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Functional & Integrative Genomics

, Volume 19, Issue 3, pp 453–465 | Cite as

Transcriptomics analysis of propiconazole-treated Cochliobolus sativus reveals new putative azole targets in the plant pathogen

  • Deepika Somani
  • Ragini Adhav
  • Ramya Prashant
  • Narendra Y. KadooEmail author
Original Article

Abstract

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is a filamentous fungus from the class Dothideomycetes. It is a pathogen of cereals including wheat and barley, and causes foliar spot blotch, root rot, black point on grains, head blight, leaf blight, and seedling blight diseases. Annual yields of these economically important cereals are severely reduced due to this pathogen attack. Evolution of fungicide resistant pathogen strains, availability of a limited number of potent antifungal compounds, and their efficacy are the acute issues in field management of phytopathogenic fungi. Propiconazole is a widely used azole fungicide to control the disease in fields. The known targets of azoles are the demethylase enzymes involved in ergosterol biosynthesis. Nonetheless, azoles have multiple modes of action, some of which have not been explored yet. Identifying the off-target effects of fungicides by dissecting gene expression profiles in response to them can provide insights into their modes of action and possible mechanisms of fungicide resistance. Moreover it can also reveal additional targets for development of new fungicides. Hence, we analyzed the global gene expression profile of C. sativus on exposure to sub-lethal doses of propiconazole in a time series. The gene expression patterns were confirmed using quantitative reverse transcriptase PCR (qRT-PCR). This study revealed overexpression of target genes from the sterol biosynthesis pathway supporting the reported mode of resistance against azoles. In addition, some new potential targets have also been identified, which could be explored to develop new fungicides and plant protection strategies.

Keywords

Bipolaris sorokiniana Cochliobolus sativus Fungicide resistance Propiconazole RNA-seq Transcriptomics analysis 

Abbreviations

ABC

ATP binding cassette

CPM

Counts per million

DEGs

Differentially expressed genes

EC50

Effective concentration to give half maximal response

FPKM

Fragments per kilobase million

Hpt

Hours post treatment

KEGG

Kyoto Encyclopedia of Genes and Genomes

LFC

Log2 fold change

NCBI

National Center for Biotechnology Information

PDA

Potato dextrose agar

qRT-PCR

Quantitative reverse transcriptase polymerase chain reaction

Notes

Acknowledgements

DS acknowledges the Junior and Senior Research fellowships from the University Grants Commission (UGC), India. The authors thank Dr. Rajeev Kumar, Dept. of Agricultural Biotechnology & Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa (India) for providing the D2 isolate of C. sativus and Dr. I.K. Kalappanwar, Dept. of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad (India) for help in microscopic identification of the pathogen. The Centre for Cellular and Molecular Platforms (C-CAMP), Bangalore (India) is acknowledged for RNA sequencing.

Funding

NK received financial support in the form of Council of Scientific and Industrial Research (CSIR), India (BSC 0117) and RP received financial support from Department of Biotechnology (DBT), India (GAP 304126).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

10142_2019_660_Fig8_ESM.png (2.4 mb)
Fig S1

Radial growth inhibition assay using PDA plates. a) Top and bottom view of culture at 2 ppm – 32 ppm concentration of propiconazole. b) Comparison of culture at 16 ppm and 32 ppm concentration of propiconazole with respect to control (picture taken on 6th day after inoculation) (PNG 2414 kb)

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High Resolution Image (TIF 3163 kb)
10142_2019_660_Fig9_ESM.png (326 kb)
Fig S2

Functional classification of differentially expressed transcripts (CC: Cellular Component, MF: Molecular Function, BP: Biological Process) (PNG 326 kb)

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High Resolution Image (TIF 409 kb)
10142_2019_660_Fig10_ESM.png (976 kb)
Fig S3

KEGG annotation of enzymes from DEGs to respective pathways at: (a) 3 hpt; (b) 6 hpt and (c) 12 hpt (PNG 976 kb)

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High Resolution Image (TIF 1367 kb)
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Fig S4

Functional protein association network of DEGs at 3 hpt, 6 hpt and 12 hpt from propiconazole treated culture (PNG 5774 kb)

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High Resolution Image (TIF 7689 kb)
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Fig S5

Fold change pattern of genes of steroid biosynthesis pathway. The numbers on Y-axis indicate the log2 fold change values (PNG 538 kb)

10142_2019_660_MOESM5_ESM.tif (637 kb)
High Resolution Image (TIF 637 kb)
10142_2019_660_MOESM6_ESM.xlsx (475 kb)
ESM 1 (XLSX 474 kb)

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Copyright information

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

Authors and Affiliations

  1. 1.Biochemical Sciences DivisionCSIR-National Chemical LaboratoryPuneIndia
  2. 2.Academy of Scientific and Innovative Research (AcSIR)New DelhiIndia
  3. 3.Faculty of Health ScienceUniversity of MacauMacauChina

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