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Genes & Genomics

, Volume 40, Issue 11, pp 1181–1197 | Cite as

Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response

  • Xiao-Xiao Gong
  • Bing-Yu Yan
  • Jin Hu
  • Cui-Ping Yang
  • Yi-Jian Li
  • Jin-Ping Liu
  • Wen-Bin Liao
Research Article

Abstract

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at 4 °C for 2 h) and LT24 (cold treatment at 4 °C for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

Keywords

Rubber tree Hevea brasiliensis Cold stress response RNA sequencing Transcriptome Transcription factor 

Notes

Acknowledgements

This work was funded by the National Natural Science Foundation of China (No. 31560573) and the Hainan Province Major Science and Technology Project (ZDZX2013023).

Author contributions

XXG, BYY and JH conducted bioinformatics studies and carried out qRT-PCR validation. CPY and YJL participated in collection of plant materials. JPL supervised the experiments and wrote the manuscript. WBL participated in the bioinformatics studies. All the authors read and approved the manuscript for publication.

Compliance with ethical standards

Conflict of interest

Xiao-Xiao Gong declares that she does not have conflict of interest. Bing-Yu Yan declares that she does not have conflict of interest. Jin Hu declares that he does not have conflict of interest. Cui-Ping Yang declares that she does not have conflict of interest. Yi-Jian Li declares that he does not have conflict of interest. Jin-Ping Liu declares that he does not have conflict of interest. Wen-Bin Liao declares that he does not have conflict of interest.

Ethical approval

This article does not contain any studies with human subjects or animals performed by any of the authors.

Supplementary material

13258_2018_681_MOESM1_ESM.doc (42 kb)
Additional file 1: PCR primer sets used in the quantitative real time PCR (qRT-PCR) (DOC 41 KB)
13258_2018_681_MOESM2_ESM.xlsx (86 kb)
Additional file 2: Up-regulated genes detected between LT2 and CT libraries (XLSX 85 KB)
13258_2018_681_MOESM3_ESM.xlsx (146 kb)
Additional file 3: Down-regulated genes detected between LT2 and CT libraries (XLSX 146 KB)
13258_2018_681_MOESM4_ESM.xlsx (197 kb)
Additional file 4: Up-regulated genes detected between LT24 and CT libraries (XLSX 196 KB)
13258_2018_681_MOESM5_ESM.xlsx (135 kb)
Additional file 5: Down-regulated genes detected between LT24 and CT libraries (XLSX 134 KB)
13258_2018_681_MOESM6_ESM.xls (63 kb)
Additional file 6: Seven pathways including Flavonoid biosynthesis, Phenylpropanoid biosynthesis, Plant hormone signal transduction, Cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, Phenylalanine metabolism and Starch and sucrose metabolism, significantly enriched in both LT2 and LT24 samples (XLS 62 KB)
13258_2018_681_MOESM7_ESM.docx (42 kb)
Additional file 7: DEGs of TFs in LT2 and L24 compared with CT (described with the reference genome sequence information (Tang et al. 2016)) (DOCX 41 KB)

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Copyright information

© The Genetics Society of Korea and Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Tropical Agriculture and Forestry InstituteHainan UniversityHaikouChina
  2. 2.Service Center of Science and Technology, Rubber Research InstituteChinese Academy of Tropical Agricultural SciencesDanzhouChina
  3. 3.Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina

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