Genomic characterisation of mycoviruses associated with members of ceratocystidaceae

Abstract

Plant pathogenic fungi represent a significant global threat, causing substantial economic losses in both agricultural crops and forests. Fungicide use, while common, faces challenges due to fungal resistance, as well as concerns over human and environmental health. Mycoviruses offer eco-friendly alternatives since some can attenuate fungal pathogenicity. However, despite their potential, mycoviruses remain underexplored in various fungal families and genera. This dissertation aimed to address this knowledge gap by focusing on the underrepresented fungal family Ceratocystidaceae. The first part of the study involved the identification and characterization of mycoviruses in publicly available fungal transcriptomes from this family. Datasets from public repositories often undergo poly-A selection during library preparation, resulting in the underrepresentation of mycoviruses lacking a poly-A tail, and potentially leading to truncation of some mycoviruses. To overcome this limitation, the second chapter of the study utilized ribo-depletion during library preparation to generate fungal transcriptomes for members of the genus Ceratocystis. This approach was able to resolve the complete genomes of three endornaviruses in Ceratocystis fimbriata, which had remained unresolved in earlier research. Overall, this investigation led to the identification of 28 mycoviruses across nine fungal species. The majority of these mycoviruses were single-stranded RNA viruses, and were tentatively classified into the viral families Mitoviridae, Mymonaviridae, and Endornaviridae, while one virga-like virus remains unclassified. The study also revealed double-stranded RNA mycoviruses in some fungal transcriptomes, which were putatively classified into the Totiviridae family. This research marks the first identification of mycoviruses in Thielaviopsis ethacetica, Thielaviopsis paradoxa, two distinct isolates of Huntiella omanensis, Ceratocystis platani, Ceratocystis eucalypticola, Ceratocystis manginecans, and Ceratocystis albifundus. Equally noteworthy is the discovery of identical mitoviruses in two fungal species from Thielaviopsis, as well as within three different fungal species from Ceratocystis, despite these occupying different ecological niches and plant hosts. While the transmission mechanism of these viruses remains uncertain, the data implies a need to assess isolation procedures, like carrot baiting, as potential sources of viral transmission in experiments. This dissertation significantly advances our knowledge of mycoviral diversity within the Ceratocystidaceae family and raises intriguing questions about the origins of these viruses. While more tests are needed to precisely determine the effects of these mycoviruses on their hosts, the insights obtained here provide a basis for future research into biocontrol strategies against these plant pathogenic fungi.