Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.
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. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de.
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.
Colin
C
Ruprecht
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.
Sebastian
S
Proost
Instituto Gulbekian De Ciencia, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
Marcela
M
Hernandez-Coronado
Instituto Gulbekian De Ciencia, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
Carlos
C
Ortiz-Ramirez
University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany.
Daniel
D
Lang
University of Marburg, Karl-von-Frisch-Str. 8, D-35043, Marburg, Germany.
Stefan A
SA
Rensing
Instituto Gulbekian De Ciencia, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
Jörg D
JD
Becker
Department of Plant Systems Biology VIB, Department of Plant Biotechnology and Bioinformatics Ghent University, Technologiepark 927, B-9052, Gent, Belgium.
Klaas
K
Vandepoele
Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, 14476, Potsdam, Germany.
Marek
M
Mutwil
D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D019068:Bryopsida / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*
D010940:Plant Proteins

Arabidopsis thaliana
; 
Oryza sativa
; 
Physcomitrella patens
; comparative co-expression; gene function; network evolution; phylogenetics; phylostratigraphy