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  • (2023) Chen, Stephanie
    There has been a recent explosion of genomic data facilitated by rapid technological advances in sequencing and bioinformatics coupled with decreasing cost. However, the distribution of species with sequenced genomes across the plant tree of life is highly uneven. The genomic era is an opportunity to accelerate our understanding of plant evolution and efforts in conservation in the face of the Anthropocene. The overarching aims of this PhD encompass the development and optimisation of genomic resources for plants. This thesis focuses on two groups of Australian native plants – Telopea (waratahs) and Myrtaceae. I assembled the first chromosome-level reference genome for Telopea speciosissima (New South Wales waratah) using Nanopore long-reads, 10x linked-reads, and Hi-C data (Chapter 2). I applied reduced representation sequencing (DArTseq; n = 244), whole-genome sequencing (n = 14), and chloroplast sequencing (n = 50) to reveal insights into the population structure and demographic history of the genus, demonstrating a downstream application of the reference genome (Chapter 3). There was a decline in effective population sizes in all lineages coinciding with the Last Glacial Maximum (LGA); the drop was especially apparent in the Monga and Victorian waratahs. I assembled reference genomes for four Myrtaceae species – Syzygium oleosum (blue lilly pilly), Rhodamnia argentea (malletwood), Rhodamnia rubescens (brush turpentine), and Rhodomyrtus psidioides (native guava) – that display varying degrees of resistance to myrtle rust (Chapter 4). The latter two species are native rainforest species in rapid decline due to the invasive fungal pathogen Austropuccinia psidii and are currently being conserved and protected in ex-situ collections. Here, I analysed DArTseq data to develop recommendations for the conservation management of these critically endangered species, and demonstrate the value of genomic resources in conservation (Chapter 5). Overall, this PhD thesis demonstrates how references genomes, complementary genomic data and bioinformatic tools are valuable resources that contribute to our understanding of the Australian flora and pave the way for the persistence of plant populations into the future.