Genome-wide identification and characterization of novel lncRNAs in Ginkgo biloba

Abstract

We identified several novel lncRNAs that play important roles in Ginkgo biloba leaf development. A large number of long non-coding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, lncRNAs and their regulatory roles remain poorly characterized in woody plants, particularly in the gymnosperm G. biloba. We performed deep strand-specific RNA sequencing (ssRNA-seq), and obtained 27.44 GB raw data from all major developmental stages of G. biloba leaves. From these sequencing data, we identified 1323 novel lncRNAs. These lncRNAs were transcribed from 947 scaffolds of G. biloba, 57.6% of which came from intergenic regions. We also confirmed that Gb-lncRNAs were shorter and had fewer exons than protein-coding genes. Target prediction for 764 lncRNAs identified 1184 target genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis revealed that these lncRNAs might be associated with photosynthesis, plant hormones, and secondary metabolism in leaves. Moreover, we constructed a network of regulatory interactions between lncRNAs and mRNAs; 89 lncRNAs were predicted as targets of 64 miRNAs and 33 lncRNAs functioned as miRNA precursors. Quantitative real-time PCR revealed that novel lncRNAs had stage- and tissue-specific expression patterns in G. biloba leaves. These results provide new insight into the function of lncRNAs in leaves and enhance our understanding of plant lncRNAs.