Functional & Integrative Genomics

, Volume 19, Issue 3, pp 391–407 | Cite as

Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat

  • Himanshu Dubey
  • Kanti Kiran
  • Rajdeep Jaswal
  • Priyanka Jain
  • Arvind M Kayastha
  • Subhash C Bhardwaj
  • Tapan Kumar Mondal
  • Tilak Raj SharmaEmail author
Original Article


Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1–1.28 million potential sRNAs and two microRNA-like small RNA (mil-RNAs) candidates were identified. Computational prediction of targets using a common set of sRNAs and P. triticina mil-RNAs (pt-mil-RNAs) within P. triticina and wheat revealed the majority of the targets as repetitive elements in P. triticina whereas in wheat, the target genes were identified to be involved in many biological processes including defense-related pathways. We found 9 receptor-like kinases (RLKs) and 14 target genes of each related to reactive oxygen species (ROS) pathway and transcription factors respectively, including significant numbers of target genes from various other categories. Expression analysis of twenty selected sRNAs, targeting host genes pertaining to ROS related, disease resistance, metabolic processes, transporter, apoptotic inhibitor, and transcription factors along with two pt-mil-RNAs by qRT-PCR showed distinct patterns of expression of the sRNAs in urediniospore-specific libraries. In this study, for the first time, we report identification of novel sRNAs identified in P. triticina including two pt-mil-RNAs that may play an important role in biotrophic growth and pathogenicity.


Puccinia triticina Rust pathogen Small RNA sequencing Pathogenicity 



TRS is thankful to the Department of Science and Technology, Govt. of India, for JC Bose National Fellowship. HD is thankful to the University Grants Commission (UGC), New Delhi, for providing Junior Research Fellowship (JRF).

Author contributions

TRS conceived and designed the experiments, HD generated data, and HD and PJ performed computational analysis. HD, KK, and RJ performed biological experiments, SCB contributed in providing biological material, and AMK and TKM provided input during manuscript writing. HD, KK, and TRS wrote the manuscript.

Supplementary material

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Copyright information

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

Authors and Affiliations

  • Himanshu Dubey
    • 1
    • 2
  • Kanti Kiran
    • 1
  • Rajdeep Jaswal
    • 3
  • Priyanka Jain
    • 1
  • Arvind M Kayastha
    • 2
  • Subhash C Bhardwaj
    • 4
  • Tapan Kumar Mondal
    • 1
  • Tilak Raj Sharma
    • 1
    • 3
    Email author
  1. 1.ICAR-National Research Centre on Plant Biotechnology, Pusa CampusNew DelhiIndia
  2. 2.School of Biotechnology, Institute of ScienceBanaras Hindu UniversityVaranasiIndia
  3. 3.National Agri-Food Biotechnology Institute (NABI)MohaliIndia
  4. 4.ICAR-Indian Institute of Wheat and Barley Research, Regional StationShimlaIndia

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