An Aspergillus lncRNA atlas reveals a novel modulator of aflatoxin biosynthesis

Long non-coding RNAs (lncRNAs) represent a significant fraction of the transcriptome and are vital regulators in eukaryotes, yet their functional landscape in fungi remains largely undefined. Here we present a transcriptomic atlas of 8,553 lncRNAs across four evolutionarily and biotechnologically diverse Aspergillus species. We observed marked diversity in the long non-coding repertoire between species, with only 39% shared between at least two species. However, conserved lncRNAs are expressed at significantly higher levels and across more conditions than species-specific ones, revealing a functional hierarchy within the non-coding transcriptome. We also identify subtelomeres and transposable elements as hotspots for lncRNA innovation in Aspergillus, albeit at the cost of reduced expression. Integrating genomic and transcriptomic data, we show that lncRNAs predominantly exhibit distance-dependent cis-coexpression with neighboring genes and, through guilt-by-association, we identify their participation in global modules governing primary and secondary metabolism. This framework enabled the discovery of aflalinc, a species- and condition-specific lncRNA in A. flavus that plays a role in regulating the aflatoxin biosynthetic gene cluster. Crucially, deletion of this lncRNA severely reduced the production of aflatoxin B, a highly potent agent of acute toxicity and driver of hepatocarcinoma, without affecting growth, conidiation, or sclerotia formation. In addition, examination of an independent dataset confirms the strength of the co-expression networks and uncovers stage-specific functions for lincRNAs in the maturation of A. fumigatus biofilms. Together, these findings establish lncRNAs as integral components of fungal biology and demonstrate that they can modulate mycotoxin production and biofilm formation, with broad implications for controlling fungal threats to food safety and human health.