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Genetic Manipulation of the Plant Pathogen Ustilago maydis to Study Fungal Biology and Plant Microbe Interactions
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LUCID: An Integrative Approach for Target Discovery and dsRNA Design in Plant Fungal Pathogens.

Lucía Jiménez-Castro1,2, Alba López-Laguna1,2, Dolores Férnandez-Ortuño1,2

  • 1Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.

Plant Biotechnology Journal
|February 12, 2026
PubMed
Summary

A new computational tool, LUCID, accelerates the development of RNA interference (RNAi)-based biofungicides. This eco-friendly approach targets essential fungal genes, offering a sustainable solution for controlling plant diseases.

Keywords:
botrytis cinereaRNAibiofungicidescomparative genomicsdsRNAphytopathogenic fungitranscriptomics

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Area of Science:

  • Agricultural Science
  • Computational Biology
  • Mycology

Background:

  • Conventional fungicides face challenges due to resistance and environmental concerns.
  • Phytopathogenic fungi threaten global food security and ecosystem stability.
  • Double-stranded RNA (dsRNA)-based fungicides present a species-specific, eco-friendly alternative.

Purpose of the Study:

  • To introduce LUCID, a computational pipeline for rapid development of RNAi-based biofungicides.
  • To integrate target identification, dsRNA design, and off-target prediction.
  • To provide a scalable, species-agnostic framework for sustainable fungal disease control.

Main Methods:

  • LUCID employs a dual-branch strategy to identify Conserved Essential Proteins (CEPs) and Conserved Non-Annotated Proteins (CNAPs).
  • Utilizes transcriptomic data and comparative genomics across diverse fungal species.
  • Integrates advanced protein language models (PLMs) for novel target discovery.

Main Results:

  • Validation in Botrytis cinerea showed 67% of proposed targets were successfully silenced.
  • Achieved an average silencing efficiency of 96% in Botrytis cinerea.
  • Identified a novel pathogenicity determinant in B. cinerea, a putative mediator complex protein.

Conclusions:

  • LUCID accelerates the design of effective and sustainable RNAi-based biofungicides.
  • The pipeline enables targeted control of fungal diseases with minimal ecological impact.
  • LUCID offers a promising framework for future development of eco-friendly crop protection strategies.