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Transcriptional regulation of chilling stress responsive long noncoding RNAs in Populus simonii

  • Min Tian
  • Dong Ci
  • Yuepeng Song
  • Deqiang ZhangEmail author
Original Article

Abstract

Key message

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.

Abstract

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.

Keywords

Chilling stress Long noncoding RNA Photosynthesis Phytohormone synthesis Regulatory network 

Notes

Acknowledgements

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).

Supplementary material

468_2019_1812_MOESM1_ESM.tiff (3.5 mb)
Supplementary material 1 Figure S1 Informatics pipeline of lncRNA and gene identification (TIFF 3632 KB)
468_2019_1812_MOESM2_ESM.tiff (2.6 mb)
Supplementary material 2 Figure S2 Genome-wide distribution of lncRNAs in two groups. The total lncRNAs are indicated in green, and lncRNAs affected by chilling stress are in orange. The outermost ring represents the 19 chromosomes of Populus simonii. The expression levels of lncRNAs are indicated by their height (TIFF 2644 KB)
468_2019_1812_MOESM3_ESM.tiff (345 kb)
Supplementary material 3 Figure S3 Biological processes enrichment of 1926 differentially expressed genes. Red nodes represent upregulated genes and green nodes represent downregulated genes. The degree of color represents the fold-change. The enriched processes as identified by gene ontology analysis are: 1, Photosynthesis; 2, major CHO metabolism; 3, minor CHO metabolism; 4, glycolysis; 5, fermentation; 6, gluconeogenesis; 7, OPP oxidative; 8, TCA; 9, mitochondrial; 10, cell wall; 11, lipid metabolism; 12, N metabolism; 13, amino acid metabolism; 14, S assimilation; 15, metal handling; 16, secondary metabolism; 17, hormone metabolism; 18, cofactor and vitamin metabolism; 19, tetrapyrrole synthesis; 20, stress; 21, redox; 22, polyamine metabolism; 23, nucleotide metabolism; 24, biodegradation of xenobiotics; 25, C1 metabolism; 26, Misc.; 27, RNA; 28, DNA; 29, protein; 30, signaling; 31, cell; 32, development; 33, transporter; and 34, other (TIFF 344 KB)
468_2019_1812_MOESM4_ESM.tiff (2.7 mb)
Supplementary material 4 Figure S4 Sequencing data verification by real-time PCR (RT-PCR). A) Linear regression model of RT-PCR data and RNA-Seq data. B) Heatmap of 2-ΔCt values in five poplar species at five time points. Red nodes represent upregulated genes and green nodes represent downregulated genes, and the degree of color represents fold-change (TIFF 2807 KB)
468_2019_1812_MOESM5_ESM.tiff (3.4 mb)
Supplementary material 5 Figure S5 Comparison of expression levels in P. simonii and P. trichocarpa. The orange line represents P. trichocarpa and the blue line represents P. simonii (TIFF 3505 KB)
468_2019_1812_MOESM6_ESM.xlsx (2.6 mb)
Supplementary material 6 Table S1 A total of 26,638 genes derived from both the conditional control (CC) and chilling stress (CS) groups were classified into upregulated (5747), downregulated (7425), and non-responsive (13,466) groups (XLSX 2693 KB)
468_2019_1812_MOESM7_ESM.xlsx (26 kb)
Supplementary material 7 Table S2 Gene ontology (GO) analyses were conducted on the genes listed in Table S1. Three groups of genes showed a diverse GO enrichment (XLSX 26 KB)
468_2019_1812_MOESM8_ESM.xlsx (1.5 mb)
Supplementary material 8 Table S3 A total of 18,779 long noncoding RNAs (lncRNAs) were predicted and identified, comprised of 14,779 lncRNAs in the CC group and 14,186 lncRNAs in the CS group (XLSX 1517 KB)
468_2019_1812_MOESM9_ESM.xlsx (95 kb)
Supplementary material 9 Table S4 Relationships between chilling response lncRNAs and genes, comprising 1807 lncRNAs and 1926 genes. Network connections indicate significant correlations of cis-targets or trans-targets. c, cis-target; t, trans-target; ct, both cis-target and trans-target relationship. The total number of connections was 4536 (XLSX 94 KB)
468_2019_1812_MOESM10_ESM.xlsx (17 kb)
Supplementary material 10 Table S5 Chilling-responsive lncRNAs targeted by conserved microRNA (miRNA) mimics (XLSX 16 KB)
468_2019_1812_MOESM11_ESM.xlsx (80 kb)
Supplementary material 11 Table S6 Chilling-responsive lncRNAs targeted by conserved miRNAs (XLSX 80 KB)
468_2019_1812_MOESM12_ESM.xlsx (300 kb)
Supplementary material 12 Table S7 Chilling responsive genes used for MapMan enrichment (XLSX 299 KB)
468_2019_1812_MOESM13_ESM.xlsx (10 kb)
Supplementary material 13 Table S8 Index and adapters information for RNA sequencing (XLSX 9 KB)
468_2019_1812_MOESM14_ESM.xlsx (12 kb)
Supplementary material 14 Table S9 Primer sequences for gene clone and qRT-PCR analysis of genes involved in the photosynthesis and hormone synthesis networks (XLSX 11 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.National Engineering Laboratory for Tree Breeding, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingPeople’s Republic of China
  2. 2.Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingPeople’s Republic of China

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