FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants

Abstract

Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant's genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen-and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html.

Two Complementary Mechanisms Underpin Cell Wall Patterning during Xylem Vessel Development

“…CSI1/POM2 was in part discovered based on coexpression of the corresponding gene with the primary wall CesA genes in Arabidopsis . We therefore explored what rice CSI1/POM2 homolog displayed the closest coexpression with the rice primary and secondary wall CesAs using FamNet (Ruprecht et al, 2016). We found that the most likely candidate for this function was Os06g11990, which we referred to as CSI-like 1 (CSIL1; Supplemental Figure 8A).…”

Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana

“…Another argument that coordinated evolution might follow WGD is the observation that the evolution of traits often involves mutations in multiple genes (Bullard et al, 2010;Fraser et al, 2011;He et al, 2016;Roop et al, 2016), which makes sense given that many traits are polygenic in nature. Inquiries into the existence of such patterns of coordinated divergence in Arabidopsis thaliana (Blanc and Wolfe, 2004a;Ruprecht et al, 2016) and Saccharomyces cerevisiae (Pereira-Leal and Teichmann, 2005;Conant and Wolfe, 2006;Wapinski et al, 2007), which were mainly assessed at the expression level, have reported such cases to be rare. One exception was provided by Ihmels et al (2005), who identified a link between the evolution of anaerobic growth and transcriptional rewiring of dozens of genes following WGD in S. cerevisiae.…”

PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants

“…It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/255067 doi: bioRxiv preprint first posted online version 27 with an e-value cutoff of 10 -5 (21,27), while Gene Ontology terms and gene families were obtained by using the CDS sequences in TRAPID (28).…”

“…To detect conserved and duplicated modules, we applied the FamNet pipeline, which identifies co-expression neighborhoods that contain same gene families and Pfam domains (21). Briefly, when two neighborhoods of sizes A and B are compared, the number of Pfam domains and gene families (labels) in common between the two neighborhoods is counted and compared to an expected number of random neighborhoods of these sizes (21).…”

“…Furthermore, gene modules conserved over large phylogenetic distances can reveal core components of shared processes, while duplicated gene modules can reflect recent adaptations combined with an increase in complexity (19)(20)(21).…”