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

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. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de.

Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

“…The proteins encoded by the lectin genes are part of a larger and complex interactome, and it will be difficult to relate the emergence of a new protein domain combination to existing pathways. Therefore, a combined analysis of these traditional approaches in combination with co-expression networks would be advantageous and could expand our knowledge since recent studies demonstrated that co-expression networks are conserved also across species [185,186]. At the same time, we cannot exclude the presence of minor mistakes in our dataset due to missing annotation of genes or unidentified protein domains.…”

Brachypodium: A Monocot Grass Model Genus for Plant Biology

“…Araport (Krishnakumar et al, 2014) and PlaNET (Ruprecht et al, 2017). This latter resource, PlaNET, 738 does host some B. distachyon datasets, but it is limited to the visualization and analysis of co-regulated 739 gene networks.…”

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

“…Recently, genomic analysis have been applied to study key events in the evolution of the green lineage such as terrestrialization (Delwiche and Cooper, 2015; de Vries et al, 2016). Nevertheless, the integration of genomics and transcriptomics to study the evolution of gene expression patterns in the green lineage has only recently been explored (Romero-Campero et al, 2013; Ruprecht et al, 2017). Photosynthetic organisms are particularly influenced by daily light/dark transitions as their main energy income is a very demanding light-dependent process.…”

“…In this work, phylogenomic and transcriptomic data integration and analysis have been performed by gene co-expression networks construction (Romero-Campero et al, 2013; Gehan et al, 2015; Ruprecht et al, 2017) and a novel algorithm for the identification of potential orthologues called Multiple Best Bi-directional Hit (MBBH). Using clustering techniques, specific gene clusters or modules that showed a rhythmic daily regulation have been identified.…”