Asian soybean rust fungus genome reveals clues to help control

Date:06-15-2023

Embrapa and other members of the International Asian Soybean Rust Genome Consortium celebrate the advances achieved by sequencing and assembling the genome of three samples (two isolates obtained in Brazil and one from Uruguay) of the fungus P. pachyrhizi, which causes Asian soybean rust. The work provides some clues about one of the most challenging characteristics of the microorganism: its high variability, which makes it quickly adapt and circumvent different control measures. The study was published in the journal Nature Communications.

The work provides some clues about the fungus' high variability, which makes it quickly adapt and circumvent different control measures.  Photo: Elizeo Garrcia

Asian soybean rust is one of the crop's main phytosanitary challenges because the fungus can adapt to control strategies, either by losing sensitivity to fungicides or by "breaking" the genetic resistance present in soybean cultivars. ″The availability of a reference genome for the fungus is essential for advances in knowledge of the biology and the factors involved in the fungus' adaptability, with the aim of accelerating the development of new control strategies,″ states the Embrapa Soybeans researcher Francismar C. Marcelino-Guimarães, one of the authors of the paper.

The researcher explains that detailed knowledge about the operation of the fungus' reference genome is essential to understand the factors that are involved in its adaptability and that thus contribute to hindering its control. ″Based on the genome, we found that about 93% is composed of repetitive DNA sequences called transposons, DNA fragments that can 'jump' or change places in the genome, which can contribute to its high variability,″ the researcher explains. ″Interestingly, we were able to observe that some of such transposons become active in the fungus and jump in the genome during an infection, especially in the first hours of contact with the host. They become active 24 to 48 hours after the infection alongside other genes that are essential for infection success known as effectors, which work by suppressing the plant's defense responses", she details.

In the study, it was also possible to identify the fungus' full set of effectors, which was shared by the three samples of the fungus, including those that were active or expressed at the crucial moments of infection. Some of these effectors have been characterized by Embrapa Soybeans, showing their action or attack against the host during the parasitism. ″Understanding the pathogen's attack strategies is crucial for the development of control strategies,″ the researcher asserts.

Guimarães also revealed that based on the genome available, comparative genomics studies with other fungal species also showed adaptive particularities stemming from the contraction or expansion of gene families. ″By comparing the genome of the soybean rust pathogen with those of 14 fungal species, we identified that gene loss is more frequent in P. pachyrhizi. This trait explains its high dependence on the plant tissue of the living host and, in some biological processes, the pathogen is completetely reliant on the host″, she reports, as she explains that learning the processes and key elements involved in parasitism is essential to develop host plants that are less attractive or more tolerant to the fungus.

According to the researcher, they also observed the occurrence of expanded gene families – involved in energy production and nutrient transportation –, which may point to a certain flexibility in their metabolism and in nutrient acquisition. ″Understanding the parasite's lifestyle at a molecular level is important to identify the genes that are essential during soybean parasitism and that are thus essential for nutrient acquisition and fungal survival,″ she explains.

Such genes can be used for the development of control strategies (e.g. via gene editing or transgenics) as they can compromise vital processes such as parasitism. ″Studies conducted at Embrapa have also tested the effectiveness of silencing some of the fungus' essential genes, a strategy with potential to reduce the severity of the disease,″ she observes.

The analysis of the genome also revealed a high level of differences (heterozygosity) between the two nuclei that constitute the fungus' genome. ″This characteristic indicates an absence of recombination between them, backing the fungus' propagation or asexual reproduction in South America.