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Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency

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Abstract

Long non-coding RNAs (lncRNAs) have been identified as important regulatory factors of gene expression in eukaryotic species, such as Homo sapiens, Arabidopsis thaliana, and Oryza sativa. However, the systematic identification of potential lncRNAs in trees is comparatively rare. In particular, the characteristics, expression, and regulatory roles of lncRNAs in trees under nutrient stress remain largely unknown. A genome-wide strategy was used in this investigation to identify and characterize novel and low-nitrogen (N)-responsive lncRNAs in Populus tomentosa; 388 unique lncRNA candidates belonging to 380 gene loci were detected and only seven lncRNAs were found to belong to seven conserved non-coding RNA families indicating the majority of P. tomentosa lncRNAs are species-specific. In total, 126 lncRNAs were significantly altered under low-N stress; 8 were repressed, and 118 were induced. Furthermore, 9 and 5 lncRNAs were detected as precursors of 11 known and 14 novel Populus miRNAs, respectively, whereas 4 lncRNAs were targeted by 29 miRNAs belonging to 5 families, including 22 conserved and 7 non-conserved miRNAs. In addition, 15 antisense lncRNAs were identified to be generated from opposite strands of 14 corresponding protein-coding genes. In total, 111 protein-coding genes with regions complementary to 38 lncRNAs were also predicted with some lncRNAs corresponding to multiple genes and vice versa, and their functions were annotated, which further demonstrated the complex regulatory relationship between lncRNAs and protein-coding genes in plants. Moreover, an interaction network among lncRNAs, miRNAs, and mRNAs was investigated. These findings enrich our understanding of lncRNAs in Populus, expand the methods of miRNA identification. Our results present the first global characterization of lncRNAs and their potential target genes in response to nitrogen stress in trees, which provides more information on low-nutrition adaptation mechanisms in woody plants.

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Acknowledgments

This work was supported by Program for Changjiang Scholars and Innovative Research Team in University (No. IRT13047), the 111 Project (No. B13007), and the National Natural Science Foundation of China (Nos. 31470668, 31370658 and 31200511).

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  1. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Min Chen, Chenlu Wang, Hai Bao, Hui Chen & Yanwei Wang

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  1. Min Chen
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  2. Chenlu Wang
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  4. Hui Chen
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Data archiving statement

RNA-Seq data of P. tomentosa treated or untreated with low-N stress can be available at the NIH Short Read Archive database (http://www.ncbi.nlm.nih.gov/sra) under the accession number SRP063920 (Alias: PRJNA296440).

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Communicated by S. Hohmann.

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Chen, M., Wang, C., Bao, H. et al. Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency. Mol Genet Genomics 291, 1663–1680 (2016). https://doi.org/10.1007/s00438-016-1210-3

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