Data from: Dissecting nutrient-related co-expression networks in phosphate starved poplars

Phosphorus (P) is an essential plant nutrient, but its availability is
often limited in soil. Here, we studied changes in the transcriptome and
in nutrient element concentrations in leaves and roots of poplars (Populus
× canescens) in response to P deficiency. P starvation resulted in
decreased concentrations of S and major cations (K, Mg, Ca), in increased
concentrations of N, Zn and Al, while C, Fe and Mn were only little
affected. In roots and leaves >4,000 and >9,000 genes were
differently expressed upon P starvation. These genes clustered in eleven
co-expression modules of which seven were correlated with distinct
elements in the plant tissues. One module (4.7% of all differentially
expressed genes) was strongly correlated with changes in the P
concentration in the plant. In this module the GO term “response to P
starvation” was enriched with phosphoenolpyruvate carboxylase kinases,
phosphatases and pyrophosphatases as well as regulatory domains such as
SPX, but no phosphate transporters. The P-related module was also enriched
in genes of the functional category “galactolipid synthesis”.
Galactolipids substitute phospholipids in membranes under P limitation.
Two modules, one correlated with C and N and the other with biomass, S and
Mg, were connected with the P-related module by co-expression. In these
modules GO terms indicating “DNA modification” and “cell division” as well
as “defense” and “RNA modification” and “signaling” were enriched; they
contained phosphate transporters. Bark storage proteins were among the
most strongly upregulated genes in the growth-related module suggesting
that N, which could not be used for growth, accumulated in typical storage
compounds. In conclusion, weighted gene coexpression network analysis
revealed a hierarchical structure of gene clusters, which separated
phosphate starvation responses correlated with P tissue concentrations
from other gene modules, which most likely represented transcriptional
adjustments related to down-stream nutritional changes and stress.