Global effort untangles huge genome of soybean fungus

The fungus Phakopsora pachyrhizi causes Asian soybean rust and is one of the most damaging plant pathogens of the past century. A global consortium of scientists has finally untangled its notoriously complex and large genome, enabling the development for more innovative and science-based solutions.

In 2019, the 2Blades research group which is based at The Sainsbury Laboratory announced the initial successful assembly of the genome of Phakopsora pachyrhizi. However, its very large size and complexity required further effort to complete the annotation and analysis.

A significant challenge with P. pachyrhizi is the presence of an additional nucleus, meaning it possesses two separate sets of genetic instructions. Each had to be separately determined, which was recently made possible by newer, long-read sequencing technology.

″Completing the genome and analysis was a major undertaking, but we brought together the resources of a unique consortium of public and private partners and produced this high quality annotated sequence″ stated Dr. Peter van Esse, former 2Blades Group Leader and current Board member.

″The unprecendented resolution provided insights into the high degree of transposable elements within the genome, a key insight for the development of resistant varieties.″

Infection cycle of P. pachyrhizi on susceptible soybean plants. The scientists were able to investigate which genes were expressed during the critical infection stages.

The researchers compared sequences of three geographically distinct P. pachyrhizi genomes and found a number of insights into the pathogen’s adaptability and broad host range. One of the most striking discoveries was that 93% of the genome consists of transposable elements (TEs), ″jumping″ DNA that can move around the genome.

Most fungi have 10-40% TEs, and the high percentage in P. pachyrhizi enables greater genetic plasticity. It helps to explain P. pachyrhizi’s adaptability to environmental conditions and a range of hosts, making it a formidable threat.

Asian Soybean Rust is ubiquitously present in the soybean growing areas of Latin America, where 210 million metric tons of soybean are projected to be produced in 2022/23 alone, representing a gross production value of U.S. $ 115 billion per season.

The largest producer of the soybean is Brazil, where the cost of managing soybean rust exceeds $2 billion per year and depends heavily on fungicides.

Asian soybean rust symptoms start to show up on the underside of soy plant leaves. Rust-coloured spots form, which then develop into pustules that break open and release masses of P. pachyrhizi spores. Photos by Peter van Esse and electron microscopy image by Kathrin Thor.

″Asian Soybean Rust has been known to destroy up to 90% of a soybean harvest, costing soybean producers billions of dollars each year. Understanding the pathogen is critical to the development of new control strategies to combat P. pachyrhizi in the field,″ says study co-author Yogesh Gupta, Project Leader at 2Blades and based at The Sainsbury Laboratory in Norwich, UK.

Yogesh continues, ″An unexpected finding was the expansion of genes related to amino-acid metabolism and energy production, atypical for a rust fungus. These genes may correlate with infection across many legume species since it may provide flexibility for nutrient acquisition from different hosts.″

The effort behind the project comprised a large and interactive international consortium of research and industry partners, including: 2Blades, The Sainsbury Laboratory, Brazilian Company of Agricultural Research (Embrapa), ETH Zürich, National Center for Genome Resources, U.S. Department of Energy Joint Genome Institute, Federal University of Technology of Paraná (UTFPR), Université de Lorraine INRAE, Syngenta Jealott’s Hill Int. Research Centre, AFMB Aix-Marseille University, Biodiversité et Biotechnologie Fongiques, King Abdulaziz University, Technical University of Denmark, Bayer SAS, KeyGene N.V., John Innes Centre, Universidade Federal de Viçosa, University of Hohenheim, Syngenta Crop Protection AG, RWTH Aachen University, Syngenta Crop Protection and the University of California, Berkeley.

Citation

Gupta, Y.K., Marcelino-Guimarães, F.C., Lorrain, C., Farmer, A., Haridas, S., Ferreira, E.G.C., Lopes-Caitar, V.S., Oliveira, L.S., Morin, E., Widdison, S. and Cameron, C., 2023. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nature Communications, 14(1), pp.1-16.

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