ArticleNucleic acids research2023
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
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- Complex multicellularity is linked with expanded specialized metabolite production in microorganisms.Nature microbiology · 2026Article
- Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.Environmental microbiome · 2026Article
- Chromosome-level assembly and phylophenetic insights of Cladosporium oxysporum A3.I.1, a fungus with the ability to degrade polyurethane polymers.G3 (Bethesda, Md.) · 2026Article
- DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.Antonie van Leeuwenhoek · 2026Review
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- The application potential ofIMA fungus · 2026Review
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- Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.Environmental microbiology · 2025Article
- When Conventional Methods Fail: First Detection of aMicroorganisms · 2025Article
- Telomeric assemblies ofbioRxiv : the preprint server for biology · 2025Article
- Gapless near Telomer-to-Telomer Assembly ofJournal of fungi (Basel, Switzerland) · 2025Article
- Genomic analyses of Purpureocillium lilacinum reveal unique DNA regions for developing isolate-specific molecular markers.BMC genomics · 2025Article
- High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap MushroomMicroorganisms · 2025Article
- Profiling the Genomes and Secreted Effector Proteins inJournal of fungi (Basel, Switzerland) · 2025Article
- Genomic and Functional Analysis of a Novel YeastJournal of fungi (Basel, Switzerland) · 2025Article
- Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes.Genome biology and evolution · 2025Article
- A conserved terpene cyclase gene in Sanghuangporus for abscisic acid-related sesquiterpenoid biosynthesis.BMC genomics · 2025Article
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
In phylogenomics the evolutionary relationship of organisms is studied by their genomic information. A common approach to phylogenomics is to extract related genes from each organism, build a multiple sequence alignment and then reconstruct evolution relations through a phylogenetic tree. Often a set of highly conserved genes occurring in single-copy, called core genes, are used for this analysis, as they allow efficient automation within a taxonomic clade. Here we introduce the Universal Fungal Core Genes (UFCG) database and pipeline for genome-wide phylogenetic analysis of fungi. The UFCG database consists of 61 curated fungal marker genes, including a novel set of 41 computationally derived core genes and 20 canonical genes derived from literature, as well as marker gene sequences extracted from publicly available fungal genomes. Furthermore, we provide an easy-to-use, fully automated and open-source pipeline for marker gene extraction, training and phylogenetic tree reconstruction. The UFCG pipeline can identify marker genes from genomic, proteomic and transcriptomic data, while producing phylogenies consistent with those previously reported, and is publicly available together with the UFCG database at https://ufcg.steineggerlab.com.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.