**5. Conclusions**

We sequenced and comparatively analyzed the transcriptomes from the leaves of wild type *B. halophila* plants and plants with salt treatment. This work enabled us to characterize gene expression profiles and identify functional genes related to salt tolerance. A total of 519 genes were differentially expressed under salt stress. These DEGs appear to be involved in many aspects, such as the SOS pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. It has been shown that one gene encoding the AT-Hook Motif Nuclear Localized transcription factor and three genes encoding dehydrins, might play important roles in response to salt stress in *B. halophila*. The results provide good candidate genes to breed salt tolerant plants, and will be helpful in understanding of the molecular mechanisms of salt stress in *B. halophila*.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/19/11/ 3412/s1. The sequencing data have been submitted to the SRA database under the accession number SRP146369.

**Author Contributions:** F.S. analyzed the data. F.S. and I.W.W. wrote the manuscript. L.Z. performed qRT-PCR. F.S. and D.Q. designed the experiment. All authors have read and approved the version of manuscript.

**Funding:** This work was supported by the National Key R & D Program of China (grant number 2016YFC0503103).

**Conflicts of Interest:** The authors declare that they have no competing interests.
