Laser capture microdissection of Pisum sativum L. nodules followed by RNA-seq analysis revealed crucial transcriptomic changes during infected cell differentiation

The development of the symbiotic nodule of legumes is accompanied by both differentiation of rhizobia into bacteroids and differentiation of the cells infected with rhizobia. The aim of this work was to study changes in transcriptomic profiles associated with the differentiation of the infected cells. Using laser capture microdissection, cells from the early infection zone, the late infection zone and the nitrogen fixation zone were isolated from 11-day-old pea wild type SGE nodule samples. RNA from these samples were sequenced using Illumina HiSeq 2500 platform. Obtained reads were filtered and mapped to the pea reference genome. Differential gene expression analysis (p-value < 0.01; LFC > |1|) and functional analysis were carried out for three comparisons: (1) cells of the late infection zone / cells of the early infection zone; (2) cells of the nitrogen fixation zone / cells of the early infection zone; (3) cells of the nitrogen fixation zone / cells of the late infection zone.