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

Authors: GARCIA, JORDAN - University Of California; FIGUEROA-BALDERAS, ROSA - University Of California; Puig, Alina; BARUAH, INDRANI - Orise Fellow; MATSON, MICHAEL - Mars, Inc; ALI, SHAHIN - Orise Fellow; BAILEY, BRYAN - Retired ARS Employee; MARELLI, JEAN-PHILIPPE - Mars, Inc; CANTU, DARIO - University Of California

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/21/2025
Publication Date: 10/27/2025
Citation: Garcia, J.F., Figueroa-Balderas, R., Puig, A.S., Baruah, I.K., Matson, M., Ali, S.S., Bailey, B.A., Marelli, J., Cantu, D. 2025. Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires. G3: Genes, Genomes, Genetics. https://doi.org/10.1101/2025.07.17.665439.
DOI: https://doi.org/10.1101/2025.07.17.665439

Interpretive Summary: Black pod disease, caused by several Phytophthora species, threatens cacao production worldwide, causing pod rot, stem cankers, and branch dieback with losses exceeding 30%. This endangers global supply chains and the multibillion-dollar chocolate industry, which relies heavily on cacao imports—especially in the United States. A newly identified, highly aggressive strain has emerged in Brazil, prompting researchers to investigate how it infects cacao and bypasses plant defenses. By analyzing the pathogen’s genome and how its genes behave during infection, researchers identified proteins that weaken cacao’s defenses and allow the pathogen to invade, particularly in the pods. A major finding was the scale and activity of the pathogen’s genetic arsenal, which enables rapid defeat of cacao’s defenses and raises concern for spread to other growing regions. These insights are vital for scientists, farmers, and industry stakeholders working to protect cacao crops and stabilize chocolate production.

Technical Abstract: Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil as an aggressive agent of black pod rot. We generated genome assemblies for two P. theobromicola isolates using long-read sequencing and five additional isolates using short reads. Comparative analysis revealed a genome size and predicted gene content comparable to P. citrophthora, a closely related species with a broad host range that includes both citrus and cacao. An intraspecies sequence-graph analysis revealed a highly dynamic genome structure with high proportion of variable effectors. Syntenic orthology analysis across 13 Phytophthora species identified orthologous gene groups conserved only in cacao pathogens and others specific to P. theobromicola. RxLR effectors and CAZymes were particularly enriched among lineage-specific syntenic groups, with RxLRs preferentially located near transposable elements and within gene-sparse, repeat-rich regions. Transcriptome analysis of infected cacao tissues showed that 88% of predicted effectors were expressed, with pods exhibiting the highest number of upregulated genes. Notably, several RxLRs classified as P. theobromicola-specific syntenic orthologs were highly expressed in infected tissues, suggesting that these lineage-specific effectors may play key roles in host-pathogen interactions unique to cacao. Together, our findings highlight the dynamic architecture and functional plasticity of the P. theobromicola genome, providing foundational insights into its virulence strategies and supporting future studies on host adaptation and effector evolution in emerging cacao pathogens.