Transcriptional regulation of chilling stress responsive long noncoding RNAs in Populus simonii
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We report genome-wide identification and functional prediction of lncRNAs under chilling stress, the present study deepened our understanding of the transcriptional regulation mechanism of poplar under chilling stress.
Chilling stress is a major threat to tree development and survival. Long noncoding RNAs (lncRNAs) are known to play a role in plant stress responses, but their transcriptional regulatory network remains elusive. We conducted genome-wide identification and functional prediction of lncRNAs under chilling stress in an ecologically important poplar species, Populus simonii. After the chilling treatment, we detected 30,769 genes and 10,186 putative lncRNAs, of which 13,172 genes and 5082 lncRNAs were differentially expressed under chilling stress in P. simonii. From these chilling-responsive transcripts, we hypothesized that five unique patterns of 21 lncRNAs acted directly on genes, and 617 lncRNAs affected gene expression by interacting with microRNAs (miRNAs). Additionally, the significantly differentially expressed genes were enriched to 198 gene ontology (GO) terms, which were prominently involved in photosynthesis and endogenous phytohormone synthesis pathways. Based on the physiological index, we found 48 genes with 15 lncRNAs, and 70 genes with 50 lncRNAs that were significantly differentially expressed in photosynthesis and endogenous phytohormone synthesis pathways, respectively. These findings improve our understanding of the potential functions of lncRNAs by refining the regulatory roles of lncRNAs in the photosynthesis and phytohormone synthesis pathways.
KeywordsChilling stress Long noncoding RNA Photosynthesis Phytohormone synthesis Regulatory network
This work was supported by the Fundamental Research Funds for Central Universities (no. BLYJ201603 and no. 2015ZCQ-SW-01), and the Program of Introducing Talents of Discipline to Universities (111 project, B13007).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
Data archiving statement
The raw sequencing data for the six libraries in this article have been deposited in the Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra, accession number SRP095225).
- Del Giudice A, Pavel NV, Galantini L, Falini G, Trost P, Fermani S et al (2015) Unravelling the shape and structural assembly of the photosynthetic GAPDH–CP12–PRK complex from Arabidopsis thaliana by small-angle X-ray scattering analysis. Acta Crystallogr Sect D Biol Crystallogr 71:2372–2385CrossRefGoogle Scholar
- Liu S, Chen W, Qu L, Gai Y, Jiang X (2013) Simultaneous determination of 24 or more acidic and alkaline phytohormones in femtomole quantities of plant tissues by high-performance liquid chromatography–electrospray ionization–ion trap mass spectrometry. Anal Bioanal Chem 405:1257–1266CrossRefGoogle Scholar
- Peng L, Shi L, Cai H, Xu F, Zeng C (2012) Transcriptional profiling reveals adaptive responses to boron deficiency stress in Arabidopsis. Z Naturforsch Sect CJ Biosci 67:510–524Google Scholar
- Sapir-Mir M, Mett A, Belausov E, Tal-Meshulam S, Frydman A, Gidoni D et al (2008) Peroxisomal localization of Arabidopsis isopentenyl diphosphate isomerases suggests that part of the plant isoprenoid mevalonic acid pathway is compartmentalized to peroxisomes. Plant Physiol 148:1219–1228CrossRefPubMedCentralGoogle Scholar