Biology subjects

Richards, J. K.

Publications and source records attributed to Richards, J. K..

6 recordsLinked to original sources

bioRxiv2026

A high-quality genome resource for Cercospora cf. flagellaris, a causal agent of Cercospora leaf blight of soybeans

A highly contiguous and complete reference genome of Cercospora cf. flagellaris, the causal agent of foliar disease on many plant hosts including Cercospora leaf blight of soybean, was assembled using a combination of PacBio and Illumina sequencing reads. The genome assembly is 33.72 Mb in length and consists of 14 nuclear scaffolds and one mitochondrial contig. Four scaffolds have telomeric repeats on both ends and represent fully assembled chromosomes, while nine scaffolds represent partially assembled chromosomes with telomeric repeats on one end. The assembly has an N50 of 2.90 Mb and an L50 of 5 scaffolds. Genome annotation identified 11,268 genes, of which 947 and 360 were predicted to encode secreted proteins and effectors, respectively. Additionally, 512 genes were predicted to encode carbohydrate-active enzymes and 60 biosynthetic gene clusters were annotated. Taken together, this annotated genome assembly will be a valuable resource for genomics, host-pathogen interactions, and population biology research in this economically important pathosystem.

genomics↗

bioRxiv2024

Rpt5 encodes a receptor-like protein that provides broad and effective net form net blotch (Pyrenophora teres f. teres) resistance in barley

The foliar disease net form net blotch (NFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt), causes significant yield and quality losses of barley worldwide. Dominant resistance conferred by the Resistance to Pyrenophora teres 5(Rpt5) gene from barley line CI5791 is the broadest and most effective resistance reported in this pathosystem. The Rpt5 locus was identified in multiple independent genetic studies utilizing diverse host populations and Ptt isolates, and harbors both dominant Rpt5 resistance and isolate-specific susceptibility genes/alleles that are dominant in the absence of Rpt5, designated susceptibility to Pyrenophora teres 1 (Spt1). Ptt virulence and avirulence effectors from diverse pathogen isolates genetically interact with the Rpt5/Spt1 locus, suggesting a complex locus with a function targeted by the evolution of a diversity of pathogen effectors. High-resolution mapping utilizing 1,920 recombinant gametes from a CI5791 x Tifang biparental population, identified 12 candidate genes in an [~]4.6 Mb delimited region in the cv Morex V3 genome assembly, but is 1.1 - 2.2 Mb in the pangenome assemblies, containing 5-12 genes. Analysis revealed a strong correlation between the CI5791 allele of a receptor-like protein (RLP), provisionally designated Rpt5 candidate gene 1, (Rcg1), and broad Rpt5-mediated resistance. Two independent transformants of the CI5791 Rcg1 allele in the susceptible cv Golden Promise background showed significantly increased resistance when challenged with Rpt5 avirulent Ptt isolates 6A, 15A, and 0-1 compared to the Golden Promise wildtype. Thus, Rpt5, encodes an RLP and is the first net blotch resistance gene cloned in barley. Significance StatementNet form net blotch (NFNB) causes substantial yield and quality losses of barley worldwide. Despite decades of ongoing research into genetic resistance to Pyrenophora teres f. teres, the causal agent of NFNB, no host resistance or susceptibility genes in this pathosystem had been previously identified. We present the identification and validation of Rpt5, which confers the broadest and most effective resistance against NFNB. To our knowledge Rpt5 is the first genetically defined resistance gene in a monocot to encode an RLP.

plant biology↗

bioRxiv2023

The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres

Centromeres are constricted chromosomal regions that are essential for cell division. In eukaryotes, centromeres display a remarkable architectural and genetic diversity. The basis of centromere accelerated evolution remains elusive. Here we focused on Pneumocystis species, a group of Mammalian-specific fungal pathogens that form a sister taxon with that of the Schizosaccharomyces pombe, an important genetic model for centromere biology research. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-Seq, we identified CENP-A bound regions in two Pneumocystis species that diverged [~]35 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. These features suggest an epigenetic specification of centromere function. Analysis of centromeric DNA across multiple Pneumocystis species suggest a vertical transmission at least 100 million years ago. Common ancestry of Pneumocystis and S. pombe centromeres is untraceable at the DNA level but the overall architectural similarity could be the result of functional constraint for successful chromosomal segregation. Significance StatementPneumocystis species offer a suitable genetic system to study centromere evolution in pathogens because of their phylogenetic proximity with the nonpathogenic yeast Schizosaccharomyces pombe, a popular model for cell biology. We used this system to explore how centromeres have evolved after divergence of the two clades [~]460 million years ago. To address this question, we established a protocol combining short-term culture and ChIP-Seq to characterize centromeres in multiple Pneumocystis species. We show that Pneumocystis have short epigenetic centromeres that function differently from those in S. pombe. One sentence summaryInsights into the formation of genic centromeres in fungal pathogens.

genomics↗

bioRxiv2023

Pathogen genetics identifies avirulence/virulence loci associated with barley chromosome 6H resistance in the Pyrenophora teres f. teres - barley interaction

Barley net form net blotch (NFNB) is a foliar disease caused by Pyrenophora teres f. teres. Barley line CIho5791, which harbors the chromosome 6H broad spectrum resistance gene Rpt5, displays dominant resistance to P. teres f. teres. To genetically characterize P. teres f. teres avirulence/virulence on the barley line CIho5791, we generated a P. teres f. teres mapping population using a cross between the Moroccan CIho5791-virulent isolate MorSM40-3, and the avirulent reference isolate 0-1. Genetic maps were generated for all 12 chromosomes (Ch) and quantitative trait locus (QTL) mapping identified two significant QTL associated with P. teres f. teres avirulence/virulence on CIho5791. The most significant QTL mapped to P. teres f. teres Ch1 where the virulent allele was contributed by MorSM40-3. A second QTL mapped to Ch8, however, this virulent allele was contributed by 0-1. The Ch1 and Ch8 loci accounted for 27 and 15% of the disease variation, respectively and the avirulent allele at the Ch1 locus was shown to be epistatic over the virulent allele at the Ch8 locus. Additionally, we used 177 sequenced P. teres f. teres isolates in a genome wide association study that identified the same Ch1 and Ch8 loci as the two most significant associations. Within the identified genomic regions, we identified several genes that encoded small secreted proteins, one or more of which may be responsible for overcoming the CIho5791 resistance. Results presented here demonstrate the complexity of avirulence/virulence in the P. teres f. teres - barley interaction.

genetics↗

bioRxiv2021

A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat

Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys a suite of effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Nine effector - host susceptibility gene interactions have been reported in this pathosystem, presumed to be governed by unique pathogen effectors. This study presents the characterization of the SnTox267 necrotrophic effector that hijacks two separate host pathways to cause necrosis. An association mapping approach identified SnTox267 and the generation of gene-disrupted mutants and gain-of-function transformants confirmed its role in Snn2-, Snn6-, and Snn7-mediated necrosis. The Snn2 and Snn6 host susceptibility genes were complementary, and together they functioned cooperatively to elicit SnTox267-induced necrosis in the same light-dependent PCD pathway. Additionally, we showed that SnTox267 targeted Snn7, resulting in light-independent necrosis. Therefore, SnTox267 co-opts two distinct host pathways to elicit PCD. SnTox267 sequence comparison among a natural population of 197 North American P. nodorum isolates revealed 20 protein isoforms conferring variable levels of virulence, indicating continuing selection pressure on this gene. Protein isoform prevalence among discrete populations indicated that SnTox267 has likely evolved in response to local selection pressures and has diversified more rapidly in the Upper Midwest. Deletion of SnTox267 resulted in the upregulation of the unrelated effector genes SnToxA, SnTox1, and SnTox3, providing evidence for a complex genetic compensation mechanism. These results illustrate a novel evolutionary path by which a necrotrophic fungal pathogen uses a single proteinaceous effector to hijack two host pathways to induce cell death.

pathology↗

bioRxiv2019

A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies sub-telomeric regions as drivers of virulence

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in sub-telomeric regions of chromosomes with 10 of the 14 accessory region QTL localizing to sub-telomeric regions. Comparative analysis of the sub-telomeric regions of P. teres f. teres chromosomes revealed translocation events where homology was detected between non-homologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the sub-telomeric accessory genomic compartments not only harbor most of the known virulence loci, but also that these regions have the capacity to rapidly evolve.

genomics↗