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Advancing Genomic Resources for Myrtle Rust Research and Management

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Advancing Genomic Resources for Myrtle Rust Research and Management Advancing genomic resources for myrtle rust research and management Stephanie H Chen1,2, Jason G Bragg2 and Richard J Edwards1 1School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia 2National Herbarium of New South Wales, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, Australia What is myrtle rust and why is it a major threat to biodiversity? Meet our native rainforest study species • First detected in Australia in 2010 on the NSW Malletwood Rhodamnia argentea Blue lilly pilly Syzygium oleosum Scrub turpentine Rhodamnia rubescens • Plant disease that affects the Myrtaceae family (includes eucalypts, Central Coast. turpentines, bottlebrushes, paperbarks, tea trees and lilly pillies). • Not able to be eradicated. • Infects ~350 native Australian species with a global host list of 480 species and subspecies. Current distribution of myrtle rust • Caused by the introduced fungal pathogen Austropuccinia psidii. • One strain (pandemic) is present in Australia. critically endangered critically • There are intra-species and inter-species variation in resistance levels. – AUSTRALIA Variable resistance Variable resistance Highly susceptible susceptible Highly Photos by S Chen. Maps from Atlas of Living Australia. Rust on the abaxial leaf surface of Rhodamnia rubescens Aims of the project from a population in Royal National Park, NSW. There is a need to rapidly establish a conservation population 1. Generate high quality reference genomes for each study species. of this critically endangered species in decline due to myrtle rust. 2. Characterise patterns of landscape genetic variation in Rhodamnia rubescens and R. argentea. Photo by R Edwards. 3. Characterise myrtle rust resistance in Syzygium oleosum. 4. Identify loci associated with myrtle rust resistance and climate variables. 5. Develop methods for designing restoration populations that are adapted and adaptable. 10X Genomics linked-read genomes Pipeline Annotation Genome Eukaryotic NCBI the by Annotated Rhodamnia argentea Syzygium oleosum Length of genome assembly (bp) 414,815,504 431,290,611 Estimated genome size (Mb) 824.80 438.62 Assembled using Supernova using Assembled Scaffolds 15,781 19,039 N50 of scaffolds (bp) 857,171 975,936 L50 of scaffolds 122 98 Contigs 23,310 30,899 N50 of contigs (bp) 63,685 31,039 L50 of contigs 1,659 3,485 GC content (%) 40.9 41.6 Br wse the genomes Genes 30,372 29,467 on NCBI Mean gene length (bp) 4,544 4,509 v2.1.1 mRNAs 42,570 38,158 Non-coding RNAs 4,533 4,802 Exons 175,669 169,577 Mean exon length (bp) 322 317 Mean exons per transcript 6.22 6.09 Completeness? Ploidy? BUSCO (Benchmarking Universal Single-Copy Orthologs) results. Smudgeplot results – gymnastics with heterozygous kmer pairs. Eucalyptus camaldulensis 78.2% E. grandis 90.0% Metrosideros polymorpha 93.9% Psidium guajava 68.0% R. argentea 91.6% S. oleosum 93.2% What’s next? • Scaffold 10X Chromium genomes with long-reads (Oxford Nanopore minION). • Assemble R. rubescens genome de novo from long-reads. • Obtain Hi-C sequencing data to improve contiguity to chromosome level. • Continue to collect leaf and fruit across the distribution of the study species for genotyping and rust resistance assays. Visit the Edwards Lab website slimsuite.unsw.edu.au and tweet us @slimsuite Email me at [email protected].
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