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Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires

Summary

Researchers sequenced the genome of Phytophthora theobromicola, a newly discovered fungal pathogen that causes serious cacao plant disease. They found the pathogen’s genome is highly variable among different isolates and contains many genes that help it attack cacao plants. By studying which of these harmful genes are active during infection, they identified specific virulence factors unique to this cacao pathogen that could be important targets for future disease control strategies.

Background

Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil causing aggressive black pod rot disease. The worldwide chocolate industry loses up to 38% of annual cacao production to disease, with over half attributed to Phytophthora species. Understanding the genome structure and virulence mechanisms of this pathogen is essential for developing effective disease management strategies.

Objective

This study generated comprehensive genome assemblies for P. theobromicola isolates using long-read and short-read sequencing technologies. The research aimed to characterize the genome structure, effector repertoires, and identify lineage-specific virulence factors through comparative analysis with other Phytophthora species.

Results

The analysis revealed a highly dynamic P. theobromicola genome with 47.5-45.6 Mbp haploid size comparable to P. citrophthora. Intraspecies sequence-graph analysis identified substantial variability in effector content, with 84% core effectors and 15.5% dispensable effectors. Transcriptome analysis showed 88% of predicted effectors were expressed during infection, with lineage-specific RxLRs and CAZymes particularly enriched in cacao pathogen-specific syntenic groups.

Conclusion

The study highlights the dynamic architecture and functional plasticity of the P. theobromicola genome, with lineage-specific effectors potentially playing key roles in cacao-specific host-pathogen interactions. These foundational genomic resources provide insights into virulence strategies and support future studies on host adaptation and effector evolution in emerging cacao pathogens.
  • Published in:G3 (Bethesda),
  • Study Type:Genomic Analysis and Comparative Genomics Study,
  • Source: PMID: 41140028, DOI: 10.1093/g3journal/jkaf256
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