Genome-wide identification and functional prediction of long non-coding RNAs in plastic growth in Alternanthera philoxeroides

Plants have a remarkable ability to alter their growth and development to adapt to fluctuating environments. Epigenetics plays a pivotal role in regulating plastic phenotypes. Based on long-read PacBio sequencing and time-course gene expression profiling, a genome-wide survey and functional prediction of lncRNAs potentially involved in submergence-induced plastic growth was conducted in <i>A. philoxeroides</i>. A total of 141 submergence-responsive lncRNAs were identified, with their <i>cis</i>- and <i>trans</i>-targeting genes being predicted. Functional annotation and validation of lncRNA targets indicated the significant roles of <i>lncRNA14247</i>, <i>lncRNA13847</i>, and <i>lncRNA12385</i> on phytohormone homeostasis by mediating crosstalk between various phytohormones upon submergence, and thereby impacting plastic development. The results also unveiled the potential roles of <i>lncRNA13847</i> and <i>lncRNA7566</i> in mediating submergence-induced growth alterations by targeting light signal components, such as PIFs. These findings highlighted the significance of lncRNAs in submergence responses and provided insights into the molecular underpinnings of phenotypic plasticity in <i>A. philoxeroides</i>.