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Phylogenetic analysis, molecular characterization and virulence profiling based on toxoflavin gene of an Indian BG1 strain of Burkholderia glumae causing panicle blight of rice

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Abstract

Bacterial panicle blight (BPB) caused by Burkholderia glumae (BG) has become significantly more prevalent in the rice-growing regions of North India. Based on virulence screening and in vitro quantification of toxoflavin, the BG strains were classified as hyper- (BG1 and BG3), moderate- (BG2, BG4, BG6, BG8, and BG9), and hypo- (BG5, BG7, and BG10) virulent. Plant inoculation assays with cell-free culture filtrate revealed strains with higher toxoflavin-producing ability had higher virulence. Based on 16S rRNA sequence, 6 isolates from Uttar Pradesh were grouped in clad C1; whereas, clad C2 exhibited 4 isolates, two each from Delhi and Uttar Pradesh. Strain BG1 being the most virulent Indian strain from Uttar Pradesh was further profiled for 11 tox genes. We found all the 11 tox genes present in strain BG1. In toxRABCDE cluster, all tox genes showed high similarity to B. glumae BGR1 except toxB, whereas in toxFGHIJ cluster toxF, toxG, toxH and toxI shared maximum similarity to B. glumae 336gr-1. tox genes of BG1 exhibited homology as well as divergence with B. gladioli. The domain prediction and protein association network analysis indicated the possible involvement of tox genes in the toxoflavin biosynthesis. As per our knowledge, this is the first report in India on characterization of tox genes cluster in B. glumae. Altogether, our study unravels a reliable method for identifying and characterizing B. glumae using tox genes and its relationship with disease production.

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Data availability

All the 16srRNA sequence data and tox gene sequence data has been submitted to NCBI under the accession number mentioned in the Table 1.

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Acknowledgements

The authors are grateful to the Plant Bacteriology lab, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi for providing all the necessary infrastructure and materials so that the study could be conducted. No external financial assistance was provided for the study.

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The authors declare that no funds, grants, or other support were received during the research work and preparation of this manuscript.

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Authors and Affiliations

  1. Division of Plant Pathology, ICAR, Indian Agricultural Research Institute, New Delhi, India

    Sanjeev Kumar, Kalyan K. Mondal, Thungri Ghoshal, Aditya Kulshreshtha, B. Sreenayana, M. Amrutha Lakshmi, S. Mrutyunjaya, E. R. Rashmi, N. S. Kalaivanan & Chandra Mani

  2. Division of Agricultural Chemicals, ICAR, Indian Agricultural Research Institute, New Delhi, India

    Aditi Kundu

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  1. Sanjeev Kumar
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  2. Kalyan K. Mondal
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Contributions

KKM: Conceptualized the research, supervised, analyzed the data and edited the MS; SK, ALM: Associated with data analysis, writing of draft manuscript; AK Estimation of toxoflavin; SK: performed research activities including BG isolation and DNA extraction; AK, SB, ALM, MS: Virulence analysis, Submission of the tox gene and 16 s sequence data; MS, RER, KNS, SK: amplification of the tox genes, and CM, TG, AK: maintained the BG strain, helped in raising the rice crops and inoculation.

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Correspondence to Kalyan K. Mondal.

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Experimental research and field studies on plants (either cultivated or wild), including the collection of plant material complies with relevant institutional (ICAR—Indian Institute of Agricultural Research, New Delhi, India), national, and international guidelines and legislations.

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Kumar, S., Mondal, K.K., Ghoshal, T. et al. Phylogenetic analysis, molecular characterization and virulence profiling based on toxoflavin gene of an Indian BG1 strain of Burkholderia glumae causing panicle blight of rice. 3 Biotech 13, 239 (2023). https://doi.org/10.1007/s13205-023-03660-6

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