Genetic and evolutionary mechanisms of endogenous viral elements in kelp

Endogenous viral elements (EVEs) are viral DNA integrated into host genomes and inherited across generations. They include active viruses and a wide range of viral fragments - many lose functionality, but some are co-opted for host functions. Previous studies, including those by the candidate, have revealed a complex landscape of EVEs in brown algal genomes, including both intact and fragmented forms related to giant viruses (Nucleocytoviricota). EVEs could drive rapid evolution in brown algae, yet their mechanisms and impacts remain largely unexplored. Their study has been limited by a lack of multi-individual genomic data, and integration with functional data. Understanding EVE dynamics is urgent in the context of climate change, which threatens key brown algal ecosystem engineers and aquaculture species like kelp. The EVOKE project will integrate genomic, transcriptomic, and functional approaches across multiple individuals of the kelp Saccharina latissima. The applicant brings a combination of expertise in brown algal biology and EVEs, complemented by the host PI’s leading expertise in eukaryotic bioinformatics and virology. Secondment partners provide expertise in kelp culturing. EVOKE will address how EVEs contribute to kelp genomes with the following Research Objectives (RO): (RO1) Characterise the genetic diversity and evolutionary mechanisms of EVEs, (RO2) Determine patterns of EVE transcriptional activity across host development, environmental stress, and virus replication, (RO3) Assess functional host impacts of EVE activity, integrating transcriptomics and cell-based assays. EVOKE will provide insights into the role of EVEs in algal biology, informing strategies for enhancing kelp resilience under climate stress, and providing a framework and genomic datasets to advance EVE study. It will enable the applicant to lead an interdisciplinary genomic project, acquire advanced training in virology, and advance their own line of research in viral evolution.