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Mangroves are a group of unique plants anchoring in and well adapting to the extreme intertidal environment with high salinity, hypoxia and high temperature and ultraviolet (UV) radiation. Sonneratia Caseolaris is a major mangrove tree widely distributed across the West-Indo Pacific region, however the genetic mechanisms of its adaptive evolution are still unclear. In the present study, we performed comparative transcriptome analyses between S. caseolaris and its two non-mangrove relatives, Trapa bispinosa and Duabanga grandiflora, to better understand the evolutionary adaptation of S. caseolaris. We obtained 39.92, 69.96 and 47.78 million high-quality paired-end reads using the Illumina platform and de novo assembled than into 47,954, 73,284 and 66,459 unigenes with low redundancy and high coverage. Of them, 20,181, 28,657 arid 25,244 unigenes were successfully assigned to level-2 Gene Ontology (GO) terms, and we found the distribution of GO terms were similar among the three species. Approximate 56% unigenes were involved in "response to stimulus" in all three species. Furthermore, we identified 23 unigenes under positive selection in S. caseolaris, which may be crucial for adaptation of this mangrove species to the extreme intertidal environment. (C) 2016 Elsevier B.V. All rights reserved.