An intergenic bidirectional promoter driven novel lncRNA (LjPLR) modulates the gene expression of a late nodulin in Lotus japonicus

Root nodules are the only sites for symbiotic nitrogen fixation (SNF) in leguminous plants. The development and functioning of these nodules are governed by a cascade of gene expressions categorized as early and late nodulins. While early nodulins are rapidly induced by Nod factors and involved in infection and cortical cell division, late nodulins support mature nodule function. The regulation of these gene expressions involves several extra- and intracellular factors along withnon-coding RNAs (ncRNAs). Despite extensive studies on ncRNAsinSNF, the role of long ncRNAs (lncRNAs) in it remains largely unexplored excepting the well-characterized early nodulin lncRNA ENOD40 and its natural antisense transcript DONE40. Here, we report the identification and characterization of a novel lncRNA, Lotus japonicus PLP-IV Long non-coding RNA (LjPLR), discovered through in-silico transcriptome analysis followed by in-vivo validation. LjPLR is an antisense transcript complementary to the LjPLP-IV gene, which encodes a phosphatidylinositol transfer protein-like protein implicated in membrane biogenesis. We have identifiedLjPLP-IV as the only putative target of LjPLR. The negatively correlated temporal gene expression patterns of LjPLP-IV and LjPLR during nodule biogenesis providea new insight into the regulatory landscape of SNF in Lotus japonicus.