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Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

View ORCID ProfilePeri A Tobias, View ORCID ProfileBenjamin Schwessinger, View ORCID ProfileCecilia H Deng, View ORCID ProfileChen Wu, View ORCID ProfileChongmei Dong, View ORCID ProfileJana Sperschneider, View ORCID ProfileAshley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, View ORCID ProfileGrant R Smith, View ORCID ProfileJosquin Tibbits, View ORCID ProfileDavid Chagné, View ORCID ProfileRobert F Park
doi: https://doi.org/10.1101/2020.03.18.996108
Peri A Tobias
1School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
2Plant & Food Research Australia, Sydney, Australia
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  • For correspondence: peri.tobias@sydney.edu.au benjamin.schwessinger@anu.edu.au
Benjamin Schwessinger
3Australia Research School of Biology, The Australian National University, Acton, ACT 2601
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  • For correspondence: peri.tobias@sydney.edu.au benjamin.schwessinger@anu.edu.au
Cecilia H Deng
4The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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Chen Wu
4The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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Chongmei Dong
5Plant Breeding Institute, University of Sydney, Private Bag 4011 Narellan, NSW 2567, Australia
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Jana Sperschneider
6Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
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Ashley Jones
3Australia Research School of Biology, The Australian National University, Acton, ACT 2601
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Zhenyan Lou
3Australia Research School of Biology, The Australian National University, Acton, ACT 2601
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Peng Zhang
5Plant Breeding Institute, University of Sydney, Private Bag 4011 Narellan, NSW 2567, Australia
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Karanjeet Sandhu
5Plant Breeding Institute, University of Sydney, Private Bag 4011 Narellan, NSW 2567, Australia
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Grant R Smith
7The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch Mail Centre, Christchurch 8140, New Zealand
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Josquin Tibbits
8Agriculture Victoria Department of Jobs, Precincts and Regions, Bundoora, Vic 3083, Australia
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David Chagné
9The New Zealand Institute for Plant & Food Research, Private Bag 11600, Palmerston North 4442, New Zealand
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Robert F Park
5Plant Breeding Institute, University of Sydney, Private Bag 4011 Narellan, NSW 2567, Australia
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Abstract

Austropuccinia 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 transposable elements and a very low overall GC content of 33.8%. The overall gene content is highly conserved, when compared to other closely related Pucciniales, yet the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • cecilia.deng{at}plantandfood.co.nz, chen.wu{at}plantandfood.co.nz, chongmei.dong{at}sydney.edu.au, jana.sperschneider{at}anu.edu.au, ashley.jones{at}anu.edu.au, zhenyan.luo{at}anu.edu.au, peng.zhang{at}sydney.edu.au, karanjeet.sandhu{at}sydney.edu.au, grant.smith{at}plantandfood.co.nz, josquin.tibbits{at}agriculture.vic.gov.au, david.chagne{at}plantandfood.co.nz, robert.park{at}sydney.edu.au

  • A substantial amount of additional data has been included investigating the transposable element content (>90%) of the Austropuccinia psidii genome. Other issues have been addressed following anonymous reviewers for Genome Biology and Evolution. These are largely to do with the removal of preliminary data analyses.

  • https://zenodo.org/record/3567172#.XnFpYKgzZaQ

  • https://github.com/peritob/myrtle-rust-genome-assembly

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Peri A Tobias, Benjamin Schwessinger, Cecilia H Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R Smith, Josquin Tibbits, David Chagné, Robert F Park
bioRxiv 2020.03.18.996108; doi: https://doi.org/10.1101/2020.03.18.996108
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Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements
Peri A Tobias, Benjamin Schwessinger, Cecilia H Deng, Chen Wu, Chongmei Dong, Jana Sperschneider, Ashley Jones, Zhenyan Lou, Peng Zhang, Karanjeet Sandhu, Grant R Smith, Josquin Tibbits, David Chagné, Robert F Park
bioRxiv 2020.03.18.996108; doi: https://doi.org/10.1101/2020.03.18.996108

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