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The Partnership Between Orchids, Fungi and Viruses

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The Partnership Between Orchids, Fungi and Viruses In bed with viruses: the partnership between orchids, fungi and viruses Thesis presented by Jamie Wan Ling Ong For the degree of Doctor of Philosophy School of Veterinary and Life Sciences Murdoch University 2016 Declaration I declare that this thesis is my own account of my research and contains as its main content, work which has not previously been previously submitted for a degree at any tertiary education institution. Jamie Wan Ling Ong ii Abstract The Orchidaceae is the largest and most diverse angiosperm family comprising of five subfamilies, over 800 genera and over 26,000 species. In Western Australia, there are over 450 indigenous orchid species across 40 genera, concentrated predominately within the South West Australian Floristic Region, but with a few species in the tropical Kimberley. The southern species are all terrestrial and most belong to the Diurideae tribe, which are primarily restricted to Australia and New Zealand. To varying degrees, orchids rely on associations with other organisms, particularly fungi for nutrient provision and insects for pollination. The partnerships between the orchids, their fungal symbionts and insect pollinators are quite well studied in some cases. However, the ecological influence of viruses, in particular indigenous viruses, within these symbiotic partnerships remains largely unexplored. Orchids cultivated for their flowers or vanilla are frequently infected by viruses, which are spread from plant to plant by vectors, husbandry tools and through vegetative propagation, and from place to place in infected propagules by trade. Only recently have wild orchids been shown to also harbour viruses. In this research, we used a combination of high throughput sequencing approach, traditional techniques and informatics to examine the leaf tissues of indigenous terrestrial orchid plants growing in their natural habitats for virus infection. Further, we isolated fungi that form mycorrhizal associations within cortical root cells of these plants and examined them for the presence of viruses. Terrestrial orchids and their fungal symbionts were sampled from 17 species across six genera (Caladenia, Diuris, Drakaea, Microtis, Paraceleana and Pterostylis) during the winter (June to iii August) and spring (September to November) growing seasons. This study represents the first of viruses from the indigenous orchids and fungal species examined. Thirty-two viruses, representing seven viral families and eight genera (Alphapartitivirus, Betapartitivirus, Endornavirus, Goravirus, Hypovirus, Mitovirus, Platypuvirus and Totivirus), were identified and characterised from wild plants of Drakaea, Microtis and Pterostylis orchids and their fungal symbionts. Four of the viruses were identified from leaves of Drakaea species and Pterostylis sanguinea orchids and the remaining 28 viruses were from six isolates of orchid mycorrhizal fungi of the genus Ceratobasidium. All but one of the viruses found were novel, and most were from taxonomic groups not previously described in the Australian continent. In three Ceratobasidium isolates studied, there were 5-13 virus species present in each. The presence of several closely-related bi-partite partitiviruses within the one host presented challenges in determining the numbers of species present and accurate pairing of virus segments. This study proposes solutions to address these problems, which will no doubt also arise in future metagenomics studies. Two of the new viruses described formed the bases of new genera (Goravirus and Platypuvirus), while other viruses could be tentatively classified within known taxa, but were often genetically divergent from existing members. For example, two novel partitiviruses represent a lineage basal to existing members of Alphapartitivirus, pointing to Australia as an important location in partitivirus evolution. The richness and uniqueness of viruses found in this study are likely a reflection of the orchid and iv fungal diversity of the region, itself a consequence of over 25 million years of relative geological and climatic stability. The surprisingly high numbers of mycoviruses detected from only a few fungal samples indicate that there is a rich virus association with fungal component of orchid biology and that orchid flora might represent a potentially enormous reservoir of novel viruses. v Table of contents Declaration .................................................................................................................................................... ii Abstract ........................................................................................................................................................ iii Table of contents .......................................................................................................................................... vi Abbreviations ............................................................................................................................................... ix Publications and presentations ................................................................................................................. xiii Acknowledgements ..................................................................................................................................... xv Chapter 1: Introduction ............................................................................................................................... 1 1.1 Vulnerability of orchids ........................................................................................................................ 1 1.2 Western Australian orchids ................................................................................................................... 3 1.3 W.A. orchids – plant/fungus/pollinator complex .................................................................................. 5 1.3.1 Orchid mycorrhizas ...................................................................................................................... 5 1.3.2 Orchid pollination ........................................................................................................................ 7 1.4 Orchid fungal and plant viruses ............................................................................................................ 8 1.5 Viruses identified from orchids of the south-west Australian floristic region ...................................... 9 1.6 Detection of plant viruses ................................................................................................................... 13 1.7 Next generation sequencing for virus discovery ................................................................................. 13 1.8 Aims of this research project .............................................................................................................. 15 Chapter 2: Characterization of the first two viruses described from wild populations of hammer orchids (Drakaea spp.) in Australia .......................................................................................................... 18 Chapter 3: The challenges of using high-throughput sequencing to track multiple new bi-partite viruses of wild orchid-fungus partnerships over consecutive years ....................................................... 34 3.1 Abstract ............................................................................................................................................... 34 3.2 Introduction......................................................................................................................................... 34 3.3 Materials and methods ........................................................................................................................ 36 3.3.1 Sample collection ........................................................................................................................36 3.3.2 Fungal isolation from underground stems ...................................................................................37 vi 3.3.3 Nucleic acids extraction, cDNA synthesis and amplification .....................................................38 3.3.4 Identification of fungi .................................................................................................................39 3.3.5 Sequencing data analysis.............................................................................................................39 3.3.6 RT-PCR amplification of partitivirus segments ..........................................................................40 3.3.7 5' UTRs alignments .....................................................................................................................40 3.4 Results ................................................................................................................................................ 41 3.4.1 Partitiviruses ...............................................................................................................................41 3.4.1.1 Partitivirus CPs ....................................................................................................................43 3.4.1.2 Partitivirus RdRps ...............................................................................................................43 3.4.2 Most partitiviruses occurred in both years ..................................................................................47 3.4.3 Matching partitivirus segments ...................................................................................................47
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