Tropical Plant Biology

, Volume 12, Issue 2, pp 55–66 | Cite as

RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress

  • Quandong Nong
  • Mingyong Zhang
  • Jiantong Chen
  • Mei Zhang
  • Huaping Cheng
  • Shuguang Jian
  • Hongfang Lu
  • Kuaifei XiaEmail author


Pitaya (Hylocereus polyrhizus) is a highly valued functional food that is widely planted in Southeast Asia. However, with increased soil salinization in cultivation areas, a better understanding of the molecular mechanisms associated with salt stress responses in red pitaya is necessary. Herein, RNA-Seq was used to de novo assemble and characterize the transcriptomic profiles of red pitaya roots in response to salt stress. A total of 73,589 transcripts were obtained and the average sequence length was 1308 bp. From these transcripts, 26,878 unique transcripts were successfully matched to 13,519 Swiss-prot proteins. Gene ontology (GO) annotations showed that within the categories of molecular function, biological function, and cell component, catalytic activity (GO:0003824), metabolic process (GO:0008152), and cell part (GO:0044464) were the most enriched, respectively. 2624 transcripts were significantly differentially expressed among three time points (3 h, 7 h, and 30 h) following exposure to 450 mM NaCl. Furthermore, 261 genes were up-regulated and 61 down-regulated in all three of the time points. Glycolysis/gluconeogenesis was one of the most significantly modulated pathways. The findings presented herein provide further insight into salt stress responses in pitaya and will provide a valuable resource for future functional studies examining salt adaptations.


Pitaya Salt stress RNA-Seq De novo Transcriptome 



Fold change


Gene ontology


False Discovery Rate


Coding sequence


Differentially expressed gene


Quantitative trait loci


Abscisic acid


6-phosphofructokinase 1


Phosphoglycerate kinase


Aspartate aminotransferase


Fructose-bisphosphate aldolase, class I


Squalene monooxygenase


Glyceraldehyde-3-phosphate dehydrogenase


Quantitative real-time PCR


Non-coding RNAs


Transposable elements


Salt 1


Streptomyces lividans K+ channel


Na + exclusion 1


Na + exclusion 2


Prolyl 4-hydroxylase


High-affinity K+ transporter


CCCH zinc finger protein



This project was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA13020500), the National Natural Science Foundation of China (31671659 and 31772384), the National Key Research and Development Program of China (2016YFC1403002), and the Guangzhou Science and Technology Project (201804010409).

Availability of Data and Materials Section

All the read data were available at DDBJ database (BioSample Accession no.: SAMD00115774- SAMD00115785).

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Quandong Nong
    • 1
    • 2
  • Mingyong Zhang
    • 1
  • Jiantong Chen
    • 1
    • 3
  • Mei Zhang
    • 1
    • 3
  • Huaping Cheng
    • 1
    • 3
  • Shuguang Jian
    • 3
  • Hongfang Lu
    • 3
  • Kuaifei Xia
    • 1
    • 3
    Email author
  1. 1.Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical GardenChinese Academy of SciencesGuangzhouPeople’s Republic of China
  2. 2.Wenshan Academy of Agricultural SciencesWenshanChina
  3. 3.Guangdong Provincial Key laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouPeople’s Republic of China

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