Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits

  • Hande Morgil
  • Mehmet Tardu
  • Gül Cevahir
  • İbrahim Halil KavakliEmail author
Original Article


Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.


Lentil Drought stress Roots Leaf De novo RNA-seq 



We would like to thank the Southeastern Anatolia Agricultural Research Institute providing us the seed of Lens culinaris Medik. cv. Sultan.

Author contributions

HM and MT carried out the experiments. MT performed the analysis. MT, HM, and GC contributed in writing the manuscript. IHK designed the experiments and wrote the manuscript.


This work was supported by an Istanbul Development Agency grant (ISTKA-TR/14/EVK/0039) to IHK, and by an Istanbul University BAP project (21207, 22583) to GC and IHK.

Supplementary material

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Figure S1 (PDF 226 kb)
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Figure S2 (PNG 289 kb)
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Table S1 (XLSX 10 kb)
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Table S2 (XLSX 9 kb)
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Table S3 Gene annotation from Swiss-Port (XLS 15017 kb)
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Table S4 Gene annotation from UniRef (XLS 15453 kb)
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Table S5 (XLSX 73 kb)
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Table S7 Identified DEGs in all samples (XLSX 2623 kb)
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Table S8 (XLSX 13 kb)
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Table S9 (XLSX 37 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Hande Morgil
    • 1
  • Mehmet Tardu
    • 2
  • Gül Cevahir
    • 1
  • İbrahim Halil Kavakli
    • 2
    • 3
    Email author
  1. 1.Department of BiologyIstanbul UniversityIstanbulTurkey
  2. 2.Department of Chemical and Biological EngineeringKoc UniversityIstanbulTurkey
  3. 3.Department of Molecular Biology and GeneticsKoc UniversityIstanbulTurkey

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