Identification and characterization of novel lncRNAs in Arabidopsis thaliana.

Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation. Bioinformatic analysis predicted potential target genes or cis-regulated genes of 91 antisense and 32 intergenic lncRNAs. Functional annotation of these potential targets and sequence motif analysis indicated that the lncRNAs participate in various biological processes underlying Arabidopsis growth and development. Seventeen of the lncRNAs were predicted targets of 22 miRNAs, and a network of interactions between ncRNAs and mRNAs was constructed. In addition, nine lncRNAs functioned as miRNA precursors. Finally, qRT-PCR revealed that novel lncRNAs have stage- and tissue-specific expression patterns in A. thaliana. Our study provides insight into the potential functions and regulatory interactions of novel Arabidopsis lncRNAs, and enhances our understanding of plant lncRNAs, which will facilitate functional research.

Rejuvenation increases leaf biomass and flavonoid accumulation in Ginkgo biloba.

Rejuvenation refers to the transition from an adult state to a juvenile state. Trunk truncation at the base of the tree can result in tree rejuvenation. However, little is known about the association of rejuvenation with leaf biomass and flavonoid accumulation. The results of this study showed that, compared with control leaves, leaves of renewed Ginkgo biloba shoots were larger, thicker, and more lobed and had higher fresh/dry weights and chlorophyll contents. The leaf biomass per hectare of rejuvenated trees was twofold higher than that of the untruncated controls. Moreover, we observed a marked increase in the accumulation of flavonol glycosides via metabolomic analysis and detected upregulated expression of genes involved in flavonoid biosynthesis, including CHS, FLS, F3'H, DFR, and LAR. Overexpression of GbCHS in ginkgo calli confirmed that GbCHS plays an important role in flavonoid biosynthesis. Interestingly, the contents of gibberellins significantly increased in the rejuvenated leaves. Moreover, exogenous gibberellin treatment significantly increased GbCHS expression and flavonoid contents. Our findings show that truncation can stimulate tree rejuvenation by altering hormone levels, representing an effective and feasible approach for enhancing the biomass and flavonoid content of G. biloba leaves.