DOI: 10.5061/dryad.2hj343f
title: Data from: Cooperation and coexpression: how coexpression networks shift in response to multiple mutualists

description: A mechanistic understanding of community ecology requires tackling the
 nonadditive effects of multispecies interactions, a challenge that
 necessitates integration of ecological and molecular complexity-- namely
 moving beyond pairwise ecological interaction studies and the ‘gene at a
 time’ approach to mechanism. Here, we investigate the consequences of
 multispecies mutualisms for the structure and function of genome-wide
 coexpression networks for the first time, using the tractable and
 ecologically-important interaction between legume Medicago truncatula,
 rhizobia, and mycorrhizal fungi. First, we found that genes whose
 expression is affected nonadditively by multiple mutualists are more
 highly connected in gene networks than expected by chance and had 94%
 greater network centrality than genes showing additive effects, suggesting
 that nonadditive genes may be key players in the widespread transcriptomic
 responses to multispecies symbioses. Second, multispecies mutualisms
 substantially changed coexpression network structure of host plants and
 symbionts. Less than 50% of the plant and 10% of mycorrhizal fungi
 coexpression modules detected with rhizobia present were preserved in its
 absence, indicating that third-party mutualists can cause significant
 rewiring of plant and fungal molecular networks. Third, we identified
 unique sets of coexpressed genes that explain variation in plant
 performance only when multiple mutualists were present. Finally, an
 ‘across-symbiosis’ approach identified sets of coexpressed plant and
 mycorrhizal genes that were significantly associated with plant
 performance, were unique to the multiple mutualist context, and suggested
 coupled responses across the plant-mycorrhizal interaction to third-party
 mutualists. Taken together, these results show multispecies mutualism have
 substantial effects on the molecular interactions in host plants,
 microbes, and across symbiotic boundaries.
description: Differential
 Coexpression ScriptThis script contains the
 use of previously normalized data to execute the DiffCoEx computational
 pipeline on an experiment with four treatment groups.differentialCoexpression.rNormalized Transformed Expression Count DataNormalized, transformed expression count data of Medicago truncatula and mycorrhizal fungi is given as an R data frame where the columns denote different genes and rows denote different samples. This data is used for downstream differential coexpression analyses.Expression_Data.zipNormalization and Transformation of Raw Count Data ScriptRaw count data is transformed and normalized with available R packages and RNA-Seq best practices.dataPrep.rRaw_Count_Data_Mycorrhizal_FungiRaw count data from HtSeq for mycorrhizal fungi reads are later transformed and normalized for use in differential coexpression analysis. 'R+' indicates that the sample was obtained from a plant grown in the presence of both mycorrhizal fungi and rhizobia. 'R-' indicates that the sample was obtained from a plant grown only in the presence of mycorrhizal fungi.Raw Count Data Medicago truncatulaRaw count data from HtSeq for Medicago truncatula reads are later transformed and normalized for use in differential coexpression analysis. 'M+R+' indicates that the sample was obtained from a plant grown in the presence of both mycorrhizal fungi and rhizobia. 'M+R-' indicates that the sample was obtained from a plant grown only in the presence of mycorrhizal fungi. 'M-R+' indicates that the sample was obtained from a plant grown only in the presence of rhizobia. 'M-R-' indicates that the sample was obtained from a plant grown in a sterile environment.Raw_Count_Data_Medicago_truncatula.zip