Large-scale de novo transcriptome analysis reveals specific gene expression and novel simple sequence repeats markers in salinized roots of the euhalophyte Salicornia europaea

  • Jinbiao Ma
  • Xinlong Xiao
  • Li Li
  • Albino Maggio
  • Dayong Zhang
  • Osama Abdalla Abdelshafy Mohamad
  • Michael Van Oosten
  • Gang Huang
  • Yufang Sun
  • Changyan TianEmail author
  • Yinan YaoEmail author
Original Article


Glycophytic plants suffer from severe stress and injury when roots are exposed to high salinity in the rhizosphere. In contrast, the euhalophyte Salicornia europaea grows well at 200 mM NaCl and can withstand up to 1000 mM NaCl in the root zone. Analysis of gene expression profiles and the underlying molecular mechanisms responsible for this tolerance have been largely overlooked. Using the Illumina sequencing platform and the short-reads assembly programme Trinity, we generated a total of 40 and 39 million clean reads and further 140,086 and 122,728 unigenes from the 200 mM NaCl and 0 mM NaCl treated tissues of S. europaea roots, respectively. All unigenes in this study were functionally annotated within context of the COG, GO and KEGG pathways. Unigene functional annotation analysis allowed us to identify hundreds of ion transporters related to homeostasis and osmotic adaptation as well as a variety of proteins related to cation, amino acid, lipid and sugar transport. We found significant enrichment in response to stress including the functional categories of “antioxidant activity”, “catalytic activity” and “response to stimuli”. These findings represent for a useful resource for the scientific community working on salt tolerance mechanisms. Conversely, a total of 8639 EST-SSRs from 131,594 unigenes were identified and 4539 non-redundant SSRs primers pairs were developed. These data provide a good foundation for future studies on molecular adaptation mechanisms of euhalophytes roots under saline environments and will likely facilitate the identification of critical salt tolerance traits to be transferred in economically important crops.


Abiotic stress Illumina/Solexa sequencing Salicornia europaea root Transcriptome qRT-PCR 



This work was supported by Natural Science Foundation in China (Grant no. U1703106), Youth Innovation Promotion Association, CAS (2016381), and the Open Fund of the Shanghai Key Laboratory of Bio-Energy Crops.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

11738_2018_2702_MOESM1_ESM.fa (77.1 mb)
Supplementary file S1: All-Unigene sequences of S. europaea roots (Description: Sequences with no gap and with a length longer than 200 bp were selected from the assembly results) (FA 78994 KB)
11738_2018_2702_MOESM2_ESM.xls (31.8 mb)
Supplementary file S2: Functional annotation of All-Unigenes, including GO, COG, and KEGG analyses (Description: All-Unigene sequences were searched against protein databases (Nr, Swiss-prot database, KEGG, COG, and GO) using BLASTX (E-value Nr, -5)) (XLS 32526 KB)
11738_2018_2702_MOESM3_ESM.xls (7.3 mb)
Supplementary file S3: Summary of functional annotation of identified DEGs (Description: Unigenes with an absolute value of |log2Ratio| ≥ 1 and FDR ≤ 0.001 were identified as DEGs. GO and KEGG analyses of DEGs were based on a cutoff E-value of less than or equal to 10-5) (XLS 7464 KB)
11738_2018_2702_MOESM4_ESM.xls (428 kb)
Supplementary file S4: GO categories of DEGs between salt-free and salt-treated roots of S. europaea (Description: DEGs were divided into three major categories: molecular functions, cellular components and biological processes. Gene numbers and gene ID are listed in this file) (XLS 428 KB)
11738_2018_2702_MOESM5_ESM.xlsx (62 kb)
Supplementary file S5: Summary of DEGs enriched in KEGG pathways (Description: Pathways and backbone gene numbers are given in the table. The q-values for all pathways are less than or equal to 0.05) (XLSX 61 KB)
11738_2018_2702_MOESM6_ESM.xls (21.5 mb)
Supplementary file S6: The transcriptome data comparison between shoot and root (Description: The gene length, rowreads number, RPKM value, gene annotation were given in form) (XLS 22034 KB)
11738_2018_2702_MOESM7_ESM.xlsx (202 kb)
Supplementary file S7: Summary of SSR primers (Description: The gene ID and primer pairs were given in form) (XLSX 202 KB)


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Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2018

Authors and Affiliations

  • Jinbiao Ma
    • 1
    • 3
  • Xinlong Xiao
    • 1
    • 2
  • Li Li
    • 1
  • Albino Maggio
    • 4
  • Dayong Zhang
    • 5
  • Osama Abdalla Abdelshafy Mohamad
    • 1
    • 6
  • Michael Van Oosten
    • 4
  • Gang Huang
    • 1
  • Yufang Sun
    • 1
    • 2
  • Changyan Tian
    • 1
    Email author
  • Yinan Yao
    • 1
    Email author
  1. 1.Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and GeographyChinese Academy of ScienceÜrümqiChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.Shanghai Key Laboratory of Bio-Energy CropsShanghaiChina
  4. 4.Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
  5. 5.Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnologyJiangsu Academy of Agricultural SciencesNanjingChina
  6. 6.Institute for Post Graduate Environmental Studies, Environmental Science DepartmentArish UniversityNorth SinaiEgypt

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