Tobias, P. A.Schwessinger, BenjaminDeng, C. H.Wu, ChenDong, ChongmeiSperschneider, JanaJones, AshleyLuo, ZhenyanZhang, PengSandhu, Karanjeet S.Smith, Grant RTibbits, JosquinChagne, DavidPark, R. F.2022-10-312022-10-312160-1836http://hdl.handle.net/1885/276822Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.This work was supported by the New Zealand Department of Primary Industries via RFP 18608 Myrtle rust research programme 2017–2019: understanding the pathogen, hosts, and environmental influences; the New Zealand Institute for Plant and Food Research Limited for access to the highperformance computing facility PowerPlant. This work was also supported by an Australian Research Council DECRA (DE150101897) and Future Fellowship (FT180100024) to B.S. and an Australian Research Council DECRA (DE190100066)to J.S. The provision of financial support to the University of Sydney by Judith and David Coffey and family is gratefully acknowledged.application/pdfen-AU© 2020 The Author(s)http://creativecommons.org/licenses/by/4.0/myrtle rustPucciniomycotinafungal genome evolutionMyrtaceaetransposable elements2020-11-2710.1093/g3journal/jkaa0152021-11-28Creative Commons Attribution License