Ferreira, E. G. C. | Search bioRxiv

bioRxiv2025

The dominant lineage of Phakopsora pachyrhizi in the United States of America does not have a Brazilian origin

O_LIAsian soybean rust (ASR), caused by the obligate biotrophic fungus, Phakopsora pachyrhizi, was first reported in the continental United States of America (USA) in 2004 and over the years has been of concern to soybean production in the USA. The prevailing hypothesis is that P. pachyrhizi spores were introduced into the USA via hurricanes originating from South America, particularly Hurricane Ivan. C_LIO_LITo investigate the genetic diversity and global population structure of P. pachyrhizi, we employed exome-capture based sequencing on 84 field isolates collected from different geographic regions worldwide. We compared the gene-encoding regions from all these field isolates and found that four major haplotypes are prevalent worldwide. Here, we provide genetic evidence supporting multiple incursions that have led to the currently established P. pachyrhizi population of the USA. Phylogenetic analysis of mitochondrial genes further supports this hypothesis. C_LIO_LINotably, we observed limited genetic diversity in P. pachyrhizi populations in Brazil, suggesting a clonal population structure in that country that contrasts to populations from the USA and Africa. C_LIO_LIThis study provides the first comprehensive characterization of P. pachyrhizi population structures defined by genetic evidence from populations across major soybean growing regions. C_LI

evolutionary biology↗

bioRxiv2024

The genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi has been driven by two major evolutionary lineages

Phakopsora pachyrhizi, an obligate biotrophic rust fungus, is the causal agent of Asian Soybean Rust (ASR) disease. Here, we utilized whole-genome data to explore the evolutionary patterns and population structure across 45 P. pachyrhizi isolates collected from 1972 to 2017 from diverse geographic regions worldwide. We also characterized in-silico mating-type (MAT) genes of P. pachyrhizi, in the predicted proteome of three isolates, to investigate the sexual compatibility system. Our molecular phylogenetic analysis in P. pachyrhizi inferred two distinct evolutionary lineages structured on a temporal scale, with lineage Pp1 grouping isolates obtained from 1972 to 1994, while more recently collected isolates formed a second lineage, Pp2. We found high levels of genetic diversity in lineage Pp1, whereas lineage Pp2 exhibited a strong clonal genetic structure, with a significant lower diversity. The widespread propagation of P. pachyrhizi clonal spores across soybean-growing regions likely explains the absence of a large-scale spatial genetic structure within each lineage. Two independent isolates (TW72-1 and AU79-1) showed moderate levels of genetic admixture, suggesting potential somatic hybridization between the two P. pachyrhizi lineages. We observed no clear congruence between virulence levels of P. pachyrhizi isolates and their phylogenetic patterns. Our findings support a probable tetrapolar mating system in P. pachyrhizi. Taken together, our study offers new insights into the evolutionary history of P. pachyrhizi and demonstrates that multiple MAT genes are highly expressed during the later stages of soybean infection, suggesting their potential role in the formation of urediniospores within the life cycle of P. pachyrhizi. AUTHOR SUMMARYThe Asian Soybean Rust (ASR) disease, caused by basidiomycetes fungus P. pachyrhizi, represents a critical threat to soybean crops worldwide. With the recent availability of high-quality genome assemblies for P. pachyrhizi, we are committed to exploring the genetic diversity of this destructive pathogen. This study analyzed whole-genome resequencing data from P. pachyrhizi isolates collected over several decades in various geographic regions. We identified recent diversification patterns in P. pachyrhizi, with two major lineages. The origin of the two lineages is likely due to temporal shifts in the genetic structure of P. pachyrhizi. Additionally, we investigated the genes responsible for sexual compatibility, known as mating-type (MAT) genes. Transcriptome data indicated that MAT genes are actively expressed during the later stages of the P. pachyrhizi-soybean infection. We conclude that the evolutionary dynamic of P. pachyrhizi is shaped by divergent lineages, which exhibit varying levels of virulence on differential soybean lines containing ASR resistance genes.

evolutionary biology↗

bioRxiv2022

The soybean rust pathogen Phakopsora pachyrhizi displays transposable element proliferation that correlates with broad host-range adaptation on legumes

Asian soybean rust, caused by Phakopsora pachyrhizi, is one of the worlds most economically damaging agricultural diseases. Despite P. pachyrhizis impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. We simultaneously sequenced three P. pachyrhizi genomes uncovering a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. The proliferation of TEs within the genome occurred in several bursts and correlates with the radiation and speciation of the legumes. We present data of clear de-repression of TEs that mirrors expression of virulence-related candidate effectors. We can see a unique expansion in amino acid metabolism for this fungus. Our data shows that TEs play a dominant role in P. pachyrhizis genome and have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity of the genome.

microbiology↗