Hovhannisyan, Hrant, 1992-Rodríguez Sánchez, Antonio JoséSaus, EsterVaneechoutte, MarioGabaldón Estevan, Juan Antonio, 1973-2023-06-202023-06-202023Hovhannisyan H, Rodríguez A, Saus E, Vaneechoutte M, Gabaldón T. Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples. Front Cell Infect Microbiol. 2023 Jan 24;13:1093178. DOI: 10.3389/fcimb.2023.10931782235-2988http://hdl.handle.net/10230/57240The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.application/pdfeng© 2023 Hovhannisyan, Rodríguez, Saus, Vaneechoutte and Gabaldón. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.info:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fcimb.2023.1093178CandidaHost-pathogen interactions in vivoRNA-SeqProbe-based enrichmentLong non-coding RNA (IncRNA)info:eu-repo/semantics/openAccess