Genomic and phenomic approaches for studying Puccinia sorghi-maize interactions DOI Open Access
Katerina L. Holan

Опубликована: Янв. 1, 2023

Rust fungal pathogens comprise the largest group of plant pathogenic fungi. Due to limitations their study, like an inability be cultured or difficulty in making genetic modifications, there are many gaps knowledge base these organisms. One rust species, Puccinia sorghi, is a worldwide pathogen maize that can cause significant yield losses. Much research for P. sorghi focuses on qualitative disease phenotypes various isolates different backgrounds, with limited information regarding key pathogenicity genes (effectors) required successful infection within this pathosystem. It imperative further develop genomic and phenomic tools available use effector characterization screens. With recent advent long-read sequencing, genome assembly has transitioned from exceedingly fragmented contigs based short-read sequencing large, repeat-resolved scaffolds. More complete genomes have led discoveries about true size, repeat content, gene content Well-annotated assemblies also allow prediction candidate proteins function as virulence determinants. In work, resources expanded highly contiguous, previously undescribed isolate (IA16). Comprehensive annotation utilizing expressed sequence tags several timepoints across cycle enabled additional effectors species. Comparison candidates other will lead particular isolate's virulence. We report members rust-specific secreted protein family present IA16 isolate. Of eight candidates, we were able demonstrate one weak suppressor hypersensitive immune response heterologous system Nicotiana benthamiana. This work utilized automated phenotyping setup acquire time lapse images leaves during experimental assays. By pairing assays platforms, increase throughput, accuracy, consistency results. Lastly, detail machine learning approach quantifying common leaves. Because plant-pathogen interactions complex, small changes phenotype undetectable by human measurements may occur, development easy-to-use computer vision-based platforms provide consistent quantitative results essential. Additionally, better understanding minimum requirements given useful future development, speed at which new developed. demonstrates viable accurate quantification symptoms, corroborating ground truth provides extensive image data applications. Overall, dissertation presents multi-disciplinary study both pipelines interactions.

Язык: Английский

From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi DOI Creative Commons
Asanka Madhushan,

Dulan Bhanuka Weerasingha,

Evgeny Ilyukhin

и другие.

Journal of Fungi, Год журнала: 2025, Номер 11(1), С. 25 - 25

Опубликована: Янв. 1, 2025

Since the domestication of plants, pathogenic fungi have consistently threatened crop production, evolving genetically to develop increased virulence under various selection pressures. Understanding their evolutionary trends is crucial for predicting and designing control measures against future disease outbreaks. This paper reviews evolution fungal pathogens from natural habitats agricultural settings, focusing on eight significant phytopathogens: Pyricularia oryzae, Botrytis cinerea, Puccinia spp., Fusarium graminearum, F. oxysporum, Blumeria graminis, Zymoseptoria tritici, Colletotrichum spp. Also, we explore mechanism used understand in these fungi. The studied evolved agroecosystems through either (1) introduction elsewhere; or (2) local origins involving co-evolution with host shifts, genetic variations within existing strains. Genetic variation, generated via sexual recombination asexual mechanisms, often drives pathogen evolution. While rare mainly occurs at center origin pathogen, mechanisms such as mutations, parasexual recombination, horizontal gene chromosome transfer, chromosomal structural are predominant. Farming practices like mono-cropping resistant cultivars prolonged use fungicides same mode action can drive emergence new pathotypes. Furthermore, range does not necessarily impact adaptation Although halting impractical, its pace be slowed by managing selective pressures, optimizing farming practices, enforcing quarantine regulations. study has been transformed advancements molecular biology, genomics, bioinformatics, utilizing methods next-generation sequencing, comparative transcriptomics population genomics. However, continuous research remains essential monitor how evolve over time proactive strategies that mitigate agriculture.

Язык: Английский

Процитировано

1
Genome biology and evolution of mating-type loci in four cereal rust fungi DOI Creative Commons
Zhenyan Luo, Alistair R. McTaggart, Benjamin Schwessinger

и другие.

PLoS Genetics, Год журнала: 2024, Номер 20(3), С. e1011207 - e1011207

Опубликована: Март 18, 2024

Permanent heterozygous loci, such as sex- or mating-compatibility regions, often display suppression of recombination and signals genomic degeneration. In Basidiomycota, two distinct loci confer mating compatibility. These encode homeodomain ( HD ) transcription factors pheromone receptor Pra )-ligand allele pairs. To date, an analysis genome level mating-type (MAT) is lacking for obligate biotrophic basidiomycetes in the Pucciniales , order containing serious agricultural plant pathogens. Here, we focus on four species Puccinia that infect oat wheat, including P . coronata f. sp. avenae graminis tritici triticina striiformis MAT are located separate chromosomes supporting previous hypotheses a tetrapolar compatibility system The genes multiallelic all while PR locus appears biallelic, except which potentially has multiple alleles. largely conserved their macrosynteny, both within between species, without strong suppression. Regions proximal to locus, however, displayed signs degeneration three with biallelic locus. Our observations support link suppression, degeneration, diversity consistent recent mathematical modelling simulations. Finally, confirm expressed during asexual infection cycle, propose this may regulating nuclear maintenance pairing spore formation. study provides insights into evolution key pathogenic species. Understanding can help predict possible combinations pairs, generated by sexual reproduction somatic recombination, potential new virulent isolates these important

Язык: Английский

Процитировано

8
Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina DOI Creative Commons
Jana Sperschneider, Tim Hewitt, David C. Lewis

и другие.

Nature Microbiology, Год журнала: 2023, Номер 8(11), С. 2130 - 2141

Опубликована: Окт. 26, 2023

Abstract In clonally reproducing dikaryotic rust fungi, non-sexual processes such as somatic nuclear exchange are postulated to play a role in diversity but have been difficult detect due the lack of genome resolution between two haploid nuclei. We examined three nuclear-phased assemblies Puccinia triticina , which causes wheat leaf disease. found that most recently emerged Australian lineage was derived by pre-existing lineages, originated Europe and North America. Haplotype-specific phylogenetic analysis reveals repeated events shuffled nuclei long-term clonal leading global P. population representing different combinations limited number genomes. Thus, seems be predominant mechanism generating emergence new strains this otherwise pathogen. Such genomics-accelerated surveillance pathogen evolution paves way for more accurate disease monitoring.

Язык: Английский

Процитировано

11
From Lesions to Lessons: Two Decades of Filamentous Plant Pathogen Genomics DOI Creative Commons
Wagner C. Fagundes,

Yu-Seng Huang,

Susanne Häußler

и другие.

Molecular Plant-Microbe Interactions, Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

Filamentous plant pathogens pose a severe threat to food security. Current estimates suggest up 23% yield losses pre- and post-harvest diseases these are projected increase due climate change (Singh et al. 2023; Chaloner 2021; Stukenbrock Gurr Fisher 2012; Steinberg 2020). Understanding how filamentous emerge, spread adapt their hosts new environmental niches is crucial address devastating impact on global agriculture. Over the past two decades, genomics has emerged as central technology advance our understanding of population dynamics coevolution pathogens. The first genome pathogen, blast fungus Magnaporthe oryzae, was sequenced 20 years ago. Since then, pathogen not only provided deep genomic makeup populations, but fundamental for gene discovery, disease diagnostics, accelerated molecular biology. In merely we have witnessed several revolutions in field, including reference genomes many pathogens, scale thousands individuals, long-read chromosome conformation sequencing highly continuous assemblies recent intersections structural Here, commemorate 20th anniversary by presenting important technological advances (Fig. 1) lessons learned from decades genomics, with focus cereal diseases.

Язык: Английский

Процитировано

0
Complete genome sequence of a novel mitovirus identified in the phytopathogenic fungus Puccinia triticina DOI
Yanhui Zhang, Na Wang,

Jinyang Li

и другие.

Archives of Virology, Год журнала: 2025, Номер 170(5)

Опубликована: Март 27, 2025

Язык: Английский

Процитировано

0
Genomics Research on the Road of Studying Biology and Virulence of Cereal Rust Fungi DOI Creative Commons
Haixia Guan, Peng Zhang, Robert Park

и другие.

Molecular Plant Pathology, Год журнала: 2025, Номер 26(4)

Опубликована: Апрель 1, 2025

ABSTRACT Rust fungi are highly destructive pathogens that pose a significant threat to crop production worldwide, especially cereals. Obligate biotrophy and, in many cases, complex life cycles make rust particularly challenging study. However, recent rapid advances sequencing technologies and genomic analysis tools have revolutionised fungal research. It is anticipated the increasing availability ongoing substantial improvements genome assemblies will propel field of biology into post‐genomic era, instigating cascade research endeavours encompassing multi‐omics gene discoveries. This case for cereal pathogens, which continental‐scale studies virulence been conducted over years historical collections viable isolates sequenced assembled. Genomic plays crucial role uncovering underlying causes high variability complexity population dynamics fungi. Here, we provide an overview progress genomics, discuss strategies employed analysis, elucidate strides drive era.

Язык: Английский

Процитировано

0
Genomic and phenomic approaches for studying Puccinia sorghi-maize interactions DOI Open Access
Katerina L. Holan

Опубликована: Янв. 1, 2023

Rust fungal pathogens comprise the largest group of plant pathogenic fungi. Due to limitations their study, like an inability be cultured or difficulty in making genetic modifications, there are many gaps knowledge base these organisms. One rust species, Puccinia sorghi, is a worldwide pathogen maize that can cause significant yield losses. Much research for P. sorghi focuses on qualitative disease phenotypes various isolates different backgrounds, with limited information regarding key pathogenicity genes (effectors) required successful infection within this pathosystem. It imperative further develop genomic and phenomic tools available use effector characterization screens. With recent advent long-read sequencing, genome assembly has transitioned from exceedingly fragmented contigs based short-read sequencing large, repeat-resolved scaffolds. More complete genomes have led discoveries about true size, repeat content, gene content Well-annotated assemblies also allow prediction candidate proteins function as virulence determinants. In work, resources expanded highly contiguous, previously undescribed isolate (IA16). Comprehensive annotation utilizing expressed sequence tags several timepoints across cycle enabled additional effectors species. Comparison candidates other will lead particular isolate's virulence. We report members rust-specific secreted protein family present IA16 isolate. Of eight candidates, we were able demonstrate one weak suppressor hypersensitive immune response heterologous system Nicotiana benthamiana. This work utilized automated phenotyping setup acquire time lapse images leaves during experimental assays. By pairing assays platforms, increase throughput, accuracy, consistency results. Lastly, detail machine learning approach quantifying common leaves. Because plant-pathogen interactions complex, small changes phenotype undetectable by human measurements may occur, development easy-to-use computer vision-based platforms provide consistent quantitative results essential. Additionally, better understanding minimum requirements given useful future development, speed at which new developed. demonstrates viable accurate quantification symptoms, corroborating ground truth provides extensive image data applications. Overall, dissertation presents multi-disciplinary study both pipelines interactions.

Язык: Английский

Процитировано

0