Abstract
Recent data suggests one fungus, Aspergillus fumigatus, causes more deaths annually than HIV or malaria combined. Coupled with rapid emergence of antifungal drug resistance, the limited range of effective treatments, and mortality rates of >50%, aspergillosis represents a major challenge in infectious diseases. Recent studies have identified long-noncoding RNAs (lncRNAs) involved in drug resistance and virulence in pathogenic yeasts such as Candida spp. However, there is very limited knowledge of lncRNAs in human pathogenic moulds, including A. fumigatus. Here we exploit transcriptomics data of A. fumigatus exposed to different environments to annotate transcripts mapping to 2388 genomic loci. After manual curation we generate a database of over 1000 lncRNAs. We observe that the lncRNAs display orchestrated transcriptional profiles upon drug treatment and many are proximal to genes involved in azole sensitivity. We knock out a set of intergenic lncRNAs and perform a large-scale phenotypic analysis to identify 60 lncRNA mutants displaying condition-dependent fitness changes with 35 mutants exhibiting a positive growth phenotype under azole stress. Overall, this study generates and experimentally validates an important resource that will enable the wider research community to increase understanding of the functional importance of lncRNAs in A. fumigatus, including their involvement in drug sensitivity.
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Data availability
Raw sequence data has been deposited at the NCBI sequence read archive (SRA) under accession number PRJNA861909 (ncbi.nlm.nih.gov/bioproject/861909) and PRJNA1165181 (ncbi.nlm.nih.gov/bioproject/1165181). Source data are provided with this paper, either in the supplementary Data or the Source Data File. Source data are provided with this paper.
Code availability
Code used for analysis is available at https://github.com/Danweaver1/lncRNA-prediction (https://doi.org/10.5281/zenodo.17477034) and https://github.com/harrychown/asp_lncrna (https://doi.org/10.5281/zenodo.17416843) and https://github.com/Tanda-Qi/Analysis_Phenobooth_output (https://doi.org/10.5281/zenodo.17900633).
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Acknowledgements
D.W. is funded by the NIHR Manchester Biomedical Research Centre (BRC) (NIHR203308). This work was funded by the Wellcome Trust under project number 208396/Z/17/Z (to M.J.B., P.B. and D.D.).
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P.B., D.D., M.B. conceived and planned the experimental work, P.B., D.D., T.Q., D.W., H.C., C.V. and M.B. wrote the manuscript, D.W., T.Q., M.F., C.V. and T.F. performed laboratory work, D.W., H.C., P.B., T.Q., C.V. analysed the data and D.W., H.C., R.L., L.D. and Nv.R. performed additional manual annotation steps.
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Weaver, D., Qi, T., Chown, H. et al. Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68543-9
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DOI: https://doi.org/10.1038/s41467-026-68543-9
