Alkali stress is one of the important factors in restricting agriculture production. Leymus chinensis is constructive halophyte species in alkalized grassland in China. In order to investigate the gene expression response of L. chinensis to alkali stress, we used PacBio technology to obtain reference full-length transcript sequences for transcriptomic analysis of alkali stress response. In order to elucidate the alkali tolerance mechanisms of L. chinensis, we measured the photosynthetic parameters, concentrations of ions and compatible solutes, chloroplast ultrastructure and anatomy of control and stressed plants. Our results showed that L. chinensis shares many alkali-tolerance mechanisms with glycophytes. Higher stability of photosynthetic apparatus under alkali stress may be prominent alkali-tolerance trait of L. chinensis. L. chinensis may have a strong capacity to decline the toxicity of Na + to organelles and cytoplasmic proteins. Enhanced expression of dehydrin and LEA genes and increased accumulation of carbohydrates may contribute to the development of Na +-specific stress tolerance of L. chinensis under alkali stress.

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