Academic Journal
Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus.
| Τίτλος: | Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus. |
|---|---|
| Συγγραφείς: | Huberman LB; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720., Villalobos-Escobedo JM; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.; Environmental Genomics and Systems Biology Division/Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.; Tecnologico de Monterrey, Institute for Obesity Research, Monterrey, NL 64700, México., Skerker JM; Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720., Shi R; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720., Rico-Ramírez AM; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720., Adams CA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.; Environmental Genomics and Systems Biology Division/Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720., Arkin AP; Environmental Genomics and Systems Biology Division/Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.; Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720., Deutschbauer AM; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.; Environmental Genomics and Systems Biology Division/Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720., Glass NL; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720.; Environmental Genomics and Systems Biology Division/Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720. |
| Πηγή: | Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2026 Sep; Vol. 123 (35), pp. e2616888123. Date of Electronic Publication: 2026 Aug 25. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Washington, DC : National Academy of Sciences |
| Ιατρικοί όροι (MeSH): | Genomics*/methods , Trichoderma*/genetics , Fungi*/genetics , Gene Library* , Mutation*, Agrobacterium tumefaciens/genetics ; Genome, Fungal ; Mutagenesis, Insertional |
| Περίληψη: | Advances in sequencing technology enabling rapid and inexpensive whole-genome sequencing highlight how few genes are functionally characterized. This problem is particularly acute in filamentous fungi, where even in the best studied organisms upward of half of genes are poorly characterized or unannotated. High-throughput tools to identify gene function exist for single-celled organisms, like yeast and bacteria. However, filamentous fungi present challenges to high-throughput gene characterization, including low transformation efficiency and multinucleate cells. Filamentous fungi are critical components of nutrient cycling in ecosystems, form symbioses with plants that improve nutrient uptake, and are devastating human, plant, and animal pathogens causing millions of deaths and substantial crop loss each year. Thus, it is critical to overcome challenges to rapid gene characterization in filamentous fungi. We generated a library of hundreds of millions of uniquely barcoded plasmids containing a broad host-range drug resistance marker for ectopic insertion into filamentous fungal genomes by Agrobacterium tumefaciens. We then optimized A. tumefaciens mediated transformation of the biocontrol agent Trichoderma atroviride and made an insertional mutagenesis library containing 83,311 barcoded insertions, disrupting 5,331 of 11,863 predicted genes. This library enables high-throughput screens to rapidly connect genotype to phenotype. Quantifying relative barcode abundance in the pooled library before and after exposure to experimental conditions identified candidate genes and recovered known pathway components in amino acid biosynthetic, fructose utilization, and xylose utilization pathways. This resource establishes a scalable platform for high-throughput functional genomics in filamentous fungi, enabling investigations of fungal biology to improve medical outcomes, biotechnology, and sustainable agriculture. |
| Competing Interests: | Competing interests statement:Reviewers D.B.-P. and R.B.B. were co-authors on a state of the field summary manuscript in 2025 with co-author N.L.G. |
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| Grant Information: | R35 GM150926 United States GM NIGMS NIH HHS; R35GM150926 HHS | NIH | National Institute of General Medical Sciences (NIGMS); DE-AC02-05CH11231 U.S. Department of Energy (DOE) |
| Contributed Indexing: | Keywords: Trichoderma; barcoded mutant library; filamentous fungi; high-throughput functional genomics; high-throughput screen |
| Entry Date(s): | Date Created: 20260825 Date Completed: 20260825 Latest Revision: 20260904 |
| Update Code: | 20260904 |
| PubMed Central ID: | PMC13534542 |
| DOI: | 10.1073/pnas.2616888123 |
| PMID: | 42640796 |
| Βάση Δεδομένων: | MEDLINE |
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