{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T14:51:00Z","timestamp":1791384660086,"version":"4.3.3"},"reference-count":94,"publisher":"Pensoft Publishers","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/share-your-work\/public-domain\/cc0\/"}],"funder":[{"DOI":"10.13039\/100000155","name":"Division of Environmental Biology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000155","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["7721995"],"award-info":[{"award-number":["7721995"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["imafungus"],"abstract":"<jats:p>\n                    The genomic signatures of microbial domestication remain poorly understood within the context of natural population variation. Here, we demonstrate that\n                    <jats:italic>Aspergillus oryzae<\/jats:italic>\n                    , the filamentous fungus used in soy sauce and sake production, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of\n                    <jats:italic>Aspergillus flavus<\/jats:italic>\n                    (population C).\n                    <jats:italic>A. oryzae<\/jats:italic>\n                    isolates also overlap with the recently described, clinically enriched\n                    <jats:italic>A. flavus<\/jats:italic>\n                    population D, suggesting multiple domestication events. All isolates tested retained pathogenicity in a zebrafish infection model. At the transcriptomic level, populations are significantly differentiated and respond differently to spore density, suggesting population-specific adaptations to ecological conditions. Although most transcriptomic variation was consistent with phylogenetic relationships, several co-expression modules exhibited significantly greater divergence than expected from phylogeny alone, suggesting that phenotypic diversification may sometimes occur through the reorganization of transcriptomic architectures.\n                    <jats:italic>A. oryzae<\/jats:italic>\n                    also displayed elevated expression of a carbohydrate-metabolism module; however, this pattern was consistent with phylogenetic differentiation, suggesting that enhanced carbohydrate metabolism may have begun evolving prior to domestication or may be most apparent under fermentation-relevant conditions. Population-specific variation is also evident among secondary metabolite (SM) gene clusters. While\n                    <jats:italic>A. oryzae<\/jats:italic>\n                    shows markedly reduced expression of aflatoxin biosynthesis genes, this trend does not extend across the entire secondary metabolome. Using machine-learning-based gene regulatory network inference, we identified population-specific transcriptomic differences linked to distinct transcription factors, with evidence for both cis- and trans-acting regulatory divergence, but no changes in global regulators such as\n                    <jats:italic>laeA<\/jats:italic>\n                    . Together, these findings provide new insights into the domestication of\n                    <jats:italic>A. oryzae<\/jats:italic>\n                    , its global significance, and the microevolution of fungal secondary metabolic pathways.\n                  <\/jats:p>","DOI":"10.3897\/imafungus.17.195218","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:55:56Z","timestamp":1791381356000},"source":"Crossref","is-referenced-by-count":0,"title":["Population-specific transcriptomic shifts underlie secondary metabolic diversification in Aspergillus flavus Link and the domestication of Aspergillus oryzae (Ahlb.)"],"prefix":"10.3897","volume":"17","author":[{"given":"Milton T.","family":"Drott","sequence":"first","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yen-Wen","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of Public Health, New Haven, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. Anne","family":"Hatmaker","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, United States of America"},{"name":"Department of Plant Pathology, University of Georgia, Athens, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nayanna M.","family":"Mercado-Soto","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Mitch","family":"Elmore","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dianiris","family":"Luciano-Rosaro","sequence":"additional","affiliation":[{"name":"U.S. Department of Agriculture-Agricultural Research Service, Food Quality Laboratory, Beltsville, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jae-Hyuk","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Bacteriology, University of Wisconsin, Madison, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonis","family":"Rokas","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Vanderbilt University, Nashville, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John G.","family":"Gibbons","sequence":"additional","affiliation":[{"name":"Department of Food Science, College of Natural Sciences, University of Massachusetts Amherst, Amherst, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Huttenlocher","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kunlong","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy P.","family":"Keller","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States of America"},{"name":"Department of Plant Pathology, University of Wisconsin, Madison, United States of America"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2258","published-online":{"date-parts":[[2026,10,7]]},"reference":[{"key":"195218_B1","doi-asserted-by":"publisher","DOI":"10.3390\/toxins4090695"},{"key":"195218_B2","unstructured":"Alexa A, Rahnenfuhrer J (2010) topGO: enrichment analysis for gene ontology. 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