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

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Abstract

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.

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Acknowledgements

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

Funding

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.

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Author notes

  1. Hande Morgil and Mehmet Tardu contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, Istanbul University, 34134 Suleymaniye, Istanbul, Turkey

    Hande Morgil & Gül Cevahir

  2. Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey

    Mehmet Tardu & İbrahim Halil Kavakli

  3. Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Sariyer, Istanbul, Turkey

    İbrahim Halil Kavakli

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  1. Hande Morgil
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  2. Mehmet Tardu
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  3. Gül Cevahir
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  4. İbrahim Halil Kavakli
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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.

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Correspondence to İbrahim Halil Kavakli.

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Gene annotation from Swiss-Port (XLS 15017 kb)

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Gene annotation from UniRef (XLS 15453 kb)

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Identified DEGs in all samples (XLSX 2623 kb)

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Morgil, H., Tardu, M., Cevahir, G. et al. Comparative RNA-seq analysis of the drought-sensitive lentil (Lens culinaris) root and leaf under short- and long-term water deficits. Funct Integr Genomics 19, 715–727 (2019). https://doi.org/10.1007/s10142-019-00675-2

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  • DOI: https://doi.org/10.1007/s10142-019-00675-2

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