Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified IncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (s5RNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel IncRNAs 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 IncRNAs. Functional annotation of these potential targets and sequence motif analysis indicated that the IncRNAs participate in various biological processes underlying Arabidopsis growth and development. Seventeen of the IncRNAs were predicted targets of 22 miRNAs, and a network of interactions between ncRNAs and mRNAs was constructed. In addition, nine IncRNAs 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 IncRNAs, and enhances our understanding of plant IncRNAs, which will facilitate functional research. (C) 2017 Elsevier Inc. All rights reserved.