Bioinformatics Approaches for Disease Diagnosis in Plants

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Authors

  • Section of Extension and Social Sciences, ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram-695017, Kerala ,IN

Keywords:

Bioinformatics, Plant disease diagnosis, NGS, Metagenomics, System biology.

Abstract

To study the interactions between plants and their disease-causing pathogens under diverse environmental conditions, wide range of tools and techniques are employed. These include traditional microbiological methods, high-throughput DNA sequencing, metagenomics, molecular biological approaches, functional genomics, metabolomics, and advanced microscopic techniques. But, tools like bioinformatics and data analysis empower the researchers to unravel the complex mechanisms of pathogen interaction and helps in precise diagnosis in plants, ultimately contributing to crop resilience and sustainable agriculture. The present review provides comprehensive approaches to the appropriate bioinformatic tools and supply clues on mechanisms of pathogen pathogenicity and plant immunity as well as strategies on the diagnosis and treatment of plant disease.

Published

2024-10-24

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References

Adams, I. P., Glover, R. H., Monger, W. A., Mumford, R., Jackeviciene, E. et al. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol. Plant Pathol., 10(4): 537-545. https: //doi.org/10.1111/j.1364-3703.2009.00545.x

Knief C. 2014. Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci., 5: 216. doi: 10.3389/fpls.2014.00216

Ko, G., Kim P.-G., Yoon J., Han G., Park S.-J. et al. 2018. Bioinformatics workflow system for the analysis of massive sequencing data. BMC Bioinformatics, 19: 43. https://doi.org/10.1186/s12859-018-2019-3

Mishra, B., Kumar, N. and Mukhtar, M. S., 2019. Systems biology and machine learning in plant-pathogen interactions. Mol. Plant Microbe Interact., 32(1): 45-55. doi: 10.1094/MPMI-08-18-0221-FI

Patel, R., Mitra, B., Vinchurkar, M., Adami, A., Patkar, R. et al. 2022. A review of recent advances in plant-pathogen detection systems. Heliyon, 8(12): e11855. doi: 10.1016/j.heliyon.2022.e11855

Shoaib, M., Shah, B., Ei-Sappagh, S., Ali, A., Ullah, A. et al. 2023. An advanced deep learning models-based plant disease detection: a review of recent research. Front. Plant Sci., 14: 1158933. doi: 10.3389/fpls.2023.1158933

Sperschneider, J. 2020. Machine learning in plant-pathogen interactions: empowering biological predictions from field scale to genome scale. New Phytol., 228(1): 35-41. doi: 10.1111/nph.15771

Thompson, J. D., Higgins, D. G. and Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22(22): 4673-4680. doi: 10.1093/nar/22.22.4673

Van der Auwera, G. A. and O’Connor, B. D. 2020. Genomics in the Cloud: using Docker, GATK, and WDL in Terra. O’Reilly Media, 496 pp.