10.5061/DRYAD.2HJ343F
Palakurty, Sathvik X.
University of Miami
Stinchcombe, John R.
University of Toronto
Afkhami, Michelle E.
University of Miami
Data from: Cooperation and coexpression: how coexpression networks shift
in response to multiple mutualists
Dryad
dataset
2018
Medicago truncatula
nonaddictive
mycorrhizal fungi
WGCNA
DiffCoEx
Ensifer meliloti
National Science Foundation
https://ror.org/021nxhr62
IOS-1401840
2018-03-19T17:12:17Z
2018-03-19T17:12:17Z
en
https://doi.org/10.1111/mec.14550
22878632 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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