Identification of oscillating genes during early stages of root nodule symbiosis

Legumes interact with nitrogen-fixing bacteria, referred to as rhizobia, and form root nodules to accommodate bacterial symbionts. Rhizobia penetrate into the host tissue through infection threads, which are host-derived tubular and membranous structures formed in root hairs that entrap bacteria. Nodule primordia develop through the division of cortical cells below the infection foci. While the symbiotic process is initiated by bacteria-produced signaling molecules, legumes control the extent of symbiosis by optimizing nodule numbers and distribution to avoid disproportionated tradeoffs and maintain root functions. The host response to symbiotic bacteria occurs discontinuously but repeatedly at the tip of the growing roots. This pattern implicates intermittent host gene expressions in response to rhizobial infection. However, the underlying regulatory mechanisms to form the discontinuous patterns have not been investigated in detail. The goal of this research is to understand the mechanism and biological significance of regulating the oscillatory expression of host genes. Therefore, RNA-seq was performed using 1.2-cm root tip segments collected every 1.5 hours to identify host genes displaying oscillatory expression patterns in the Lotus japonicus root tip inoculated with Mesorhizobium loti.