Single-base-resolution methylomes of Populus euphratica reveal the association between DNA methylation and salt stress
- 230 Downloads
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.
KeywordsDNA methylation Populus euphratica Salt stress Gene expression
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.
- Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, Salt DE (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet 6(11):e1001193CrossRefPubMedPubMedCentralGoogle Scholar
- Janz D, Behnke K, Schnitzler JP, Kanawati B, Schmitt-Kopplin P, Polle A (2010) Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms. BMC Plant Biol 10(1):150CrossRefPubMedPubMedCentralGoogle Scholar
- Lafon-Placette C, Faivre-Rampant P, Delaunay A, Street N, Brignolas F, Maury S (2013) Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene-body DNA methylation in open chromatin state. New Phytol 197(2):416–430CrossRefPubMedGoogle Scholar
- Lafon-Placette C, Le AG, Chauveau D et al (2017) Changes in the epigenome and transcriptome of the poplar shoot apical meristem in response to water availability affect preferentially hormone pathways. J Exp Bot 69(3)Google Scholar
- Li X, Zhu JD, Hu FY, Ge S, Ye M, Xiang H, Zhang G, Zheng X, Zhang H, Zhang S, Li Q, Luo R, Yu C, Yu J, Sun J, Zou X, Cao X, Xie X, Wang J, Wang W (2012) Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics 13:300CrossRefPubMedPubMedCentralGoogle Scholar
- Liang D, Zhang Z, Wu H et al (2014) Single-base-resolution methylomes of Populus trichocarpa reveal the association between DNA methylation and drought stress. BMC Genet 15(S1):1–11Google Scholar
- Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322CrossRefPubMedPubMedCentralGoogle Scholar
- Ma T, Wang J, Zhou G, Yue Z, Hu Q, Chen Y, Liu B, Qiu Q, Wang Z, Zhang J, Wang K, Jiang D, Gou C, Yu L, Zhan D, Zhou R, Luo W, Ma H, Yang Y, Pan S, Fang D, Luo Y, Wang X, Wang G, Wang J, Wang Q, Lu X, Chen Z, Liu J, Lu Y, Yin Y, Yang H, Abbott RJ, Wu Y, Wan D, Li J, Yin T, Lascoux M, DiFazio SP, Tuskan GA, Wang J, Liu J (2013b) Genomic insights into salt adaptation in a desert poplar. Nat Commun 4(4):2797CrossRefPubMedGoogle Scholar
- Ma JC, Wan DS, Duan BB, Bai X, Bai Q, Chen N, Ma T (2018a) Genome sequence and genetic transformation of a widely distributed and cultivated poplar. Plant Biotechnol J. https://doi.org/10.1111/pbi.12989
- Ma T, Wang K, Hu Q, Xi Z, Wan D, Wang Q, Feng J, Jiang D, Ahani H, Abbott RJ, Lascoux M, Nevo E, Liu J (2018b) Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. Proc Natl Acad Sci U S A 115(2):E236–E243CrossRefPubMedGoogle Scholar
- Ottow EA, Brinker M, Teichmann T, Fritz E, Kaiser W, Brosché M, Kangasjärvi J, Jiang X, Polle A (2005) Populus euphratica displays apoplastic sodium accumulation, osmotic adjustment by decreases in calcium and soluble carbohydrates, and develops leaf succulence under salt stress. Plant Physiol 139(4):1762–1772CrossRefPubMedPubMedCentralGoogle Scholar
- Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515CrossRefPubMedPubMedCentralGoogle Scholar