou University of Traditional Chinese Medicine Guizhou550025 China State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing100193 China Research Center for Clinical&Translational Medicine Fifth Medical Center for General Hospital of PLABeijing100039 China

Lonicera japonica Thunb.,a traditional Chinese herb,has been used for treating human diseases for thousands of years.Recently,the genome of L.japonica has been decoded,providing valuable information for research into gene function.However,no comprehensive database for gene functional analysis and mining is available for L.japonica.We therefore constructed LjaFGD(***/LjaFGD and ***/LjaFGD),a database for analyzing and comparing gene function in L.japonica.We constructed a gene co-expression network based on 77 RNA-seq samples,and then annotated genes of L.japonica by alignment against protein sequences from public databases.We also introduced several tools for gene functional analysis,including Blast,motif analysis,gene set enrichment analysis,heatmap analysis,and JBrowse.Our co-expression network revealed that MYB and WRKY transcription factor family genes were co-expressed with genes encoding key enzymes in the biosynthesis of chlorogenic acid and luteolin in L.japonica.We used flavonol synthase 1(LjFLS1)as an example to show the reliability and applicability of our database.LjaFGD and its various associated tools will provide researchers with an accessible platform for retrieving functional information on L.japonica genes to further biological discovery.

关键词： co-expression network functional annotation functional analysis tools Lonicera japonica

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Glucocorticoids Significantly Influence the Transcriptome of Bone Microvascular Endothelial Cells of Human Femoral Head

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Chinese Medical Journal 2015年第14期128卷 1956-1963页

作者： Qing-Sheng Yu Wan-Shou Guo Li-Ming Cheng Yu-Feng Lu Jian-Ying Shen Ping Li Department of Orthopedics China-Japan Friendship Hospital Beijing 100029 China Beijing Key Laboratory for Immune-Mediated Inflammatory Diseases Beijing 100029 China Artemisinin Research Center Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing 100700 China Department of Pharmacology Institute of Clinical Medical Sciences China-Japan Friendship Hospital Beijing 100029 China

Background： Appropriate expression and regulation of the transcriptome, which mainly comprise ofmRNAs and lncRNAs, are important for all biological and cellular processes including the physiological activities of bone microvascular endothelial cells （BMECs）. Through an intricate intraeellular signaling systems, the transcriptome regulates the pharmacological response of the cells. Although studies have elucidated the impact of glucocorticoids （GCs） cell-specific gene expression signatures, it remains necessary to comprehensively characterize the impact of lncRNAs to transcriptional changes. Methods： BMECs were divided into two groups. One was treated with GCs and the other left untreated as a paired control. Differential expression was analyzed with GeneSpring software V12.0 （Agilent, Santa Clara, CA, USA） and hierarchical clustering was conducted using Cluster 3,0 software. The Gene Ontology （GO） analysis was performed with Molecular Annotation System provided by CapitalBio corporation. Results： Our results highlight the involvement of genes implicated in development, differentiation and apoptosis following GC stimulation. Elucidation of differential gene expression emphasizes the importance of regulatory gene networks induced by GCs. We identified 73 up-regulated and 166 down-regulated long noncoding RNAs, the expression of 107 of which significantly correlated with 172 mRNAs induced by hydrocortisone. conclusions： Transcriptome analysis of BMECs from human samples was performed to identify specific gene networks induced by GCs. Our results identified complex RNA crosstalk underlying the pathogenesis of steroid-induced necrosis of femoral head.

关键词： co-expression network Intracellular Signaling Pathway Microvascular Endothelial Ceils Noncoding RNAs Osteonecrosis

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Genome-Wide Identification,Phylogeny and expressional Profiles of Autophagy Gene Family in Bread Wheat(Triticum aestivum L.)

Genome-Wide Identification,Phylogeny and Expressional Profil...

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第八届全国小麦基因组学及分子育种大会

作者： Wenjie Yue Licao Cui Weining Song Xiaojun Nie State Key Laboratory of Crop Stress Biology in Arid Areas College of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F University

Autophagy is a highly conserved intracellular degradation system that eukaryotic organism evolved for self-defense and protect cells from damage.Extensive studies have conducted to demonstrate that autophagy played the crucial role in regulating plant growth and development as well as in response to diverse stresses.However,little is known about ATG genes in wheat(Triticum aestivum L.),especially those involved in the regulatory network of stress processes.In this study,a total of 108 putative ATG(autophagy-associated genes) genes in wheat were obtained using a genome-wide search approach.Phylogenetic analysis classified them into 13 subfamilies,of which the ATG16 subfamily contained 29 members ranking the largest subfamily.The conserved motif composition as well as phylogenetic relationship of these TaATGs was systematically analyzed and strongly supported the classification.Besides,the exon-intron structure analysis showed that gene structure of the homoelogous genes tended to be similarity during the process of wheat polypolidation In addition,a total of 114 putative cis-elements were found and cis-elements related to light responsiveness were abundantly presented in the promoter regions.Furthermore,co-expression network analysis found that YAMP727 is the node of the whole network structure and complex interactions were identified among the members of interaction network.Finally,the expression profiles of wheat ATGs among different tissues and under abiotic stresses were investigated and several tissue-specific and stress-induced genes were identified and TaATG8 subfamily was found to play a crucial role in tissue autophagy and stress defense,which could be considered as the candidates for further functional study.This was the first study to report the characteristics of ATG family in wheat,which ultimately provided important clues for further functional analysis and also facilitate to reveal the evolution mechanism of ATG genes in wheat and beyond.

关键词： Wheat Autophagy-associated gene family expression pattern co-expression network

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