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Tree Genetics & Genomes

, 14:86 | Cite as

Single-base-resolution methylomes of Populus euphratica reveal the association between DNA methylation and salt stress

  • Yutao Su
  • Xiaotao Bai
  • Wenlu Yang
  • Weiwei Wang
  • Zeyuan Chen
  • Jianchao Ma
  • Tao Ma
Original Article
Part of the following topical collections:
  1. Genome Biology

Abstract

DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. In this study, we examined single-base resolution methylomes of Populus euphratica under control and salt stress conditions using high-throughput bisulfite sequencing. Our data showed that the methylation levels of methylated cytosines in upstream 2 kb, downstream 2 kb, and repetitive sequences increased after salt treatment in leaves, but decreased in roots. We also found that heavy methylation in 100-bp upstream of the transcriptional start site repressed gene expression, while methylations within downstream 2 K and within the gene body were positively associated with gene expression. A total of 1893 and 1817 significant differentially methylated regions (DMRs) corresponding to 251 and 191 differentially methylated genes (DMGs) were identified in leaf and root tissues, respectively. These DMGs may play important roles in salt stress responses of P. euphratica through the changes of their DNA methylation levels. Overall, these findings provide valuable insights into our understanding of the interaction between gene expression and methylation of salt responses in poplars.

Keywords

DNA methylation Populus euphratica Salt stress Gene expression 

Notes

Funding

Funding for this work is provided by the National Natural Science Foundation of China (31500502), National Key Research and Development Program of China (2016YFD0600101), One Thousand Young Talents program from Sichuan Province and the Fundamental Research Funds for the Central Universities.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Data archiving statement

The bisulfite sequencing data have been submitted to the NCBI Sequence Read Archive under accession number SRP133971. The transcriptome data is available under NCBI Sequence Read Archive with the project accession number SRP116293.

Supplementary material

11295_2018_1298_MOESM1_ESM.pdf (387 kb)
Supplementary Fig. S1 Pie chart representing the proportion of regions covering gene models, repeats or intergenic loci in the whole-genome BS-Seq of leaf (a) and root (b) tissues (PDF 386 kb)
11295_2018_1298_MOESM2_ESM.pdf (345 kb)
Supplementary Fig. S2 The percentage of methylated cytosines (mCs) that identified in leaf (a) and root (b) tissues in each sequence context (CG, CHG and CHH). (PDF 344 kb)
11295_2018_1298_MOESM3_ESM.pdf (271 kb)
Supplementary Fig. S3 Relative methylation levels of the corresponding genomic regions in leaf (a) and root (b) tissues. The y-axis shows the relative methylation level in each element of genomic regions (x-axis), which contains upstream2k (up2k), downstream2k (down2k), mRNA, and intergenic sequences. Asterisk on error bars indicates significant differences at p < 0.05 (t test) (PDF 271 kb)
11295_2018_1298_MOESM4_ESM.pdf (796 kb)
Supplementary Fig. S4 Relationship between levels of gene expression and DNA methylation in different genomic regions (upstream 2 kb, gene body, and downstream 2 k) for leaf (a, b) and root (c, d) tissues under normal and salt conditions (PDF 796 kb)
11295_2018_1298_MOESM5_ESM.pdf (318 kb)
Supplementary Fig. S5 Relationship between levels of gene expression and DNA methylation in the 100-bp upstream of the transcriptional start site for leaf (a) and root (b) tissues. The left and right panels refer to normal and salt stress conditions, respectively. (PDF 317 kb)
11295_2018_1298_MOESM6_ESM.pdf (376 kb)
Supplementary Fig. S6 Gene ontology (GO) enrichment analysis of DMGs in leaf (a) and root (b) tissues (PDF 375 kb)
11295_2018_1298_MOESM7_ESM.pdf (697 kb)
Supplementary Fig. S7 Genome browser screen of DNA methylation for leaf-specific (a–e) and root-specific (f–i) DMGs. Top to bottom tracks: DNA methylation in leaf under normal and salt stress conditions, DNA methylation in root under normal and salt stress conditions, and gene model of P. euphratica. The gene number and gene name of Arabidopsis homologous was showed on the top left corner. The DMRs was presented by the red box (PDF 697 kb)
11295_2018_1298_MOESM8_ESM.xlsx (18 kb)
Supplementary Table S1 Description of the BS-Seq data for leaf and root tissues of Populus euphratica under normal and salt stress conditions. (XLSX 18 kb)
11295_2018_1298_MOESM9_ESM.xlsx (211 kb)
Supplementary Table S2 Number of differentially methylated regions (DMRs) in leaf tissue. LN = leaf normal condition; LS = leaf salt stress condition. (XLSX 210 kb)
11295_2018_1298_MOESM10_ESM.xlsx (197 kb)
Supplementary Table S3 Number of differentially methylated regions (DMRs) in root tissue. RN = root normal condition; RS = root salt stress condition. (XLSX 197 kb)
11295_2018_1298_MOESM11_ESM.xlsx (236 kb)
Supplementary Table S4 Number of differentially methylated genes (DMGs) in leaf tissue. The level of gene expression was showed, and the differentially expressed genes (DEGs) were highlighted. (XLSX 235 kb)
11295_2018_1298_MOESM12_ESM.xlsx (239 kb)
Supplementary Table S5 Number of differentially methylated genes (DMGs) in root tissue. The level of gene expression was showed, and the differentially expressed genes (DEGs) were highlighted. (XLSX 238 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Yutao Su
    • 1
  • Xiaotao Bai
    • 2
  • Wenlu Yang
    • 1
  • Weiwei Wang
    • 1
  • Zeyuan Chen
    • 1
  • Jianchao Ma
    • 2
  • Tao Ma
    • 1
  1. 1.Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life SciencesSichuan UniversityChengduPeople’s Republic of China
  2. 2.State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life SciencesLanzhou UniversityLanzhouPeople’s Republic of China

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