Functional Module Detection in the Palm Tree Phoenix dactylifera by Co-expression and Co-conservation Analysis

Palm trees, the common name for the monocotyledonous family Arecaceae, comprise more than 2,600 species mainly found in tropical, subtropical and warm temperate climate zones. The family contains many economically important species for nutrition, construction and industrial processes. Due to their adaption to heat, soil salinity and extreme drought conditions, Date palms (Phoenix dactylifera) are cultivated for their edible fruits throughout northern Africa and the Middle East and provide major essential nutrients to the population of these countries. To gain a molecular understanding of this adaption, we generated a large set of date palm RNA-Seq data comprising drought, heat and osmotic stress conditions as well as treatments with abscisic acid, a major stress signal and plant hormone. In combination with additional public transcriptome data from a variety of tissues including fruits, flowers, leaves and roots, a probabilistic co-expression network identified temporal, spatial and conditional functional modules of palm genes co-acting in biological processes related to drought, heat and osmotic stress conditions. The obtained modules were contrasted with pathways and genes in Arabidopsis that are known to be functional in these stress conditions. To further explore the mechanistic model of our co-expressed clusters, we used phylogenetic footprinting to identify and visualize candidate cis-modules underlying the co-expressed modules. Orthologous one-to-one gene pairs were obtained from a high-resolution, genome-level syntenic map between two related palm trees, date and oil palm. Cis-regulatory candidate regions were subsequently identified by their evolutionary conservation, network-level conservation and co-expression and corroborated our previously identified functional modules.

We acknowledge funding by the DSFP programme of the King Saud University, Riyad