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Populus pruinosa and P. euphratica, are two desert poplars characterized by extreme adaptation to salt stress. In contrast, P. trichocarpa and P. tomentosa are two salt sensitive congeners. In order to identify the adaptations to salt stress that are common to each type of these poplars, we compared transcriptome changes in the four poplar species after exposure to continuous salt stress. We identified 7822 1:1 orthologs between the four species and 702 differentially expressed genes (DEGs) during the 48 h time course. The result of hierarchical clustering suggested that the patterns of gene expression were significantly different between the two types of poplar. These genes were mainly involved in ’Oxidoreductase activity’, ’Primary metabolic processes’, ’Transport’ and ’Nucleic acid binding transcription factor activity’. Among these DEGs, in which the functions related to responses to salt exposure are significantly over-represented, 11 genes were found to be continuously up or down-regulated in response to salt stress in the two types. We also found that most of the orthologous candidate genes evolved under purifying selection and one ortholog (GDSL) showed positive selection. These genes probably played important roles when their ancestral Glade underwent adaptive divergence into the two types, differentiated by habitat salt-content. (C) 2017 Elsevier Ltd. All rights reserved.