Schwessinger Group - Plants, fungi, evolution

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Our team focuses on questions around plant biosecurity in Australia by studying the interaction between plants and their fungal pathogen. Specifically, we work on agronomic important wheat rust fungi and the environmental important myrtle rust fungus that infects a wide range of myrtacea (e.g. eucalyptus trees).

Key questions are:

  • How do these invasive fungal pathogens infect host plants?
  • What are the genes underlying host adaptation enabling infection?
  • How does evolution and adaptation shape genome structure in agricultural vs. natural ecosystems?
  • Can we develop cutting edge sequence based methods for pathogen detection?
  • How do microbial communities in plant leaves change during the infection with invasive pathogens?

Many of these questions are also applicable to other study systems, hence we are a really collaborative team. We work with other groups at RSB and beyond on plant, animal, and fungal genomics.

The science in the 'lab':

We are a highly collaborative and interactive team that studies the interaction of fungi and plants, as main focus. We use a wide varity of tools reaching from biochemistry, bioinformatics, genomics, to environmental sampling. Modern biology is best mixed by combining good 'old school' biochemistry with modern data science stired with interesting biological questions.

Plants and fungi are simply awesome.

We study these plant-fungi interactions on multiple molecular and temporal scales. This includes many aspects:

  • Detailed molecular interaction studies of plant and fungal proteins leading to disease or immunity. The seconds to days timescale.
  • Detailed genome evolution and adaptation of fungal pathogens, especially the wheat stripe rust and myrtle rust fungus, in response to wild and agricultural ecosystems. The months to years timescale.
  • Detailed comparative and population genomics analysis of rust fungi with a focus on wheat rusts. The decades to millions of year timescale.

 

Projects in the 'lab' in 2024 onward:

Fungal genomics, evolution, and host adaptation (Summer, Honours, Master, and PhD students)

Detection of fungal pathogens and their associated microbiome (Summer, Honours, and Master students)

A synthetic biology approach to detect pathogen molecules in crops (Summer, Honours, and Master students)

We aim to publish work performed by students on its own or as part of a bigger manuscript. Everyone will be clearly rewarded with appropriate authorship.

 

The science beyond the 'lab':

Beyond being nerds, we aim to contribute to a welcoming and progressive academic environment. Group members are actively encouraged to contribute to community events, outreach science communication, and university commities. For example, group members were part of eLife's Early Career Advisory Board, ambassador for the protocol sharing webpage protocols.io, members of the RSB Equity Committee and others. And of course we love open access and reproducible science.

 

Plant-microbe interactions
Phylogenetics, population genetics and biodiversity
Evolutionary genetics and genomics
Bioinformatics and bio-mathematical modelling
Host-microbe biology

Technologies Specialist

Group Leader

Postdoctoral Fellows

Technical Officer

Divisional Visitors

Masters Students

PhD Students

Senior Research Officer

Special Project Student

Technical Assistants

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Project Status
A synthetic biology approach to detect pathogen molecules in crops Current
Detection of fungal pathogens and their associated microbiome Current
Fungal genomics, evolution, and host adaptation Current

Please refer to Google Scholar or Pubmed for our latest publications.

Not up-to-date list.

# refereed publications: 42

# public preprints: 3

3471 citations (Google Scholar, 06/2018)

 

[OA] represents publication in open access journals

# represents shared first authorship

$ represents corresponding author

Junior researchers supervised by Dr Schwessinger are underlined

Citation data is from Google Scholar, June 2018

 

Peer-reviewed Journal Articles

  1. [OA] Thomas, N.C., Oksenberg, N., Liu, F., Caddell, D., Nalyvayko, A., Nguyen, Y., Schwessinger, B.$, Ronald, P.$, 2017. The Rice XA21 Ectodomain Fused to the Arabidopsis EFR Cytoplasmic Domain Confers Resistance to Xanthomonas oryzae pv. oryzae. PeerJ 6, e4456. Citations = 0
  2. [OA] Schwessinger, B.$, Sperschneider, J., Cuddy, W.$, Miller, M., Garnica, D., Taylor, J., Dodds, P., Figueroa, M., Robert, P., Rathjen, J.$, 2017. A near complete haplotype-phased genome of the dikaryotic wheat stripe rust fungus Puccinia striiformis f. sp. tritici reveals high inter-haplome diversity. mBio 9, e02275-17 Citations = 2
  3. [OA] Miller, M.E., Zhang, Y., Omidvar, V., Sperschneider, J., Schwessinger, B., Raley, C., Palmer, J.M., Garnica, D., Upadhyaya, N., Rathjen, J., Taylor, J.M., Park, R.F., Dodds, P.N., Hirsch, C.D., Kianian, S.F., Figueroa, M., 2018. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust. mBio 9, e01650-17. Citations = 3
  4. [OA] Pornsiriwong, W., Estavillo, G.M., Chan, K.X., Tee, E.E., Ganguly, D., Crisp, P.A., Phua, S.Y., Zhao, C., Qiu, J., Park, J., Yong, M.T., Nisar, N., Yadav, A.K., Schwessinger, B., Rathjen, J., Cazzonelli, C.I., Wilson, P.B., Gilliham, M., Chen, Z.-H., Pogson, B.J., 2017. A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. Elife 6. doi:10.7554/eLife.23361 Citations = 22
  5. [OA] Pruitt, R.N., Joe, A., Zhang, W., Feng, W., Stewart, V., Schwessinger, B., Dinneny, J.R., Ronald, P.C., 2017. A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone. New Phytol. 215, 725–736. doi:10.1111/nph.14609 Citations = 2
  6. [OA] Schwessinger, B.$, 2017. Fundamental wheat stripe rust research in the 21st century. New Phytol. 213, 1625–1631. doi:10.1111/nph.14159 Citations = 13
  7. [OA] Singh, V., Perraki, A., Kim, S.Y., Shrivastava, S., Lee, J.H., Zhao, Y., Schwessinger, B., Oh, M.-H., Marshall-Colon, A., Zipfel, C., Huber, S.C., 2017. Tyrosine-610 in the Receptor Kinase BAK1 Does Not Play a Major Role in Brassinosteroid Signaling or Innate Immunity. Front. Plant Sci. 8. doi:10.3389/fpls.2017.01273 Citations = 0
  8. Thynne, E., Saur, I.M.L., Simbaqueba, J., Ogilvie, H.A., Gonzalez-Cendales, Y., Mead, O., Taranto, A., Catanzariti, A.-M., McDonald, M.C., Schwessinger, B., Jones, D.A., Rathjen, J.P., Solomon, P.S., 2017. Fungal phytopathogens encode functional homologues of plant rapid alkalinization factor (RALF) peptides. Mol. Plant Pathol. 18, 811–824. doi:10.1111/mpp.12444 Citations = 17
  9. Bahar, O., Mordukhovich, G., Luu, D.D., Schwessinger, B., Daudi, A., Jehle, A.K., Felix, G., Ronald, P.C., 2016. Bacterial Outer Membrane Vesicles Induce Plant Immune Responses. Mol. Plant Microbe Interact. 29, 374–384. doi:10.1094/MPMI-12-15-0270-R Citations = 11
  10. Kohler, A.C., Chen, L.-H., Hurlburt, N., Salvucci, A., Schwessinger, B., Fisher, A.J., Stergiopoulos, I., 2016. Structural Analysis of an Avr4 Effector Ortholog Offers Insight into Chitin Binding and Recognition by the Cf-4 Receptor. Plant Cell 28, 1945–1965. doi:10.1105/tpc.15.00893 Citations = 4
  11. Schwessinger, B., Li, X., Ellinghaus, T.L., Chan, L.J.G., Wei, T., Joe, A., Thomas, N., Pruitt, R., Adams, P.D., Chern, M.S., Petzold, C.J., Liu, C.C. $, Ronald, P.C. $, 2016. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integr. Biol. 8, 542–545. doi:10.1039/C5IB00232J Citations = 2
  12. [OA] Thomas, N.C.#, Schwessinger, B.#, Liu, F., Chen, H., Wei, T., Nguyen, Y.P., Shaker, I.W.F., Ronald, P.C., 2016. XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves. PeerJ 4, e2446. doi:10.7717/peerj.2446 Citations = 1
  13. Lao, J., Sharma, M.K., Sharma, R., Fernández-Niño, S.M.G., Schmutz, J., Ronald, P.C., Heazlewood, J.L., Schwessinger, B. $, 2015. Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum). Proteomics 15, 2286–2290. doi:10.1002/pmic.201400487 Citations = 7
  14. [OA] Pruitt, R.N.#, Schwessinger, B. #,$, Joe, A., Thomas, N., Liu, F., Albert, M., Robinson, M.R., Chan, L.J.G., Luu, D.D., Chen, H., Bahar, O., Daudi, A., Vleesschauwer, D.D., Caddell, D., Zhang, W., Zhao, X., Li, X., Heazlewood, J.L., Ruan, D., Majumder, D., Chern, M., Kalbacher, H., Midha, S., Patil, P.B., Sonti, R.V., Petzold, C.J., Liu, C.C., Brodbelt, J.S., Felix, G., Ronald, P.C.$, 2015. The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. Science Advances 1, e1500245. doi:10.1126/sciadv.1500245 Citations = 67
  15. [OA] Schwessinger, B. #, Bahar, O. #, Thomas, N., Holton, N., Nekrasov, V., Ruan, D., Canlas, P.E., Daudi, A., Petzold, C.J., Singan, V.R., Kuo, R., Chovatia, M., Daum, C., Heazlewood, J.L., Zipfel, C., Ronald, P.C., 2015a. Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses. PLoS Pathog 11, e1004809. doi:10.1371/journal.ppat.1004809 Citations = 47
  16. [OA] Schwessinger, B. $, Bart, R., Krasileva, K.V., Coaker, G. $, 2015. Focus issue on plant immunity: from model systems to crop species. Front. Plant Sci 6, 195. doi:10.3389/fpls.2015.00195 Citations = 5
  17. Schwessinger, B.$, Rathjen, J.P.$, 2015. Changing SERKs and priorities during plant life. Trends in Plant Science 20, 531–533. doi:10.1016/j.tplants.2015.06.006 Citations = 9
  18. [OA] Cain, B., Budke, J.M., Wood, K.J., Sweeney, N.T., Schwessinger, B.$, 2014. How postdocs benefit from building a union. eLife Sciences 3, e05614. doi:10.7554/eLife.05614 Citations = 6
  19. [OA] Chen, X.#, Zuo, S.#, Schwessinger, B.#, Chern, M., Canlas, P.E., Ruan, D., Zhou, X., Wang, J., Daudi, A., Petzold, C.J., Heazlewood, J.L., Ronald, P.C., 2014. An XA21-Associated Kinase (OsSERK2) Regulates Immunity Mediated by the XA21 and XA3 Immune Receptors. Molecular Plant 7, 874–892. doi:10.1093/mp/ssu003 Citations = 68
  20. Macho, A.P. #, Schwessinger, B. #, Ntoukakis, V. #, Brutus, A., Segonzac, C., Roy, S., Kadota, Y., Oh, M.-H., Sklenar, J., Derbyshire, P., Lozano-Durán, R., Malinovsky, F.G., Monaghan, J., Menke, F.L., Huber, S.C., He, S.Y., Zipfel, C., 2014. A Bacterial Tyrosine Phosphatase Inhibits Plant Pattern Recognition Receptor Activation. Science 343, 1509–1512. doi:10.1126/science.1248849 Citations = 71
  21. Malinovsky, F.G., Batoux, M., Schwessinger, B., Youn, J.H., Stransfeld, L., Win, J., Kim, S.-K., Zipfel, C., 2014. Antagonistic Regulation of Growth and Immunity by the Arabidopsis Basic Helix-Loop-Helix Transcription Factor HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH INCREASED LEAF INCLINATION1 BINDING bHLH1. Plant Physiol. 164, 1443–1455. doi:10.1104/pp.113.234625 Citations = 60
  22. Zuo, S., Zhou, X., Chen, M., Zhang, S., Schwessinger, B., Ruan, D., Yuan, C., Wang, J., Chen, X., Ronald, P.C., 2014. OsSERK1 regulates rice development but not immunity to Xanthomonas oryzae pv. oryzae or Magnaporthe oryzae. J. Integr. Plant Biol. 56, 1179–1192. doi:10.1111/jipb.12290 Citations = 13
  23. [OA] Bahar, O.#, Pruitt, R.#, Luu, D.D., Schwessinger, B., Daudi, A., Liu, F., Ruan, R., Fontaine-Bodin, L., Koebnik, R., Ronald, P., 2014. The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ 2, e242. doi:10.7717/peerj.242 Citations = 39
  24. Albrecht, C.#, Boutrot, F.#, Segonzac, C., Schwessinger, B., Gimenez-Ibanez, S., Chinchilla, D., Rathjen, J.P., Vries, S.C. de, Zipfel, C., 2012. Brassinosteroids inhibit pathogen-associated molecular pattern–triggered immune signaling independent of the receptor kinase BAK1. PNAS 109, 303–308. doi:10.1073/pnas.1109921108 Citations = 229
  25. Dardick, C., Schwessinger, B., Ronald, P., 2012. Non-arginine-aspartate (non-RD) kinases are associated with innate immune receptors that recognize conserved microbial signatures. Curr Opin Plant Biol 15, 358–66. doi:10.1016/j.pbi.2012.05.002 Citations = 55
  26. [OA] Han, S.-W. #, Lee, S.-W. #, Bahar, O., Schwessinger, B., Robinson, M.R., Shaw, J.B., Madsen, J.A., Brodbelt, J.S., Ronald, P.C., 2012. Tyrosine sulfation in a Gram-negative bacterium. Nat Commun 3, 1153. doi:10.1038/ncomms2157 Citations = 39
  27. Schwessinger, B., Ronald, P.C., 2012. Plant innate immunity: perception of conserved microbial signatures. Annu Rev Plant Biol 63, 451–482. doi:10.1146/annurev-arplant-042811-105518 Citations = 223
  28. Wang, E.#, Schornack, S.#, Marsh, J.F., Gobbato, E., Schwessinger, B., Eastmond, P., Schultze, M., Kamoun, S., Oldroyd, G.E.D., 2012. A Common Signaling Process that Promotes Mycorrhizal and Oomycete Colonization of Plants. Current Biology 22, 2242–2246. doi:10.1016/j.cub.2012.09.043 Citations = 170
  29. Ntoukakis, V.#, Schwessinger, B.#, Segonzac, C., Zipfel, C., 2011. Cautionary notes on the use of C-terminal BAK1 fusion proteins for functional studies. Plant Cell 23, 3871–8. doi:10.1105/tpc.111.090779 Citations = 49
  30. Roux, M.#, Schwessinger, B.#, Albrecht, C., Chinchilla, D., Jones, A., Holton, N., Malinovsky, F.G., Tor, M., de Vries, S., Zipfel, C., 2011. The Arabidopsis Leucine-Rich Repeat Receptor-Like Kinases BAK1/SERK3 and BKK1/SERK4 Are Required for Innate Immunity to Hemibiotrophic and Biotrophic Pathogens. Plant Cell 23, 2440–55. doi:10.1105/tpc.111.084301 Citations = 387
  31. [OA] Schwessinger, B., Roux, M., Kadota, Y., Ntoukakis, V., Sklenar, J., Jones, A., Zipfel, C., 2011. Phosphorylation-Dependent Differential Regulation of Plant Growth, Cell Death, and Innate Immunity by the Regulatory Receptor-Like Kinase BAK1. PLoS Genet 7, e1002046. doi:10.1371/journal.pgen.1002046 Citations = 293
  32. [OA] Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.H., Huitema, E., Jeong, D.H., Jones, A.M., Jones, J.D., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., Maclean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J., Morgan, W., Morris, P.F., Munro, C.A., O’Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R., Whisson, S.C., Judelson, H.S., Nusbaum, C., 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461, 393–8. doi:10.1038/nature08358 Citations = 924
  33. Nekrasov, V., Li, J., Batoux, M., Roux, M., Chu, Z.H., Lacombe, S., Rougon, A., Bittel, P., Kiss-Papp, M., Chinchilla, D., van Esse, H.P., Jorda, L., Schwessinger, B., Nicaise, V., Thomma, B.P., Molina, A., Jones, J.D., Zipfel, C., 2009. Control of the pattern-recognition receptor EFR by an ER protein complex in plant immunity. Embo J 28, 3428–38. doi:10.1038/emboj.2009.262 Citations = 214
  34. Conti, L., Price, G., O’Donnell, E., Schwessinger, B., Dominy, P., Sadanandom, A., 2008. Small ubiquitin-like modifier proteases OVERLY TOLERANT TO SALT1 and -2 regulate salt stress responses in Arabidopsis. Plant Cell 20, 2894–908. doi:10.1105/tpc.108.058669 Citations = 120
  35. Schwessinger, B., Zipfel, C., 2008. News from the frontline: recent insights into PAMP-triggered immunity in plants. Curr Opin Plant Biol 11, 389–95. doi:10.1016/j.pbi.2008.06.001 Citations = 293

 

Peer-reviewed book chapter

  1. Schwessinger, B. $, Rathjen, J.P., 2017. Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing. Methods Mol. Biol. 1659, 49–57. doi:10.1007/978-1-4939-7249-4_5 Citations = 1
  2. Jones, J., Zipfel, C., Schwessinger, B., Roux, M., 2008. Genetic analysis of PAMP-triggered immunity in Arabidopsis, Biology of Plant-Microbe Interactions. International Society for Molecular Plant-Microbe Interactions, St. Paul, Minnesota. Citations = unknown

 

Publicly available preprints

  1. [OA] McDonald, M.#, Schwessinger, B.#, Stewart, V., Ronald, P., 2017. Distribution and inheritance of a gene cluster encoding a sulfated tyrosine peptide in Xanthomonas spp. bioRxiv 149930. doi:10.1101/149930Citations = 0
  2. [OA] Schalamun, M., Kainer, D., Beavan, E., Nagar, R., Eccles, D., Rathjen, J., Lanfear, R., Schwessinger, B., 2018. A comprehensive toolkit to enable MinION long-read sequencing in any laboratory. bioRxiv 289579. Citations = 0
  3. [OA] Wang, W., Schalamun, M., Suarez, A.M., Kainer, D., Schwessinger, B., Lanfear, R., 2018. Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. bioRxiv 320085. https://doi.org/10.1101/320085

Fungi fighter named ACT’s emerging scientist

Story | Friday 19 August 2022
Using cutting-edge technology, biologist Dr Benjamin Schwessinger from The Australian National University (ANU) is helping to protect the biosecurity of Australia's unique flora and agricultural industry.
Wheat photo courtest of Keith/Ewing on flickr

Research working to make wheat fungus a thing of the past

Story | Sunday 24 May 2020
Researchers have a new understanding of the genetic makeup of a fungus that causes the disease Wheat Stripe Rust, one of the most destructive wheat diseases globally costing $1 billion annually.
Wheat

Killer wheat disease spreads without sex

Story | Saturday 9 November 2019
Some clever detective work by an international team of scientists has uncovered how a deadly fungus - a stem rust called Ug99 - came about through some unusual breeding habits. The discovery will help protect wheat crops around the world from devastating fungal diseases.

Benjamin Schwessinger

Story | Tuesday 4 September 2018
Benjamin Schwessinger talks about research, teaching and equity

PS Seminar Series - Sexual recombination on cereal rust fungi: epidemiological implications and potential applications for a sustainable cereal supply

Event | Wed 27 March 2024
Rust fungi are a major cause of cereal yield losses worldwide requiring frequent fungicide applications in case crop resistance is overcome by new pathogen variants.

PS PhD Exit Seminar - Positive reporters of defence induction for screening effector recognition in wheat protoplasts

Event | Fri 16 February 2024
In response to plant disease as a severe limiting factor in crop production, genomics-informed surveillance promises to support crop protection and biosecurity efforts.

PS Seminar Series: Plant Biosecurity and the Beauty of Timor-Leste

Event | Thu 16 November 2023
Timor-Leste is a beautiful island nation in the north west of Australia and is an important neighbour. This talk will introduce Timor-Leste from various perspectives. It will highlight the importance of biosecurity to Timor-Leste’s economy and why this matters to Australia.

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