Genome-wide identification and characterization of lncRNAs responding to iron deficiency in Oryza sativa

Background: Iron (Fe) plays a vital role in various cellular processes in plants, including chlorophyll biosynthesis, photosynthesis and respiration. Fe deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Long non-coding RNAs (lncRNAs) have recently been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency in plants has not been reported. In this work, genome-wide identification and characterization of lncRNAs responsive to Fe deficiency were performed by strand-specific RNA sequencing in rice. Results: In total, 6477 lncRNAs were identified. In Fe-deficient conditions, 47 lncRNAs were up-regulated and 33 lncRNAs were down-regulated in shoots, while 89 lncRNAs were up-regulated and 32 lncRNAs were down-regulated in roots compared to normal conditions. The lncRNAs that were differentially expressed under Fe-sufficient and -deficient conditions appear to be clustered in the genome. Among five monocotyledon species, 88 lncRNAs were conserved, but only 3 lncRNAs responded to Fe deficiency in shoots. Two lncRNAs were identified as putative target mimics of miRNAs that respond to Fe deficiency. Conclusions: Our results provide evidence that lncRNAs are involved in Fe-deficiency signaling pathway in plants, providing a new pathway for further investigation into Fe-regulatory and response mechanisms.