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Determination of the native floral virome in Mt Wellington Park

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Wilson, JR 2021 , 'Determination of the native floral virome in Mt Wellington Park', Honours thesis, University of Tasmania.

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Abstract

In an ever‐increasing population, plant virology is a field of growing importance. Understanding key factors such as virus flow, the transmission properties of native viruses, potential to spread and the severity of disease caused is crucial for both the conservation of our native habitats, but also increasing agricultural production in a sustainable fashion.
In order to gain a better understanding of the potential impact that native floral viruses may have on agricultural crops, we first must identify and characterize the native species present. To this date, there is very little published literature surrounding the virome of plant species that are neither ornamental nor used for agricultural purposes. This represents a large knowledge gap as human activity continues to drive virus emergence in both the natural and managed environments.
A total of 34 samples with putative viral infections were taken from two walking trails in Wellington Park, the Pipeline trail and the Lenah Valley track. Of these, 18 samples of varying species underwent RNA extraction and next generation sequencing. Bioinformatic software including Geneious Prime, Genome Detective and Virusdetect were used to analyse the reads received from sequencing, with varying success. Using the data gained from the sequence analysis, select samples underwent electron microscopy and PCR to confirm the presence of the virus species detected by the next generation sequencing. Some samples were also used to inoculate test subjects to assess the transmission properties of the viruses causing symptomatic infection within the samples obtained from Wellington Park.
The sequencing data revealed the potential presence of four viral species. This included Citrus exocortis Yucatan viroid isolate 15, Pepper cryptic virus 1 (PCV‐1), White clover mosaic virus (WCMV) and Tobacco mosaic virus (TMV). Of these viruses, the most significant findings were WCMV and TMV, due to both of these species having the potential to reduce fitness in native and agricultural species alike. The presence of TMV was first located in sample 14, Bedfordia salicina but PCR revealed its presence in sample 7, another sample of Bedfordia salicina from a different location. Using these results, it can be ascertained that B. salicina is susceptible to TMV infection, and it is present within the native virome of the park. WCMV was detected in both unknown species sample 4, and sample 5 (P. apetala). However, no Potexvirus primers were able to be obtained, so no further analysis could occur.
In summary, the native environment holds host to many viral species, and as the agro‐ecological interface continues to be manipulated by the human race, virus emergence will continue. The presence of at least one pathogenic viral species in a small sample size is cause for concern, and highlights the need for further research in the area.

Item Type: Thesis - Honours
Authors/Creators:Wilson, JR
Keywords: Native virome, RNA, plant viruses, Tasmania
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Copyright 2021 the author

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