{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T13:59:25Z","timestamp":1790171965176,"version":"4.1.0"},"reference-count":90,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC05-00OR22725"],"award-info":[{"award-number":["DE-AC05-00OR22725"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSystems"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Dark septate endophytes (DSEs) are ubiquitous root-colonizing fungi characterized by melanized, septate hyphae and a frequent association with plants in stressful or nutrient-poor environments. Although DSEs are increasingly recognized for context-dependent effects on host stress resilience, the specialized metabolic capacity of many DSE lineages remains poorly resolved.\n                      <jats:italic toggle=\"yes\">Hyaloscypha finlandica<\/jats:italic>\n                      is a recurrent root-associated fungus of\n                      <jats:italic toggle=\"yes\">Populus<\/jats:italic>\n                      and other hosts, making it a useful system for understanding symbiotic mechanisms using multi-omics analyses. Here, we combined comparative biosynthetic gene cluster (BGC) prediction across 41 ascomycete genomes with untargeted metabolomics of\n                      <jats:italic toggle=\"yes\">H. finlandica<\/jats:italic>\n                      PMI 746 grown in a defined minimal medium and a complex plant-derived medium. Benchmarking antiSMASH, FunBGCeX, and BGC-Prophet revealed broad conservation of PKS-, NRPS-, and terpene-associated biosynthetic capacity among DSEs. LC-MS\/MS profiling detected strong medium-associated shifts in the extracellular chemical footprint of\n                      <jats:italic toggle=\"yes\">H. finlandica<\/jats:italic>\n                      and identified putative terpenoid-, polyketide-, peptide-, siderophore-, and DHN-melanin-related features through spectral matching and\n                      <jats:italic toggle=\"yes\">in silico<\/jats:italic>\n                      chemical-class inference. Authentic-standard comparison supported a probable assignment of 7-oxodehydroabietic acid, whereas most other annotations remain putative or class-level assignments. Integrating genomic and metabolomic evidence identified representative candidate intersections between encoded biosynthetic capacity and observed chemistry, but definitive BGC-product links remain targets for future genetic and structural validation. Together, these results provide a public paired-omics resource for a core\n                      <jats:italic toggle=\"yes\">Populus<\/jats:italic>\n                      -associated DSE and a conservative framework for interpreting fungal multi-omics in non-model endophytes.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>\n                        <jats:bold>IMPORTANCE<\/jats:bold>\n                      <\/jats:title>\n                      <jats:p>\n                        Dark septate endophytes (DSEs) are widespread fungal symbionts that influence plant performance, yet their encoded and expressed metabolic capacities remain largely uncharacterized. This study provides a paired comparative genome-mining and untargeted metabolomics resource for\n                        <jats:italic toggle=\"yes\">Hyaloscypha finlandica<\/jats:italic>\n                        , a recurrent\n                        <jats:italic toggle=\"yes\">Populus<\/jats:italic>\n                        -associated DSE. By explicitly distinguishing biosynthetic gene cluster (BGC) prediction, spectral annotation, authentic-standard support, and unresolved BGC-Prophet assignment, this work provides a transparent reference for future studies of DSE specialized metabolism. The resulting data sets support comparative analyses across fungal endophytes and help prioritize candidate metabolites and gene clusters for targeted validation.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/msystems.00838-26","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T13:01:07Z","timestamp":1790168467000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Genome mining and metabolomics reveal context-dependent biosynthetic potential in a core poplar dark septate endophyte"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6841-2270","authenticated-orcid":true,"given":"Julian B.","family":"Cosner","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01qz5mb56","id-type":"ROR","asserted-by":"publisher"}],"name":"Biosciences Division, Oak Ridge National 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