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Background   Fraxinus hupehensis  is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA 3 ) effectively stimulated the seed germination of  F. hupehensis . However, little is known about the physiological and molecular mechanisms underlying the effect of GA 3  on  F. hupehensis  seed germination.    Results  We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA 3  (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA 3  treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA 3  contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from  F. hupehensis  transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA 3  (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA 3  signal transduction were also observed in the G group. GA 3 -regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA 3 -promoted  F. hupehensis  seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes.    Conclusion  Exogenous GA 3  increased the germination rate, vigor, and water absorption rate of  F. hupehensis  seeds .  Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA 3  on  F. hupehensis  seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1801-3) contains supplementary material, which is available to authorized users.

Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis