A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 24, 2023

Abstract Human activity impacts the evolutionary trajectories of many species worldwide. Global trade agricultural goods contributes to dispersal pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how surmount control strategies cope with new climates is crucial predicting future impact crop pathogens. Here, we address this by assembling a global thousand-genome panel Zymoseptoria tritici , major fungal pathogen wheat reported in all production areas We identify invasion routes ongoing exchange among wheat-growing regions. find that expansion was accompanied increased transposable elements weakened genomic defenses. Finally, significant standing variation adaptation encountered during spread. Our work shows large population panels enable deep insights into trajectory pathogen.

Language: Английский

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Alternaria diseases on potato and tomato

Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 25(3)

Published: March 1, 2024

Abstract Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by solani brown spot alternata are most common, but the disease complex is far more diverse. We first provide an overview of species infecting two host plants to alleviate some confusion that arises from taxonomic rearrangements this fungal genus. Highlighting diversity fungi on both solanaceous hosts, we review studies investigating genetic genomes, before present recent advances elucidating host–pathogen interactions fungicide resistances. Taxonomy Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria. Biology range adopt diverse lifestyles. specifically crops ( Solanum tuberosum ) lycopersicum ). They necrotrophic pathogens with no known sexual stage, despite signatures recombination. Disease symptoms Symptoms early blight/brown include foliar lesions as spots, depending characteristic concentric rings, which eventually lead severe defoliation considerable yield loss. Control Good field hygiene can keep pressure low. Some cultivars show differences susceptibility, there fully resistant varieties known. Therefore, main control mechanism treatment fungicides.

Language: Английский

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Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(2), P. e1011130 - e1011130

Published: Feb. 14, 2023

The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression epigenetically silenced initiates bursts transposition that be counteracted by purifying selection and defenses. However, how these forces interact determine the expansion routes within a species remains largely unknown. Here, we analyzed set 19 telomere-to-telomere genomes fungal wheat Zymoseptoria tritici. Phylogenetic reconstruction ancestral state estimates individual TE families revealed have undergone distinct activation repression periods resulting highly uneven copy numbers between same species. Most are clustered gene poor niches, indicating strong against insertions near coding sequences, as consequence insertion site preferences. with high low sequence divergence signatures defense mechanisms (i.e., RIP). In contrast, small non-autonomous MITEs) less impacted located close proximity genes. Individual experienced multiple burst events generated many nearly identical copies. We found Copia element was initiated from recent copies inserted substantially closer genes compared older Overall, tended initiate GC-rich niches escaped inactivation genomic Our work shows specific environments features provide triggers for proliferation genomes.

Language: Английский

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Research on Genome Data Recognition and Analysis based on Louvain Algorithm

Published: July 16, 2024

In genomics analysis, with the development of sequencing technology and rapid growth data volume, how to effectively identify analyze important information in genomic from massive has become an challenge. Identify key patterns features through advanced community testing methods. First, often contains a lot noise redundant that needs be processed steps such as normalization, filtering, dimensionality reduction. Normalization makes at different scales comparable, filtering out points low quality or missing values, reduction reduces dimensions principal component analysis (PCA) retains main information. The gene co-expression network establishes connection relationship between genes by calculating expression similarity matrix genes, applies Louvain algorithm maximize modularity network, aggregate nodes layer layer, form structure, complex potential structure genes. Finally, we utilize cancer dataset evaluate proposed model. From our extensive experimental results, can observe Louvain's indicates outperformances accuracy recognition data.

Language: Английский

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Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: March 9, 2022

Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand molecular bases of their pathogenic lifestyles, we compared newly assembled genomes single strains fructicola, M. fructigena laxa, with those Botrytis cinerea Sclerotinia sclerotiorum, closest within Sclerotiniaceae. Phylogenomic analysis orthologous proteins syntenic investigation suggest that laxa is closer to than other investigated Sclerotiniaceae species. This indicates was earliest result speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). fructicola showed older bursts TE insertions, which affected (mainly in fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence sexual process fructicola. More recent expansion linked low RIP action fructigena, very little S. sclerotiorum B. cinerea. The detection active non-syntenic TEs indicative horizontal transfer has resulted alterations specific functions. Analysis candidate effectors, biosynthetic clusters secondary metabolites carbohydrate-active enzymes, indicated genus multiple virulence mechanisms infect host plants, including toxins, cell-death elicitor, putative factors cell-wall-degrading enzymes. Some species-specific might explain differences terms plant organ preferences between two

Language: Английский

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Transposable elements and their role in aging

Ageing Research Reviews, Journal Year: 2023, Volume and Issue: 86, P. 101881 - 101881

Published: Feb. 10, 2023

Language: Английский

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Update on the Basic Understanding of Fusarium graminearum Virulence Factors in Common Wheat Research

Plants, Journal Year: 2024, Volume and Issue: 13(8), P. 1159 - 1159

Published: April 22, 2024

Wheat is one of the most important food crops, both in China and worldwide. production facing extreme stresses posed by different diseases, including Fusarium head blight (FHB), which has recently become an increasingly serious concerns. FHB significant destructive diseases affecting wheat crops all over world. Recent advancements genomic tools provide a new avenue for study virulence factors relation to host plants. The current review focuses on recent progress strains infection. presence genome-wide repeat-induced point (RIP) mutations causes mutations, eventually leading plant susceptibility against invasion. Furthermore, effector proteins disrupt resistance mechanism. In this study, we proposed systematic modification genome using modern biological facilitate foreign We also suggested number scientific strategies, such as gene cloning, developing more powerful functional markers, haplotype marker-assisted selection, further improve associated breeding methods.

Language: Английский

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A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

Microbial Genomics, Journal Year: 2022, Volume and Issue: 8(4)

Published: April 26, 2022

is a fungal pathogen that causes leaf mould of tomato. The reference genome this was released in 2012 but its high repetitive DNA content prevented contiguous assembly and further prohibited the analysis architecture. In study, we combined third generation sequencing technology with Hi-C chromatin conformation capture technique, to produce high-quality near complete gene annotation Race 5 isolate

Language: Английский

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Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

Frontiers in Fungal Biology, Journal Year: 2022, Volume and Issue: 3

Published: Sept. 14, 2022

The genus

Language: Английский

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Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions

Biochemical Society Transactions, Journal Year: 2022, Volume and Issue: unknown

Published: May 6, 2022

DNA methylation is an epigenetic modification with a very long evolutionary history. However, evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of diversifies in different lineages, and lost altogether frequently. growing availability genomic epigenomic sequencing organisms highlights this diversity but also illuminates potential factors that could explain why both the machinery its evolve so rapidly. Key to are new discoveries about fitness costs associated methylation, theories how fundamental biochemical mechanisms introduction maintenance patterns evolve.

Language: Английский

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