Identification and characterization of long noncoding RNA in Paulownia tomentosa treated with methyl methane sulfonate.

Paulownia is a tree native to China, with important ecological and economic value. Long noncoding RNAs (lncRNAs) are known to play important roles in eukaryotic gene regulation. However, no lncRNAs have been reported in Paulownia so far. We performed RNA sequencing of two Paulownia tomentosa lncRNA libraries constructed from the terminal buds of normal untreated seedlings and 60 mg L-1 MMS-treated seedlings, and obtained a total of 2531 putative lncRNAs. The average length of the lncRNA transcripts was much less than the average length of the mRNA transcripts in the P. tomentosa libraries. A few of the Paulownia lncRNAs were conserved among ten species tested. We identified seven lncRNAs as precursors of 13 known miRNAs, 15 lncRNAs may act as target mimics of 19 miRNAs, and 351 unique noncoding sequences belonging to 133 conserved lncRNA families. In addition, we identified 220 lncRNAs responsive to methyl methane sulfonate (MMS), including seven phytohormone-related lncRNAs and one lncRNAs involved in base excision repair. This is the first time that lncRNAs have been explored in Paulownia. The lncRNA data may also provide new insights into the MMS-response in P. tomentosa.