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 ChakdarEmail author
  • Alok Kumar Srivastava
  • Anil Kumar Saxena
Original Research Article


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.


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



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)


  1. 1.
    Siciliano I, Ortu G, Gilardi G, Gullino ML, Garibaldi A (2015) Mycotoxin production in liquid culture and on plants infected with Alternaria spp. isolated from rocket and cabbage. Toxins 7(3):743–754CrossRefGoogle Scholar
  2. 2.
    Scott PM (2001) Analysis of agricultural commodities and foods for Alternaria mycotoxins. J AOAC Int 84:1809–1817PubMedGoogle Scholar
  3. 3.
    Valueva TA, Kudryavtseva NN, Sofyin AV et al (2015) Serine exoproteinases secreted by the pathogenic fungi of Alternaria genus. J Plant Pathol Microb. 6:6CrossRefGoogle Scholar
  4. 4.
    Weidenborner M (2001) Encyclopedia of food mycotoxins. Springer, DordrechtCrossRefGoogle Scholar
  5. 5.
    Haggblom P, Niehans WG (1986) Light effects on polyketide metabolism in Alternaria alternata. Exp Mycol 10:252–255CrossRefGoogle Scholar
  6. 6.
    Dutkiewicz L (1997) Bacteria and fungi in organic dust as potential health hazard. Ann Agric Environ Med 4:11–16Google Scholar
  7. 7.
    Field D, Wills C (1998) Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc Natl Acad Sci USA 95(4):1647–1652CrossRefGoogle Scholar
  8. 8.
    Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981CrossRefGoogle Scholar
  9. 9.
    Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function and evolution. Mol Biol Evol 21(6):991–1007CrossRefGoogle Scholar
  10. 10.
    Huang TS, Lee CC, Chang AC et al (2003) Shortening of microsatellite deoxy (CA) repeats involved in GL331-induced down-regulation of matrix metalloproteinase-9 gene expression. Biochem Biophys Res Commun 300(4):901–907CrossRefGoogle Scholar
  11. 11.
    Weiser JN, Love JM, Moxon ER (1989) The molecular mechanism of phase variation of H. influenzae lipopolysaccharide. Cell 59:657–665CrossRefGoogle Scholar
  12. 12.
    Grover A, Aishwarya V, Sharma PC (2007) Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genom 277(5):469–480CrossRefGoogle Scholar
  13. 13.
    Baron Samuel (1996) Medical microbiology, 4th edn. Medical Branch at Galveston, University of Texas, Galveston (ISBN 10: 0-9631172-1-1) Google Scholar
  14. 14.
    Genome (2004) National Library of Medicine (US), National Center for Biotechnology Information, Bethesda. Accessed 30 June 2016
  15. 15.
    Martins WS, Lucas DCS, Neves KFS, Bertioli DJ (2009) WebSat—a web software for microsatellite marker development. Bioinformation 3(6):282–283CrossRefGoogle Scholar
  16. 16.
    Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(Suppl 1):10.1–10.12CrossRefGoogle Scholar
  17. 17.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefGoogle Scholar
  18. 18.
    Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30CrossRefGoogle Scholar
  19. 19.
    Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associate with non-repetitive DNA in plant genomes. Nat Genet 30:194–200CrossRefGoogle Scholar
  20. 20.
    Grover A, Sharma PC (2011) Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution? Curr Sci 100:6Google Scholar
  21. 21.
    Qu J, Huang C, Zhang J (2015) Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene 575(2 Pt 2):524–530PubMedGoogle Scholar
  22. 22.
    Saha D, Fetzner R, Burkhardt B et al (2012) Identification of a polyketide synthase required for alternariol (AOH) and alternariol-9-methyl ether (AME) in Alternaria alternata. PLoS One 7(7):e40564CrossRefGoogle Scholar
  23. 23.
    Zhao J, Liu K, Lu J et al (2012) Alternariol induces DNA polymerase β expression through the PKA-CREB signaling pathway. Int J Oncol 40:1923–1928PubMedGoogle Scholar
  24. 24.
    Zhao J, Ma J, Lu J et al (2016) Involvement of p38MAPK–ATF2 signaling pathway in alternariol induced DNA polymerase β expression. Oncol Lett 12:675–679CrossRefGoogle Scholar
  25. 25.
    Dong ZM, Zheng NG, Wu JL, Li SK, Wang YL (2006) Difference in expression level and localization of DNA polymerase beta among human esophageal cancer focus, adjacent and corresponding normal tissues. Dis Esophagus 19:172–176CrossRefGoogle Scholar
  26. 26.
    Tan XH, Zhao M, Pan KF et al (2005) Frequent mutation related with overexpression of DNA polymerase beta in primary tumors and precancerous lesions of human stomach. Cancer Lett 220:101–114CrossRefGoogle Scholar
  27. 27.
    Albertella MR, Lau A, O’Connor MJ (2005) The overexpression of specialized DNA polymerases in cancer. DNA Repair 4:583–593CrossRefGoogle Scholar
  28. 28.
    Wang H, Jones C, Zanella JC, Holt T, Gilchrist DG, Dickman MB (1996) Fumonisins and Alternaria alternata lycopersici toxins: Shinganine analog mycotoxins induce apoptosis in monkey kidney cells. Proc Natl Acad Sci USA 93:3461–3465CrossRefGoogle Scholar
  29. 29.
    Gené J, Azón-Masoliver A, Guarro J, Ballester F, Pujol I, Llovera M, Ferrer C (1995) Cutaneous phaeohyphomycosis caused by Alternaria longipes in an immunosuppressed patient. J Clin Microbiol 33(10):2774–2776PubMedPubMedCentralGoogle Scholar
  30. 30.
    Liu GT, Qian YZ, Zhang P, Dong WH, Qi YM, Guo HT (1992) Etiological role of Alternaria alternata in human esophageal cancer. Chin Med J 105(5):394–400PubMedGoogle Scholar
  31. 31.
    Zhen YZ, Xu YM, Liu GT et al (1991) Mutagenicity of Alternaria alternata and Penicillium cyclopium isolated from grains in an area of high incidence of oesophageal cancer–Linxian, China. IARC Sci Publ 105:253–257Google Scholar
  32. 32.
    Romano C, Valenti L, Miracco C et al (1997) Two cases of cutaneous phaeohyphomycosis by Alternaria alternata and Alternaria tenuissima. Mycopathologia 137:165CrossRefGoogle Scholar
  33. 33.
    Bush RK, Prochnau JJ (2004) Alternaria-induced asthma. J Allergy Clin Immunol 113(2):227–234CrossRefGoogle Scholar
  34. 34.
    Burkhardt B, Pfeiffer E, Metzler M (2009) Absorption and metabolism of the mycotoxins alternariol and alternariol-9-methyl ether in Caco-2 cells in vitro. Mycotoxin Res 25(3):149–157CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Prassan Choudhary
    • 1
  • Prem Lal Kashyap
    • 2
  • Sanjay Kumar Goswami
    • 1
  • Hillol Chakdar
    • 1
    Email author
  • 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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