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Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules

(2017) PLANT JOURNAL. 90(3). p.447-465
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants.
Keywords
PROTEIN-PROTEIN INTERACTIONS, MICROARRAY DATA SETS, CELLULOSE SYNTHASE, COMPARATIVE GENOMICS, ARABIDOPSIS-THALIANA, PLASMA-MEMBRANE, GREEN, PLANTS, CELL-WALLS, ALGAE, IDENTIFICATION, comparative co-expression, network evolution, phylostratigraphy, phylogenetics, gene function, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens

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Chicago
Ruprecht, Colin, Sebastian Proost, Marcela Hernandez-Coronado, Carlos Ortiz-Ramirez, Daniel Lang, Stefan A Rensing, Jorg D Becker, Klaas Vandepoele, and Marek Mutwil. 2017. “Phylogenomic Analysis of Gene Co-expression Networks Reveals the Evolution of Functional Modules.” Plant Journal 90 (3): 447–465.
APA
Ruprecht, C., Proost, S., Hernandez-Coronado, M., Ortiz-Ramirez, C., Lang, D., Rensing, S. A., Becker, J. D., et al. (2017). Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. PLANT JOURNAL, 90(3), 447–465.
Vancouver
1.
Ruprecht C, Proost S, Hernandez-Coronado M, Ortiz-Ramirez C, Lang D, Rensing SA, et al. Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules. PLANT JOURNAL. 2017;90(3):447–65.
MLA
Ruprecht, Colin, Sebastian Proost, Marcela Hernandez-Coronado, et al. “Phylogenomic Analysis of Gene Co-expression Networks Reveals the Evolution of Functional Modules.” PLANT JOURNAL 90.3 (2017): 447–465. Print.
@article{8523541,
  abstract     = {Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large-scale genomic and phylogenetic data with gene co-expression networks to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co-expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants.},
  author       = {Ruprecht, Colin and Proost, Sebastian and Hernandez-Coronado, Marcela and Ortiz-Ramirez, Carlos and Lang, Daniel and Rensing, Stefan A and Becker, Jorg D and Vandepoele, Klaas and Mutwil, Marek},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {PROTEIN-PROTEIN INTERACTIONS,MICROARRAY DATA SETS,CELLULOSE SYNTHASE,COMPARATIVE GENOMICS,ARABIDOPSIS-THALIANA,PLASMA-MEMBRANE,GREEN,PLANTS,CELL-WALLS,ALGAE,IDENTIFICATION,comparative co-expression,network evolution,phylostratigraphy,phylogenetics,gene function,Arabidopsis thaliana,Oryza sativa,Physcomitrella patens},
  language     = {eng},
  number       = {3},
  pages        = {447--465},
  title        = {Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules},
  url          = {http://dx.doi.org/10.1111/tpj.13502},
  volume       = {90},
  year         = {2017},
}

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