Elms, especially Ulmus minor and Ulmus americana, are carrying out a hard battle against Dutch elm disease (DED). This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i) obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii) perform a functional annotation of the assembled transcriptome, (iii) identify genes potentially involved in the molecular response to environmental stress, and (iv) develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the ... : Ulmus_minor_INFO_unigenesUnigenes description. This document shows the sequence lenght; protein name; information from the best blast hit; GO terms associated to the sequence; Enzyme Codes (ECs); Domains; Sequence assiated to abiotic; biotic or both stimulus; Sequences with SNPs.Ulmus_minor_INFO_redundant_sequencesRedundant sequences description. This document shows the sequence lenght; protein name; information from the best blast hit; GO terms associated to the sequence; Enzyme Codes (ECs); Domains; Sequence assiated to abiotic; biotic or both stimulus; Sequences with SNPs.Ulmus_minor_KEEG_annotation_unigenesUnigenes associated to different KEEG pathwaysUlmus_minor_GO_annotation_unigenesGO annotation of UnigenesUlmus_minor_POLYMORPHISM_identificationIdentification and location of SNPs and other polymorphismsUlmus_minor_transcriptomeSequences from full transcriptoma in Fasta formatFungus_transcripts181 Unique transcripts that show homology with genome of inoculated organisms. ...