phylogenomics – Page 2

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

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Fungi are found everywhere on Earth and play critical roles in breaking down organic matter, supporting plant growth, and providing food and medicines. Scientists have recently reorganized how fungi are classified into nine major groups using genetic analysis, which has helped clarify evolutionary relationships that were previously unclear. This comprehensive review explains what distinguishes each fungal group, how they are related to each other evolutionarily, and why fungi deserve more attention in biology education given their importance to human life and global ecosystems.

Genome sequence of the novel Cystobasidiomycetes fungal isolate EMM_F5

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Researchers isolated and sequenced the genome of a previously unclassified yeast called EMM_F5 found on Magnolia tree leaves. Through genetic analysis, they determined this yeast belongs to the Cystobasidiomycetes class and likely represents a new family called Microsporomycetaceae. This discovery fills an important gap in fungal genomics by providing the first genetic information available for this family of fungi.

Diploid-dominant life cycles characterize the early evolution of Fungi

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Scientists studied the evolutionary history of fungi by sequencing the genomes of 69 water-dwelling fungi. They discovered that contrary to what textbooks say, many fungi actually have diploid-dominant life cycles (like animals) rather than haploid-dominant ones (with single copies of genes). The ancient ancestor of all fungi was likely diploid, and different fungal groups lost this trait at different times in evolution.

The First Whole Genome Sequence and Methylation Profile of Gerronema lapidescens QL01

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Scientists have sequenced the complete genome of Lei Wan (Gerronema lapidescens), a medicinal mushroom used in traditional Chinese medicine for treating parasitic infections and digestive problems. The research reveals the mushroom’s genetic blueprint, including genes responsible for producing beneficial compounds and adapting to rocky mountain environments. This foundational work aims to enable sustainable cultivation of this rare fungus and development of new medicinal treatments, addressing current conservation threats from over-harvesting.

Genomic characterization and fermentation study of the endophyte Stemphylium sp. (Aa22), a producer of bioactive alkyl-resorcinols

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Scientists have studied a beneficial fungus called Stemphylium sp. Aa22 that lives inside wormwood plants and produces natural insect-repelling compounds called alkyl-resorcinols. By reading the complete genetic code of this fungus, researchers identified the gene responsible for making these compounds and found that growing the fungus in liquid culture produces more of the desired compounds than growing it on solid rice. This research could lead to developing natural, environmentally-friendly pesticides to protect crops from aphids and other pests.

A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus

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Scientists developed a new method to accurately identify and distinguish different strains of button mushrooms using genetic markers derived from core genes. This method is more accurate and simpler than previous approaches and can be applied to other mushroom species and fungi. The research helps mushroom farmers and breeders properly identify cultivars and protect their varieties from unauthorized propagation.

Haplotype-Phased Chromosome-Level Genome Assembly of Floccularia luteovirens Provides Insights into Its Taxonomy, Adaptive Evolution, and Biosynthetic Potential

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Scientists have created the most detailed genetic map of the yellow mushroom (Floccularia luteovirens), a highly valued medicinal and edible fungus from the Tibetan Plateau. Using advanced sequencing technology, they mapped its 13 chromosomes and identified 15 pathways that the mushroom uses to make potentially useful healing compounds. The research also solved a long-standing mystery about the mushroom’s family tree, proving it is not actually related to Armillaria mushrooms as previously thought. This genetic blueprint opens new possibilities for developing medicines from this special fungus.

What’s in a name? Fit-for-purpose bacterial nomenclature: meeting report

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Scientists are discovering and renaming bacteria so rapidly that doctors and other professionals sometimes don’t recognize the new names, which can cause confusion in patient care and food safety. This meeting brought together experts to discuss the problem and create better systems for managing these changes. The key finding is that when bacteria get new scientific names, there needs to be better communication with the practical users like clinicians so they stay informed and can provide proper treatment.

Trichoderma tlahuicanensis sp. nov. (Hypocreaceae), a novel mycoparasite of Fusarium oxysporum and Phytophthora capsici isolated from a traditional Mexican milpa

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Scientists discovered and formally named a new fungal species called Trichoderma tlahuicanensis, found in traditional Mexican farming fields. This fungus naturally attacks harmful plant diseases like those caused by Fusarium and Phytophthora, making it valuable for protecting crops without synthetic chemicals. The researchers used advanced DNA sequencing to confirm it was indeed a new species, distinct from known Trichoderma relatives.

Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

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Researchers sequenced the complete genome of a wild button mushroom strain (ARP23) that has been successfully bred with commercial mushrooms to create the ‘Heirloom’ variety. This strain is larger and contains more genes than other known button mushroom strains, making it valuable for breeding disease-resistant varieties. The genome sequence reveals that all button mushroom strains share core genes for breaking down plant material in compost, but have diverse collections of optional genes. This genetic resource provides a foundation for developing mushrooms more resistant to diseases and viruses.

Research Keyword: phylogenomics