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 fo...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 WheatCENet.WheatCENet 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 wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.展开更多
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.31970629 and 31771467 to ZS,and 31870209 to YJ).
文摘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 WheatCENet.WheatCENet 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 wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.
