Biology subjects

Pedley, K. F.

Publications and source records attributed to Pedley, K. F..

8 recordsLinked to original sources

bioRxiv2026

Haplotype-phased, chromosome-level, annotated genome assembly of the soybean rust pathogen Phakopsora pachyrhizi

Phakopsora pachyrhizi, the causal agent of soybean rust, is among the most aggressive and economically impactful pathogens affecting soybean (Glycine max) production worldwide. As a dikaryotic rust fungus, P. pachyrhizi maintains its genetic information as two discrete haplotypes that are sequestered within separate nuclei for most of its life cycle as it reproduces asexually via the production of infectious urediniospores. Previous genomes of three P. pachyrhizi isolates collected in South America revealed a large genome with a high transposable element content, measuring up to 1.25 Gb and 93%, respectively. Although these efforts provided valuable foundational resources, the complexity of the genome resulted in highly fragmented assemblies. Here, we generated a highly contiguous, substantially improved, annotated genome resource from the P. pachyrhizi isolate LA04-1, collected during the initial outbreak of soybean rust in the continental United States in 2004. The assembly is haplotype-phased, with each haplotype assembled into 18 chromosomes totaling 572 Mb and 569 Mb in size. The isolate contains unique mating-type genes and does not share haplotype genomes with any available isolates with whole-genome sequencing datasets. This resource will be valuable to future investigations into the underlying mechanisms of virulence in this important plant pathogen.

genomics↗

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↗

bioRxiv2023

A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase

The devastating soybean rust (SBR) pathogen, Phakopsora pachyrhizi, encodes many secreted proteins, but only two have been functionally characterized for their roles in rust virulence. Here, we demonstrate that transient expression of P. pachyrhizi effector candidate 15 (PpEC15), an aspartic protease, leads to enhanced bacterial growth in planta, suppression of callose deposition, reduced expression of plant defense-related marker genes and suppression of pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species (ROS). Stable expression of PpEC15 in soybean suppresses PAMP-induced ROS production and enhances bacterial growth, indicating that, collectively, PpEC15 suppresses host and non-host innate immune responses. Yeast-two-hybrid and proximity labeling identified putative PpEC15 interacting partners including a peptide-chain release factor (PCRF), a NAC83 (NAM, ATAF, and CUC) transcription factor, and a DAHP (3-deoxy-7-phosphoheptulonate) synthase. We further show that PpEC15 can cleave DAHP but does not cleave PCRF or NAC83. Virus-induced gene silencing of NAC83, PCRF and DAHP altered PAMP-induced ROS production and salicylic acid production, indicating that these proteins may be involved in immune signaling. Collectively, our data show that PpEC15 is conserved across P. pachyrhizi isolates and other economically important rust species and is involved in the suppression of plant basal defense responses. Understanding the role of PpEC15 in P. pachyrhizi virulence will provide a foundation for designing targeted intervention strategies to generate rust-resistant crops.

plant biology↗

bioRxiv2022

A Re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling

Wheat blast, caused by the Triticum lineage of Pyricularia oryzae (PoT), is a serious disease that first emerged in Brazil and quickly spread to neighboring countries. The recent appearance of this disease in Bangladesh and Zambia highlights a need to understand the population biology and epidemiology of the disease so as to mitigate pandemic outbreaks. Current knowledge in these areas is largely based on analyses of wheat blast isolates collected in Brazil, and their comparison with isolates from non-wheat, endemic grasses. Those studies concluded that wheat blast is caused by a highly diverse P. oryzae population that lacks host specificity and, as a result, undergoes extensive gene flow with populations infecting non-wheat hosts. Additionally, based on genetic similarity between wheat blast and isolates infecting Urochloa species, it was proposed that the disease originally emerged via a host jump from this grass, and the widespread use of Urochloa as a pasture grass likely plays a central role in wheat blast epidemiology. Inconsistencies with earlier phylogenetic studies prompted us to re-analyze the Brazilian data in the context of a comprehensive, global, phylogenomic dataset. We now show that the seminal studies failed to sample the P. oryzae populations normally found on endemic grasses and, instead, repeatedly sampled PoT and P. oryzae Lolium (PoL) members that happened to be present in these hosts. The resulting lack of accurate and representative information about the grass-infecting populations in Brazil means that current conclusions about wheat blasts evolution, population biology and epidemiology are unsubstantiated and could be equivocal.

microbiology↗

bioRxiv2022

Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Global wheat production is seriously threatened by the filamentous fungal pathogen, Magnaporthe oryzae, causing wheat blast disease. The pathogen was first identified in South America and recently spread across continents to Bangladesh (South Asia) and Zambia (South-central Africa). M. oryzae strains closely related with a South American field isolate B71 was found to have caused the wheat blast outbreaks in South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Using an improved reference genome for B71 and whole genome sequences of isolates from Bangladesh, Zambia, and South America, we found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates. Structural variation analysis using whole genome short-read sequencing data indicate all isolates closely related to B71 maintained at least one supernumerary mini-chromosome and, interestingly, some Zambian isolates contain more than one mini-chromosome. Long-read sequencing and de novo genome assemblies of two Zambian isolates show that both contain a mini-chromosome similar to the B71 mini-chromosome, although pervasive structural variation exists among them. Genome assemblies also provide evidence that one Zambian isolate carries an additional mini-chromosome that is highly divergent from the B71 mini-chromosome. Our findings show that while the core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome during the multiple introductions, and the rapid sequence and structural variation suggests the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.

genomics↗

bioRxiv2021

Recombination of standing variation in a multi-hybrid swarm drove adaptive radiation in a fungal pathogen and gave rise to two pandemic plant diseases

Adaptive radiations fuel speciation and are characterized by rapid genetic diversification and expansion into new ecological niches. Historically, these processes were believed to be driven by selection on novel mutations but genomic analyses now indicate that standing variation and gene flow often have prominent roles. How "old" variation is combined, however, and its resulting genetic architecture within newly-adapted populations is not well understood. We reconstructed a recent radiation in the fungus, Pyricularia oryzae, that spawned a population pathogenic to eleven grass genera, and caused two new plant diseases: wheat blast - already a serious threat to global agriculture - and gray leaf spot of ryegrasses. We show that the new population evolved in a multi-hybrid swarm using only the standing variation that was present in seven individuals from five distinct, host-specialized lineages. Sexual and parasexual recombination within the swarm reassorted key host-specificity factors and generated more diversity in possibly just a few weeks than existing lineages had accumulated over hundreds to thousands of years. We suggest that the process was initiated by sexual opportunity arising when a fertile fungal strain was imported into Brazil on Urochloa introduced as forage for beef production; and we further contend that the host range expansion was largely fortuitous, with host selection playing little, if any, role in driving the process. Finally, we believe that our findings point to an overlooked role for happenstance in creating situations that allow organisms to skirt rules that would normally hold evolution in check. Commercial Endorsement DisclaimerMention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. Equal Opportunity/Non-Discrimination StatementUSDA is an equal opportunity provider and employer.

evolutionary biology↗

bioRxiv2019

Mai1 protein acts between host recognition of pathogen effectors and MAPK signaling

The molecular mechanisms acting between host recognition of pathogen effectors by NOD-like receptor (NLR) proteins and mitogen-activated protein kinase (MAPK) signaling cascades are unknown. MAPKKK (M3K) activates MAPK signaling leading to programmed cell death (PCD) associated with NLR-triggered immunity. We identified a tomato M3K-interacting protein, SlMai1, that has 80% amino acid identity with Arabidopsis brassinosteroid kinase 1 (AtBsk1). SlMai1 has a protein kinase domain and a C-terminal tetratricopeptide repeat domain which interacts with the kinase domain of M3K. Virus-induced gene silencing of Mai1 homologs in Nicotiana benthamiana increased susceptibility to Pseudomonas syringae and compromised PCD induced by four NLR proteins. PCD was restored by expression of a synthetic SlMai1 gene that resists silencing. Expression of AtBsk1 did not restore PCD in Mai1-silenced plants, suggesting SlMai1 is functionally divergent from AtBsk1. PCD caused by overexpression of M3K or MKK2 was unaffected by Mai1 silencing indicating Mai1 acts upstream of these proteins. Co-expression of Mai1 with M3K in leaves enhanced MAPK phosphorylation and accelerated PCD. These findings reveal Mai1 as a molecular link acting between host recognition of pathogens and MAPK signaling. Author SummaryPlants use intracellular immune receptors to detect and respond to specific effector proteins which pathogens translocate into the host cell as part of their infection process. Localized programmed cell death (PCD) involving a mitogen-activated protein kinase (MAPK) cascade is an important host response associated with effector-triggered immunity, although the molecular connections between immune receptors and MAPK signaling is unknown. The Mai1 protein was found to act downstream of multiple immune receptors in Nicotiana benthamiana and to physically interact with MAPKKK. The Mai1-MAPKKK interaction enhances MAPK phosphorylation, triggers PCD and promotes disease resistance.

plant biology↗

bioRxiv2017

Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae, and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously-used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the eco-evolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multi-host pathogen.\n\nImportanceInfection of novel hosts is a major route for disease emergence by pathogenic micro-organisms. Understanding the evolutionary history of multi-host pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multi-host fungus that causes serious cereal diseases, including the devastating rice blast disease, and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that inter-lineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

microbiology↗