HI-PHY: PHYTOMYXID-HOST-INTERACTIONS

Phytomyxea (phytomyxids; Endomyxa, Rhizaria) are obligate, biotrophic protist parasites of plants, diatoms, oomycetes and brown algae and are best known as pathogens or vectors for viruses of arable crops (e.g. clubroot in brassicas, powdery potato scab, and rhizomania in sugar beet). They are inseparable from their hosts; hence phytomyxid biology and phytomyxid-host-interactions are notoriously difficult to study. HI-PHY aims to overcome these restraints by combining comparative transcriptome analyses with in-situ transcript visualisation. HI-PHY will aim to answer fundamental, longstanding questions related to phytomyxid-host-interactions by identifying key genetic processes in the transcriptome data, and by then monitoring and resolving these processes on the cellular level using FISH methods. The main aims of HI-PHY are (i) to identify shared and monopolised processes in pathogen defence in taxonomically different hosts; (ii) to discriminate phytomyxid induced local and systemic changes in the host, hereby evaluating the impact of phytomyxids on the host fitness and (iii) to generate fundamental insights into the biology of phytomyxids and life cycle related processes. Transcriptomes of the clubroot pathogen Plasmodiophora brassicae (in its host Arabidopsis thaliana), Maullinia ectocarpii (in its host, the brown algae Ectocarpus fasciculatus), and Woronina pythii (in its oomycete host Pythium sp.) will be generated and analysed. This will result in the first direct comparison of the phytomyxid orders Plasmodiophorida (P. brassicae, W. pythii) and Phagomyxida (M. ectocarpii) which will significantly expand our understanding of phytomyxid biology and genetics. But more importantly, these transcriptomes provide the unique opportunity for a targeted comparison of pathogen response in angiosperms (A. thaliana) and stramenopiles (E. fasciculatus, Pythium spp.), potentially revealing fundamental genetic processes of eukaryotes. These transcriptome data alone will already tremendously increase our knowledge on phytomyxid-host-interactions. Such analyses, however, can only provide a snap-shot of the transcriptional processes at the time point of sampling. Hence a major aim of HI-PHY is to link mRNA signals to specific host cells and specific life cycle stages of the parasite, using high resolution FISH methods. This will lay the foundation for spatiotemporal analyses of mRNAs while concurrently linking transcripts and their respective function to specific host cells and to phytomyxid life cycle stages. Subsequently these findings will be complemented by transcriptome data and accompanying FISH analyses of phytomyxid-host- interactions subjected to abiotic stress. This will help to understand the importance of key genetic processes during infection and host colonisation, but will also considerably increase our knowledge of the impact of phytomyxid infection on host fitness. The novel, and innovative combination of transcriptome analyses and in-situ transcript visualisiation forming the basis of HI-PHY will permit fundamental, novel insights into phytomyxid biology and eukaryote pathogen defence and cell biology, massively increasing our knowledge about an enigmatic, but important group of eukaryote parasites.

Phytomyxea, microscopic parasites affecting plants, brown algae, and oomycetes play a crucial role in ecosystems and agriculture, often acting as pathogens and virus carriers that threaten valuable crops. The HI-PHY Project (Phytomyxid Host Interactions) delivered novel findings on their taxonomy, genetics, and biology, improving our understanding of these enigmatic organisms and emphasising their broader ecological and economic significance. Phytomyxea are now recognized as part of the eukaryotic group Rhizaria which is unrelated to other groups of plant pathogens such as fungi. Plasmodiophora brassicae exemplifies the serious agricultural threat posed by phytomyxean plant pathogens, responsible for a 10% reduction in global brassica production. The HI-PHY Project discovered new species parasitizing kelps, resurrected historical records of species not seen for decades, and highlighted their widespread presence in both agricultural and natural ecosystems. Our discoveries and new collections have allowed for a more precise classification of Phytomyxea and a greater understanding of their environmental adaptations. The project illuminated the intricate interactions between Phytomyxea and their hosts, focusing on how they extract nutrients and alter energy dynamics. Through HI-PHY's findings, it was determined that phagocytosis plays a vital role in the nutrition of the growing parasite by absorbing nutrients from plant and stramenopile hosts and inducing energy-draining changes in host tissue. Investigations into circadian rhythms in photosynthetic hosts, such as Arabidopsis thaliana and the marine alga Ectocarpus siliculosus, demonstrate how Phytomyxea disrupt host energy cycles, offering insights into parasite-host relationships. HI-PHY provided entirely new genomic and transcriptomic data, opening doors for future studies to explore the intricate details of these organisms' biology. Using single-molecule RNA techniques, the team tracked communication between parasite and host throughout the infection cycle, overcoming long-standing challenges in studying these obligate biotrophs with intricate life stages. By redefining the taxonomy and ecological understanding of Phytomyxea, the HI-PHY Project has laid a critical foundation for addressing their agricultural impact and their ecological significance. These discoveries could open doors to innovative research and strategies for managing these parasites, advancing both science and sustainable agriculture.