{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T07:30:51Z","timestamp":1791531051952,"version":"4.3.4"},"reference-count":61,"publisher":"National Academy of Sciences","issue":"35","license":[{"start":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T00:00:00Z","timestamp":1787616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"HHS | NIH | National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM150926"],"award-info":[{"award-number":["R35GM150926"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:p>\n                    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\n                    <jats:italic toggle=\"yes\">Agrobacterium tumefaciens<\/jats:italic>\n                    . We then optimized\n                    <jats:italic toggle=\"yes\">A. tumefaciens<\/jats:italic>\n                    mediated transformation of the biocontrol agent\n                    <jats:italic toggle=\"yes\">Trichoderma atroviride<\/jats:italic>\n                    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.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2616888123","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T16:36:09Z","timestamp":1787675769000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":2,"title":["Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus"],"prefix":"10.1073","volume":"123","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2638-8528","authenticated-orcid":false,"given":"Lori B.","family":"Huberman","sequence":"first","affiliation":[{"name":"Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University","place":["Ithaca"]},{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 M.","family":"Villalobos-Escobedo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]},{"id":[{"id":"https:\/\/ror.org\/02jbv0t02","id-type":"ROR","asserted-by":"publisher"}],"name":"Environmental Genomics and Systems Biology Division\/Biosciences Area, Lawrence Berkeley National Laboratory","place":["Berkeley"]},{"id":[{"id":"https:\/\/ror.org\/03ayjn504","id-type":"ROR","asserted-by":"publisher"}],"name":"Tecnologico de Monterrey, Institute for Obesity Research","place":["Monterrey, M\u00e9xico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2653-1566","authenticated-orcid":false,"given":"Jeffrey M.","family":"Skerker","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Bioengineering, University of California Berkeley","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ran","family":"Shi","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana M.","family":"Rico-Ram\u00edrez","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catharine A.","family":"Adams","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]},{"id":[{"id":"https:\/\/ror.org\/02jbv0t02","id-type":"ROR","asserted-by":"publisher"}],"name":"Environmental Genomics and Systems Biology Division\/Biosciences Area, Lawrence Berkeley National Laboratory","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam P.","family":"Arkin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02jbv0t02","id-type":"ROR","asserted-by":"publisher"}],"name":"Environmental Genomics and Systems Biology Division\/Biosciences Area, Lawrence Berkeley National Laboratory","place":["Berkeley"]},{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Bioengineering, University of California Berkeley","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2728-7622","authenticated-orcid":false,"given":"Adam M.","family":"Deutschbauer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01an7q238","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Plant and Microbial Biology, University of California Berkeley","place":["Berkeley"]},{"id":[{"id":"https:\/\/ror.org\/02jbv0t02","id-type":"ROR","asserted-by":"publisher"}],"name":"Environmental Genomics and Systems Biology Division\/Biosciences Area, Lawrence Berkeley National Laboratory","place":["Berkeley"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4844-2890","authenticated-orcid":false,"given":"N. 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