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Background   Salicornia europaea,  a succulent obligatory halophyte is the most salt-tolerant plant species in the world. It survives salt concentrations of more than 1 M. Therefore, it is a suitable model plant to identify genes involved in salt tolerance mechanisms that can be used for the improvement of crops. The changes in a plant’s gene expression in response to abiotic stresses may depend on factors like soil conditions at the site, seasonality, etc. To date, experiments were performed to study the gene expression of  S. europaea  only under controlled conditions. Conversely, the present study investigates the transcriptome and physicochemical parameters of  S. europaea  shoots and roots from two different types of saline ecosystems growing under natural conditions.    Results  The level of soil salinity was higher at the naturally saline site than at the anthropogenic saline site. The parameters such as EC e , Na + , Cl − , Ca + , SO 4  2−  and HCO 3  −  of the soils and plant organs significantly varied according to sites and seasons. We found that Na +  mainly accumulated in shoots, whereas K +  and Ca 2+  levels were higher in roots throughout the growing period. Moreover, changes in  S. europaea  gene expression were more prominent in seasons, than sites and plant organs. The 30 differentially expressed genes included enzymes for synthesis of S-adenosyl methionine, CP47 of light-harvesting complex II, photosystem I proteins, Hsp70 gene, ATP-dependent Clp proteases, ribulose bisphosphate carboxylase/oxygenase (Rubisco), phenylalanine ammonia-lyase (PAL), cytochrome c oxidase (COX) and ATP synthase.    Conclusion  The comparisons made based on two seasons, plant organs and two different sites suggest the importance of seasonal variations in gene expression of  S. europaea . We identify the genes that may play an important role in acclimation to season-dependent changes of salinity. The genes were involved in processes such as osmotic adjustment, energy metabolism and photosynthesis.

Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation