ArticleScientific reports2017
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 49 citations in OpenAlex.
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.PLoS biology · 2024Article
- Are there conserved biosynthetic genes in lichens? Genome-wide assessment of terpene biosynthetic genes suggests ubiquitous distribution of the squalene synthase cluster.BMC genomics · 2024Article
- Exploration on cold adaptation of Antarctic lichen via detection of positive selection genes.IMA fungus · 2024Article
- De Novo Genome Assembly ofGenes · 2024Article
- Utilizing Deep Neural Networks to Fill Gaps in Small Genomes.International journal of molecular sciences · 2024Article
- Symbionts out of sync: Decoupled physiological responses are widespread and ecologically important in lichen associations.Science advances · 2024Article
- DL-TODA: A Deep Learning Tool for Omics Data Analysis.Biomolecules · 2023Article
- Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota).Genome biology and evolution · 2023Article
- Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics.Journal of fungi (Basel, Switzerland) · 2023Review
- Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens.Frontiers in fungal biology · 2022Article
- Prediction of Genes That Function in Methanogenesis and COMicroorganisms · 2021Article
- Depside and Depsidone Synthesis in Lichenized Fungi Comes into Focus through a Genome-Wide Comparison of the Olivetoric Acid and Physodic Acid Chemotypes ofBiomolecules · 2021Article
- Microbial Communities ofMicroorganisms · 2021Article
- An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota.Life (Basel, Switzerland) · 2020Review
- Fungal evolution: cellular, genomic and metabolic complexity.Biological reviews of the Cambridge Philosophical Society · 2020Article
- What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.Genome biology and evolution · 2020Article
- IMA Genome - F13: Draft genome sequences ofIMA fungus · 2020Article
- Improved metagenomic analysis with Kraken 2.Genome biology · 2019Article
- Fungal evolution: major ecological adaptations and evolutionary transitions.Biological reviews of the Cambridge Philosophical Society · 2019Review
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86-90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
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