Long intergenic noncoding RNAs (lincRNAs) are widespread in cellular organisms, however, the origins and functions of many lincRNAs remain to be explored. Transposable elements (TEs) are widely distributed in many eukaryotic genomes, and often account for large fractions of plant and animal genomes. By using strand-specific RNA sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified TE-associated lincRNAs (TE-lincRNAs). Stress regulation of some TE-lincRNAs was observed in Arabidopsis. Our findings indicate that TE-associated lincRNAs potentially play important roles in plant abiotic stress responses. Moreover, in the Arabidopsis chromatin remodelling mutant ddm1 that has an altered chromatin state, novel lincRNAs including TE-lincRNAs were generated. The novel lincRNAs were inherited in the subsequent generations in the wild type background, suggesting that lincRNAs could act as an adaptive reservoir in eukaryotes. Overall design: High-depth paired-end RNA-seq from wild type and linRNA mutant Arabidopsis, Each sample contains 3 biological replicates.