The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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Genome Wide Analysis of the Potato Soft Rot Pathogen Pectobacterium carotovorum Strain ICMP 5702 to Predict Novel Insights into Its Genetic Features

  • Mallick, Tista (Department of Biotechnology, Rama Devi Women's University) ;
  • Mishra, Rukmini (School of Applied Sciences, Centurion University of Technology and Management) ;
  • Mohanty, Sasmita (Department of Biotechnology, Rama Devi Women's University) ;
  • Joshi, Raj Kumar (Department of Biotechnology, Rama Devi Women's University)
  • Received : 2021.12.28
  • Accepted : 2022.02.07
  • Published : 2022.04.01
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Abstract

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a gram-negative, broad host range bacterial pathogen which causes soft rot disease in potatoes as well as other vegetables worldwide. While Pectobacterium infection relies on the production of major cell wall degrading enzymes, other virulence factors and the mechanism of genetic adaptation of this pathogen is not yet clear. In the present study, we have performed an in-depth genome-wide characterization of Pcc strain ICMP5702 isolated from potato and compared it with other pathogenic bacteria from the Pectobacterium genus to identify key virulent determinants. The draft genome of Pcc ICMP5702 contains 4,774,457 bp with a G + C content of 51.90% and 4,520 open reading frames. Genome annotation revealed prominent genes encoding key virulence factors such as plant cell wall degrading enzymes, flagella-based motility, phage proteins, cell membrane structures, and secretion systems. Whereas, a majority of determinants were conserved among the Pectobacterium strains, few notable genes encoding AvrE-family type III secretion system effectors, pectate lyase and metalloprotease in addition to the CRISPR-Cas based adaptive immune system were uniquely represented. Overall, the information generated through this study will contribute to decipher the mechanism of infection and adaptive immunity in Pcc.

Keywords

Acknowledgement

The authors are thankful to Vice Chancellor, Rama Devi Women's University for her guidance and support. Dr Joshi's lab is supported by research grants from the Dept. of Biotechnology (BT/PR23412/BPA/118/284/2017), Govt of India and Science and Engineering Research Board (SERB) (EMR/2016/005234), Dept. of Science & Technology (DST), Govt of India.

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