nanopore sequencing – mycolab.ai

Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research

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Mushrooms and related fungi in the basidiomycete group produce many useful medicines and agricultural chemicals. Scientists have traditionally struggled to study these fungi because they grow slowly and have complex genomes. Recent technological breakthroughs—including faster DNA sequencing and gene-editing tools—are now making it much easier to discover and understand the helpful compounds these fungi produce, potentially leading to new medicines.

Gapless near Telomer-to-Telomer Assembly of Neurospora intermedia, Aspergillus oryzae, and Trichoderma asperellum from Nanopore Simplex Reads

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Scientists developed an automated computer workflow that can assemble complete fungal genomes using data from a single type of DNA sequencer. They tested this method on three industrially important fungi and successfully created high-quality, gap-free genome maps for all three. This breakthrough means researchers can now generate high-quality fungal genome sequences faster and more cheaply than before, which will help improve our understanding of these organisms.

Integrated Transcriptomics and Metabolomics Provide Insight into Degeneration-Related Molecular Mechanisms of Morchella importuna During Repeated Subculturing

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Morel mushrooms are prized edible fungi that unfortunately degrade when repeatedly cultured in the laboratory, becoming slower-growing and less productive. Researchers used advanced genetic and chemical analysis to discover that degeneration occurs when the mushroom stops producing flavonoids, natural antioxidants that protect cells from damage. A specific gene called NR-PKS is responsible for making these protective flavonoids, and it shuts down in degraded strains. The study suggests that preservation methods using cold storage or adding antioxidants could help maintain healthy, productive morel cultures.

Clinical and Genomic Insights into Antifungal Resistance in Aspergillus Isolates from Thailand

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Researchers in Thailand identified a dangerous fungal infection caused by Aspergillus fumigatus that is resistant to azole antifungal drugs. This is the first time this specific drug-resistant strain has been found in a patient sample in Thailand, though it had been previously detected in environmental samples. The study used genetic testing to understand how the fungus developed resistance and found that it has altered genes that help it survive the antifungal medications commonly used to treat infections.

Integrated Transcriptomics and Metabolomics Provide Insight into Degeneration-Related Molecular Mechanisms of Morchella importuna During Repeated Subculturing

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Morel mushrooms lose quality when repeatedly cultured in laboratories, becoming slower-growing and less vibrant. Scientists discovered this happens because genes controlling antioxidant production shut down, allowing harmful free radicals to damage cells. By avoiding frequent subculturing and using cold storage or antioxidant supplements, farmers can keep their morel strains healthy and productive for longer.

Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand

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Researchers in Thailand studied a fungal infection called sporotrichosis that affects both cats and people. They used advanced DNA sequencing technology to identify the specific type of fungus and understand how it’s related to similar fungi found in other parts of the world. They also tested how well common antifungal medications work against these fungi and found that some isolates are becoming harder to treat.

Clinical and Genomic Insights into Antifungal Resistance in Aspergillus Isolates from Thailand

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Researchers in Thailand found that certain fungal infections caused by Aspergillus fumigatus are becoming resistant to common antifungal medications like voriconazole. They identified a specific genetic mutation called TR34/L98H in one patient sample that makes the fungus resistant to azole drugs used to treat these serious infections. By analyzing the genetic makeup of these resistant fungi, scientists discovered additional changes beyond the known resistance gene, suggesting these organisms may adapt in multiple ways to survive treatment. This is the first time this particular resistance mutation has been detected in a clinical patient sample in Thailand, indicating that antifungal resistance in Aspergillus is spreading and requires closer monitoring and testing.

Detection of Multiple Nosocomial Trichosporon asahii Transmission Events via Microsatellite Typing Assay, South America

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Researchers developed a new genetic fingerprinting method to identify and track Trichosporon asahii, a dangerous fungal infection that spreads in hospitals. Using this tool on clinical samples from South America, they discovered multiple separate outbreak events where the same fungal strains infected patients across different hospitals and years. This method is faster and cheaper than other genetic tests, making it useful for hospitals worldwide to detect and prevent fungal outbreaks.

De novo genome sequencing and comparative analyses of the clinically relevant species Mucor ardhlaengiktus, Mucor circinelloides, Mucor griseocyanus, and Mucor janssenii

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Scientists have sequenced and analyzed the complete genomes of four species of Mucor fungus that cause serious infections in humans. Using advanced long-read sequencing technology, they created high-quality genetic blueprints for these organisms, which will help doctors better identify which Mucor species is causing infections and enable faster diagnosis and treatment of these dangerous fungal infections.

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study

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This study shows that Nanopore DNA sequencing can reliably identify fungi in decaying wood. Researchers developed guidelines for quality filtering of Nanopore data to ensure accurate identification of fungal species. They found that specific mycorrhizal fungi, particularly Laccaria amethystina and Tomentella sublilacina, colonize young beech trees growing on decaying logs and help them obtain nutrients.

Research Keyword: nanopore sequencing