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Genome-Wide Analysis of Microsatellites in Alternaria arborescens and Elucidation of the Function of Polyketide Synthase (PksJ)

  • Prassan Choudhary
  • Prem Lal Kashyap
  • Sanjay Kumar Goswami
  • Hillol Chakdar
  • Alok Kumar Srivastava
  • Anil Kumar Saxena
Original Research Article

Abstract

Microsatellites or simple sequence repeats (SSRs) have been the most widely applied class of molecular markers used in genetic studies, having applications in genetic conservation, population studies, as well as diagnostics of fungi. Mining and analysis of SSRs of the whole genome sequence have been carried out in this study for the fungus Alternaria arborescens causing early blight of tomato and well known for producing mycotoxins like alternariol (AOH), alternariol monomethyl ether (AME), etc. A total of 4097 microsatellites were identified in A. Arborescens genome. Contig 1 was identified as the most SSR-rich region which was further analyzed to correlate the presence of SSRs with different biological processes. A total of 246 putative genes were predicted in this study and KEGG pathway analysis of 155 predicted genes indicated that SSRs can be linked with important metabolic pathways, molecular functioning, signal transduction, and cellular processes. The prediction of fungal mycotoxin inducer gene Polyketide synthase (PksJ) linked with SSR in this study may be a potential candidate participating in oncogenic signal transduction in human. Our study is the first report of PksJ gene in A. arborescens, a precursor of AOH and AME.

Keywords

Microsatellites Alternaria arborescens Polyketide synthase (PksJ) KEGG Early blight of tomato 

Notes

Acknowledgements

The study is a part of AMAAS network project entitled “Development of microarray based gene chip for major fungal plant pathogens under the background of DNA barcodes using multi-locus gene phylogeny” with financial support from the Indian Council of Agricultural Research (ICAR).

Authors’ Contribution

All the authors have equal contribution in the collection of data, analysis, and manuscript preparation.

Compliance with Ethical Standards

Conflict of interest

The authors have declared no competing interests.

Supplementary material

12539_2017_251_MOESM1_ESM.docx (50 kb)
Supplementary material 1 (DOCX 50 kb)

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Prassan Choudhary
    • 1
  • Prem Lal Kashyap
    • 2
  • Sanjay Kumar Goswami
    • 1
  • Hillol Chakdar
    • 1
  • Alok Kumar Srivastava
    • 1
  • Anil Kumar Saxena
    • 1
  1. 1.Microbial Technology UnitICAR–National Bureau of Agriculturally Important MicroorganismsMaunath BhanjanIndia
  2. 2.ICAR–Indian Institute of Wheat and Barley Research (IIWBR), Regional StationShimlaIndia

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