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共表达网络分析是利用海量生物学数据研究基因表达模式与功能关系的重要方法。在共表达网络中,具有相同表达模式的基因可能也具有功能上的一致性,这为我们提供了发掘未知基因功能信息的理论基础。本研究整合了60个玉米(Zea mays)和40个高粱(Sorghum bicolor),组织的转录组测序数据,首先在每个物种内利用全数据集和子集分别构建共表达网络,以测试所选样本数量对于共表达基因网络构建的影响;然后搜寻物种间成对的直系同源共线性基因,并利用其中一个物种的基因模块信息将另一物种的模块分割成在功能上更细的子模块;最后对不同大小的基因模块进行GO富集以确定其功能特征。本研究表明,共表达网络聚类基因在表达模式上具有组织特异性,且物种间有32%的共线性基因表达模式一致,GO富集分析结果显示物种间模块交叉分割亚模块的方法能得到在功能上更为相似的基因簇。另外,玉米亚基因组间有48.5%的双拷贝基因也具有相同的基因表达模式。本研究利用共表达基因网络的构建为传统的基因功能富集研究提供了新的视角,并通过物种间共表达基因网络的比较解析了直系同源共线性基因间的表达模式,从而进一步鉴定了这些在物种间具有相同表达模式和组织特异性基因的功能特征。
Abstract：Co-expression network analysis is an important approach to study the relationship between gene expression patterns and functions in large biological data sets. In co-expression networks, genes with the same expression pattern may also have functional consistency, which provides us with a theoretical basis for exploring information on the function of unknown genes. This study integrates transcriptome sequencing data from 60 maize(Zea mays) and 40 sorghum(Sorghum bicolor) tissues, firstly constructing a co-expression network using a full data set and subsets within each species to test the effect of selected sample size on the construction of co-expressed gene networks; then searching for pairs of orthologous syntenic genes between species and using the gene module of one species to subdivided the modules of another species into smaller sub-networks. The subn etworks defined from the same original cluster tend to be enriched in different known functions in GO enrichment analysis. This study demonstrated that the co-expression network clustering gene was tissue-specific and 32% of the syntenic genes were consistent in expression patterns among species. The results of GO enrichment analysis show that data from multiple closely related species can be used to increase the resolution of gene co-expression networks. In addition, 48.5% of maize duplicate genes were observed identical expression patterns in sorghum and both subgenomes while the rests were showed divergence of expression patterns between the maize1 and maize2.In this study, the construction of co-expressed gene network provides a new perspective for traditional gene function enrichment, and the expression pattern between orthologous syntenic genes was analyzed through comparing co-expressing networks, which in further identified the functional characteristics of genes with the same expression pattern and tissue-specificity.
Allen J.D.,Xie Y.,Chen M.,Girard L.,and Xiao G.H.,2012,Comparing statistical methods for constructing large scale gene networks,PLoS ONE,7(1):e29348.
Ashburner M.,Ball C.A.,Blake J.A.,Botstein D.,Butler H.,Cherry J.M.,Davis A.P.,Dolinski K.,Dwight S.S.,Eppig J.T.,Harris M.A.,Hill D.P.,Issel-Tarver L.,Kasarskis A.,Lewis S.,Matese J.C.,Richardson J.E.,Ringwald M.,Rubin G.M.,and Sherlock G.,2000,Gene ontology:tool for the unification of biology.The Gene Ontology Consortium,Nat.Genet.,25(1):25-29.
Bolduc N.,Yilmaz A.,Mejia-Guerra M.K.,Morohashi K.,O'Connor D.,Grotewold E.,and Hake S.,2012,Unraveling the KNOTTED1 regulatory network in maize meristems,Gene Dev.,26(15):1685-1690.
Chang Y.M.,Liu W.Y.,Shih A.C.C.,Shen M.N.,Lu C.H.,Lu M.Y.J.,Yang H.W.,Wang T.Y.,Chen S.C.C.,Chen S.M.,Li W.H.,and Ku M.S.B.,2012,Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis,Plant Physiol.,160(1):165-177.
Chettoor A.M.,Givan S.A.,Cole R.A.,Coker C.T.,Unger-Wallace E.,Vejlupkova Z.,Vollbrecht E.,Fowler J.E.,and E-vans M.M.,2014,Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes,Genome Biol.,15(7):414.
Davidson R.M.,Gowda M.,Moghe G.,Lin H.N.,Vaillancourt B.,Shiu S.H.,Jiang N.,and Buell C.R.,2012,Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution,Plant J.,71(3):492-502.
Davidson R.M.,Hansey C.N.,Gowda M.,Childs K.L.,and Buell C.R.,2011,Utility of RNA sequencing for analysis of maize reproductive transcriptomes,Plant Genome,4(3):191-203.
Downs G.S.,Bi Y.M.,Colasanti J.,Wu W.Q.,Chen X.,Zhu T.,Rothstein S.J.,and Lukens L.N.,2013,A developmental transcriptional network for Zea mays defines coexpression modules,Plant Physiol.,161(4):1830-1843.
Dugas D.V.,Monaco M.K.,Olsen A.,Klein R.R.,Kumari S.,Ware D.,and Klein P.E.,2011,Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid,BMC Genomics,12(1):514.
Ficklin S.P.,and Feltus F.A.,2011,Gene coexpression network alignment and conservation of gene modules between two grass species:maize and rice,Plant Physiol.,156(3):1244-1256.
Ficklin S.P.,Luo F.,and Feltus F.A.,2010,The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks,Plant Physiol.,154 (1):13-24.
Force A.,Lynch M.,Pickett F.B.,Amores A.,Yan Y.L.,and Postlethwait J.,1999,Preservation of duplicate genes by complementary,degenerative mutations,Genetics,151 (4):1531-1545.
Gaut B.S.,and Doebley J.F.,1997,DNA sequence evidence for the segmental allotetraploid origin of maize,Proc.Natl.A-cad.Sci.USA,94(13):6809-6814.
Hansen B.O.,Vaid N.,Musialak-Lange M.,Janowski M.,and Mutwil M.,2014,Elucidating gene function and function evolution through comparison of co-expression networks of plants,Front.Plant Sci.,5:394.
Kakumanu A.,Ambavaram M.M.R.,Klumas C.,Krishnan A.,Batlang U.,Myers E.,Grene R.,and Pereira A.,2012,Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-seq,Plant Physiol.,160(2):846-867.
Klopfenstein D.V.,Zhang L.S.,Pedersen B.S.,Ramírez F.,Vesztrocy A.W.,Naldi A.,Mungall C.J.,Yunes J.M.,Botvinnik O.,Weigel M.,Dampier W.,Dessimoz C.,Flick P.,and Tang H.B.,2018,GOATOOLS:A Python library for Gene Ontology analyses,Sci.Rep.,8(1):10872.
Kogelman L.J.A.,Cirera S.,Zhernakova D.V.,Fredholm M.,Franke L.,and Kadarmideen H.N.,2014,Identification of co-expression gene networks,regulatory genes and pathways for obesity based on adipose tissue RNA sequencing in a porcine model,BMC Med.Genomics,7(1):57.
Kommadath A.,Bao H.,Arantes A.S.,Plastow G.S.,Tuggle C.K.,Bearson S.M.D.,Guan L.L.,and Stothard P.,2014,Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding,BMC Genomics,15(1):452.
Lai X.J.,Behera S.,Liang Z.K.,Lu Y.L.,Deogun J.S.,and Schnable J.C.,2017,STAG-CNS:An order-aware conserved noncoding sequences discovery tool for arbitrary numbers of species,Mol.Plant,10(7):990-999.
Langfelder P.,and Horvath S.,2008,WGCNA:an R package for weighted correlation network analysis,BMC Bioinformatics,9(1):559.
Leal L.G.,López C.,and López-Kleine L.,2014,Construction and comparison of gene co-expression networks shows complex plant immune responses,PeerJ,2(5):e610.
Li H.,Handsaker B.,Wysoker A.,Fennell T.,Ruan J.,Homer N.,Marth G.,Abecasis G.,and Durbin R.,1000 Genome Project Data Processing Subgroup,2009,The sequence alignment/map format and SAMtools,Bioinformatics,25 (16):2078-2079.
Li P.H.,Ponnala L.,Gandotra N.,Wang L.,Si Y.Q.,Tausta S.L.,Kebrom T.H.,Provart N.,Patel R.,Myers C.R.,Reidel E.J.,Turgeon R.,Liu P.,Sun Q.,Nelson T.,and Brutnell T.P.,2010,The developmental dynamics of the maize leaf transcriptome,Nat.Genet.,42(12):1060-1067.
Martin M.,2011,Cutadapt removes adapter sequences from high-throughput sequencing reads,EMBnet.J.,17(1):10-12.
Mizuno H.,Kawahigashi H.,Kawahara Y.,Kanamori H.,Ogata J.,Minami H.,Itoh T.,and Matsumoto T.,2012,Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction,BMC Plant Biol.,12(1):121.
Obertello M.,Shrivastava S.,Katari M.S.,and Coruzzi G.M.,2015,Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice,Plant Physiol.,168(4):1830-1843.
Polanski K.,Rhodes J.,Hill C.,Zhang P.J.,Jenkins D.J.,Kiddle S.J.,Jironkin A.,Beynon J.,Buchanan-Wollaston V.,Ott S.,and Denby K.J.,2014,Wigwams:identifying gene modules co-regulated across multiple biological conditions,Bioinformatics,30(7):962-970.
Renny-Byfield S.,Rodgers-Melnick E.,and Ross-Ibarra J.,2017,Gene fractionation and function in the ancient subgenomes of maize,Mol.Biol.Evol.,34(8):1825-1832.
Rhee S.Y.,and Mutwil M.,2014,Towards revealing the functions of all genes in plants,Trends Plant Sci.,19(4):212-221.
Schnable J.C.,Springer N.M.,and Freeling M.,2011,Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss,Proc.Natl.Acad.Sci.USA,108(10):4069-4074.
Serin E.A.R.,Nijveen H.,Hilhorst H.W.M.,and Ligterink W.,2016,Learning from co-expression networks:possibilities and challenges,Front.Plant Sci.,7(1):394.
Swigonova Z.,Lai J.S.,Ma J.X.,Ramakrishna W.,Llaca V.,Bennetzen J.L.,and Messing J.,2004,On the tetraploid origin of the maize genome,Comp.Funct.Genom.,5(3):281-284.
Trapnell C.,Roberts A.,Goff L.,Pertea G.,Kim D.,Kelley D.R.,Pimentel H.,Salzberg S.L.,Rinn J.L.,and Pachter L.,2012,Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks,Nat.Protoc.,7(1):562-578.
Turco G.,Schnable J.C.,Pedersen B.,and Freeling M.,2013,Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses,Front.Plant Sci.,4(1):170.
Wang X.F.,Elling A.A.,Li X.Y.,Li N.,Peng Z.Y.,He G.M.,Sun H.,Qi Y.J.,Liu X.S.,and Deng X.W.,2009,Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to m RNA and small RNA transcriptomes in maize,Plant Cell,21(4):1053-1069.
Waters A.J.,Makarevitch I.,Eichten S.R.,Swanson-Wagner R.A.,Yeh C.T.,Xu W.,Schnable P.S.,Vaughn M.W.,Gehring M.,and Springer N.M.,2011,Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm,Plant Cell,23(12):4221-4233.
Wu T.D.,and Nacu S.,2010,Fast and SNP-tolerant detection of complex variants and splicing in short reads,Bioinformatics,26(7):873-881.
Zhang B.,and Horvath S.,2005,A general framework for weighted gene co-expression network analysis,Stat.Appl.Genet.Mol.Biol.,4(1):Article17.
基本信息:
DOI：10.13417/j.gab.040.002323
中图分类号:S513;S514
引用信息:
[1]赖先军,张义正,James C.Schnable,等.共表达网络分析玉米和高粱物种间基因表达模式及功能富集[J].基因组学与应用生物学,2021,40(Z1):2323-2337.DOI:10.13417/j.gab.040.002323.
基金信息:
四川省科技厅应用基础项目(2019YJ0546); 西昌学院高层次人才引进科研启动项目(50180108; 50190005)共同资助
2021-06-25
2021-06-25
2019-12-11