Genome-Wide Characterization and Functional Discovery Provides New Insights into the Landscape of Long Noncoding RNAs in Panax ginseng

Long noncoding RNAs (lncRNAs) have been implicated with diverse biological roles including genome regulation, various developmental processes and diseases. However, a comprehensive identification and functional prediction of lncRNAs in plants is still fall behind. Through systematic pipeline using ~104 billion sequencing RNA reads from various tissues, stages of growth, and abiotic stress treatments of Panax ginseng, we catalogued 19,495 lncRNAs and identified more than 100 candidate lncRNAs involved in abiotic stress responses to drought, salt, cold, heat and methyl jasmonate (MeJA) and 2,607 candidates involved in specialized function in specific tissues and growth stages of P. ginseng. Gene Ontology enrichments for genes that showed expression correlation and RNA-RNA interaction with a set of lncRNAs participate in important biological processes that are crucial targets of research in P. ginseng. Although lncRNAs are less conserved, we have identified two new well-conserved lncRNAs in P. ginseng and found their potential roles in mitochondrial protection and respiration chain. Finally, single nucleotide polymorphism (SNPs) investigation between P. ginseng cultivars and Panax species revealed the cause of SNPs in functional variations and rapid divergence at interspecies level over intraspecies. Our study provides new insights into the functional perspectives of lncRNAs in ginseng.