Ulmus minor response to Dutch elm disease: de novo transcriptome assembly and annotation

Abstract

Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (ONU), has devastated elm populations across Europe and North America since the 20th century. In this work, a de novo transcriptome assembly of Ulmus minor in response to ONU is presented. We used two DED-resistant genotypes, MDV2.3 and VAD2, and one DED-susceptible genotype, MDV1, to capture responses to ONU at four time points post-inoculation (6, 24, 72, and 144 hours). RNA from collected samples was isolated and sequenced producing 60.88 M 100 bp paired-end reads per sample. We performed a de novo transcriptome assembly combining data from the three genotypes. The assembly was functionally annotated and validated through differential gene expression analysis of the response. This dataset provides a valuable resource for studying molecular mechanisms of DED resistance in elms, contributing to broadening our understanding of tree immunity and facilitating potential applications in functional annotation of future genome assemblies.