Transcriptome-based mining and expression profiling of Pythium responsive transcription factors in Zingiber sp.

  • Vishnu Sukumari Nath
  • Sayuj Koyyappurath
  • Teena Elizabeth Alex
  • Kiran Ayyanperumal Geetha
  • Lesly Augustine
  • Alka Nasser
  • George ThomasEmail author
Original Article


Transcription factors (TFs) fine-tune the host defense transcriptome in response to pathogen invasions. No information is available on Zingiber zerumbet (Zz) TFs involved in defense response against Pythium myriotylum. Here, we provide a global identification, characterization, and temporal expression profiling of Zz TFs following an incompatible interaction with P. myriotylum using a transcriptome sequencing approach. We identified a total of 903 TFs belonging to 96 families based on their conserved domains. Evolutionary analysis clustered the Zz TFs according to their phylogenetic affinity, providing glimpses of their functional diversities. High throughput expression array analysis highlighted a complex interplay between activating and repressing transcription factors in fine-tuning Zz defense response against P. myriotylum. The high differential modulation of TFs involved in cell wall fortification, lignin biosynthesis, and SA/JA hormone crosstalk allows us to envisage that this mechanism plays a central role in restricting P. myriotylum proliferation in Zz. This study lays a solid foundation and provides valuable resources for the investigation of the evolutionary history and biological functions of Zz TF genes involved in defense response.


Biotic stress Defense response Ginger Plant-pathogen interaction Transcriptional reprogramming 



VSN and LA gratefully acknowledge Kerala State Council for Science, Technology and Environment (KSCSTE), Government of Kerala Post-Doctoral Fellowship (Award No: 001-11/PDF/2016/KSCSTE) and research fellowship (Award No. 010-55/FHSP/2010/CSTE), respectively. SK thanks Science and Engineering Research Board (SERB), Government of India for National Post-Doctoral Fellowship (File No. PDF/2017/002022). KG gratefully acknowledges Council for Scientific and Industrial Research (CSIR), Government of India for research fellowship (F. No. 9/716(0103)/2008- EMR-I). GT acknowledges CSIR, Government of India for a research grant (No. 38(1397)/14EMR-II). We thank the anonymous reviewers for their valuable comments in improving the manuscript.

Authors’ contributions

VSN executed the bioinformatics pipelines, performed data analysis, and drafted the manuscript. SK contributed to the bioinformatics analysis and drafting the manuscript. TEA contributed to the data analysis. KAG performed transcriptome sequencing and assembly. LA performed microarray analysis. AN contributed to data analysis. GT conceived and supervised the study. All authors read, commented on, and approved the final version of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Plant Disease Biology and BiotechnologyRajiv Gandhi Centre for BiotechnologyThiruvananthapuramIndia
  2. 2.Department of Molecular GeneticsInstitute of Plant Molecular Biology (IPMB)České BudějoviceCzech Republic
  3. 3.Department of Genome Structural Biology, Temasek Life Science Laboratory, 1-Research LinkNational University of SingaporeSingaporeSingapore
  4. 4.Department of BiotechnologyKerala Agricultural UniversityThiruvananthapuramIndia
  5. 5.Department of BotanySacred Heart CollegeErnakulamIndia

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