Genomic tools to investigate and characterise emerging and reemerging disease in aquatic invertebrates

Emerging and re-emerging diseases in aquatic invertebrates present significant challenges to global aquaculture, threatening food security, livelihoods, and ecosystem health. This thesis addresses critical knowledge gaps in the detection, characterisation, and management of aquatic invertebrate diseases by developing and applying a tiered genomic approach – integrating targeted, semi-targeted, and untargeted tools. By developing and validating long-amplicon sequencing methods to generate full ribosomal RNA (rRNA) arrays for key microeukaryotic pathogens of aquatic invertebrates, I improved the taxonomic resolution and enabled the design of robust diagnostic assays for closely related protist species. These methods were then applied to two closely related Marteilia species, which resolved longstanding taxonomic ambiguities and provided evidence for the separation of Marteilia refringens sensu stricto and M. pararefringens as distinct species. These results will be able to inform how infection with these species is governed by policy, and enable comparative genomic investigations into adaptive radiations between closely related taxa. Semi-targeted metagenomic approaches were used to characterise the virome of an economically important shrimp species in the context of health and disease, and characterise a novel viral pathogen associated with mortalities of a bivalve species. I report the discovery and genomic characterisation of a novel iridovirus, bivalve iridovirus 1 (BiIV1), associated with mortality events in the common cockle (Cerastoderma edule), and demonstrate that multiple pathogens and environmental stressors could contribute to poor health outcomes in bivalves. In shrimp (Penaeus monodon), comprehensive virome profiling revealed that healthy individuals harbour a richer and more diverse viral community, particularly CRESS-like viruses, than diseased counterparts, suggesting that virome composition is a critical, yet underappreciated, component of aquatic animal health. Finally, I demonstrated how mining of untargeted public sequencing datasets can be used to monitor and understand the distribution and dynamics of emerging aquatic pathogens by leveraging new databases and computational resources. This is exemplified through an in-depth meta-analysis of Macrobrachium rosenbergii golda virus (MrGV), an emerging viral threat to freshwater prawn aquaculture. This approach uncovered the global spread and host associations of MrGV, providing insights into its epidemiology and informing surveillance strategies. By utilising large-scale, cloud-enabled databases such as the Logan platform, I was able to efficiently screen hundreds of publicly available sequencing datasets – an approach that would have previously required large amounts of time, storage, and computational power Collectively, this body of work advances the application of genomic tools for the study of aquatic invertebrate diseases, challenges the “one disease, one pathogen” concept, and highlights the importance of integrating molecular, pathological, ecological, and epidemiological data. The contents of this thesis have direct implications for diagnostics, policy, and the sustainable management of aquaculture in a changing environment, paving the way for future research to understand the fundamental biology and ecology of aquatic systems using integrated genomic tools.<p></p>

Author dc:creator

• Chantelle Hooper (21064967)

• aquatic disease
• aquaculture
• genomics
• emerging disease
• bivalves
• crustaceans
• aquatic invertebrate
• cefas

Statement dc:rights

• OGL v3.0
• Open Access after 2027-12-08

Identifier

10779/exe.32578590.v1

OAI identifier oai:identifier

oai:figshare.com:article/32578590