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In this study, we performed comprehensive whole-genome sequencing and annotation of\n                    <jats:italic>Xylaria<\/jats:italic>\n                    sp. VDL4 using third-generation sequencing technology, followed by comparative genomic analysis. Integrated multi-omics analyses were employed to investigate the secondary metabolites and their biosynthetic pathways in\n                    <jats:italic>Xylaria<\/jats:italic>\n                    sp. VDL4 under various culture conditions. The results of genomic analysis showed that the genome of\n                    <jats:italic>Xylaria<\/jats:italic>\n                    sp. VDL4 spanned 48.5\u2009Mb, comprised 56 scaffolds with a GC content of 51.77%. Gene prediction annotated 12,457 protein-coding genes, including 76 biosynthesis gene clusters. Among these, we identified 31 polyketide synthase (PKS) genes, 17 terpene synthase (TPS) genes and 16 non-ribosomal peptide synthase (NRPS) genes, in addition to 171 transcription factors. Phylogenomic analysis showed that\n                    <jats:italic>Xylaria<\/jats:italic>\n                    sp. VDL4 and\n                    <jats:italic>Xylaria arbuscula<\/jats:italic>\n                    B clustered in the same branch, and the divergence time was about 62.8\u2009million years ago. Principal component analysis showed that the differential metabolites could be divided into three distinct groups: one for MSF, one for DM and a third group comprising CK and BWS. No significant difference was observed between the BWS and CK treatments, indicating that valproic acid did not exert a notable regulatory effect on secondary metabolite accumulation. Metabolomics analysis revealed that cytochalasin D and ganoderic acid Mf increased ~61.5-fold in solid cultures supplemented with tapioca compared with yeast malt broth cultures, while 10-hydroxycamptothecin was highly expressed under rice culture conditions. Transcriptomic analysis showed that five PKS genes and five TPS genes exhibited higher expression levels under solid culture conditions (DM and MSF), while three PKS and two TPS genes were more actively expressed under liquid culture conditions (CK and MY-BWS). Integrated with the multi-omics analysis, it was speculated that\n                    <jats:italic>Xylaria<\/jats:italic>\n                    sp. VDL4 polyketide synthase \u2013 non-ribosomal peptide synthetase 2 (\n                    <jats:italic>XyPKS-NRPS2<\/jats:italic>\n                    ) gene \u2013 may be responsible for the biosynthesis of cytochalasin D,\n                    <jats:italic>XyPKS-NRPS1<\/jats:italic>\n                    may catalyse the synthesis of swainsonine and\n                    <jats:italic>XyPKS30<\/jats:italic>\n                    gene may catalyse the synthesis of 6-methylsalicylic acid.\n                    <jats:italic>Xy-TPS11<\/jats:italic>\n                    may play a key role in the biosynthesis pathway of 10-hydroxycamptothecin, and\n                    <jats:italic>Xy-TPS4<\/jats:italic>\n                    is related to the biosynthesis of ganoderic acid Mf. The present study provides new insights into the biosynthetic mechanism of secondary metabolites in\n                    <jats:italic>Xylaria<\/jats:italic>\n                    and provides an important theoretical basis for subsequent related studies.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001658","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T15:15:49Z","timestamp":1777389349000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic features and the transcriptional regulation of secondary metabolite biosynthesis of endophytic fungus Xylaria sp. 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