In the era of available reference genomes, plant ncRNA annotation has become more visible because of its regulatory roles in response to many biotic and abiotic stressors. Characterizing and elucidating functional roles of lncRNAs and their targets from different species is critical to better understand functional roles and epigenetic effects of certain important genes. Collective knowledge about lncRNAs is currently very limited. However, recently published reference sequences of many plant genomes are an excellent target as promising resources for the improved understanding of not only lncRNAs, but any class of molecules. This knowledge of lncRNAs expands and improves genome editing, understanding epigenetics roles, and will likely define novel functional targets in plants. In this collection, we will compile a set of method articles including but not limited to machine learning and deep learning tools.