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Background  Dove tree ( Davidia involucrata  Baill.) is a rare and endangered species. Natural reproduction of dove tree is extremely difficult due to its low fecundity. Serious seed abortion is one of the key factors restraining its sexual reproduction. Understanding the inducements of seed abortion is critical for addressing the issue of offspring production and the survivability of such an endangered species. However, studies on the molecular mechanism of seed abortion in woody plants are lacking, and the dearth of genomic resources for dove tree restricts further research.    Results  In this study, using the Illumina platform, we performed  de novo  transcriptome sequencing of the fruit and seed in dove tree. A total of 149,099 transcripts were isolated and then assembled into 72,885 unigenes. Subsequently, differentially expressed genes (DEGs) between normal and abortive seeds were screened. Genes involved in response to stress, hormone signal transduction, programmed cell death, lignin biosynthesis, and secondary cell wall biogenesis showed significant different expression levels between normal and abortive seeds.    Conclusion  Combined results indicated that the abortive seeds were under the adversity stress, which should be controlled by the maternal plant. Maternally controlled development of integument is assumed to be a critical process for abortion regulation. MYB and WRKY transcription factors, receptor kinase and laccase are considered to be important regulators in seed abortion. Moreover, mass sequence data facilitated further molecular research on this unique species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0772-x) contains supplementary material, which is available to authorized users.

De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.)