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Background  Halophytes such as  Salicornia europaea  have evolved to exhibit unique mechanisms controlled by complex networks and regulated by numerous genes and interactions to adapt to habitats with high salinity. However, these mechanisms remain unknown.    Methods  To investigate the mechanism by which halophytes tolerate salt based on changes in the whole transcriptome, we performed transcriptome sequencing and functional annotation by database search. Using the unigene database, we conducted digital gene expression analysis of  S. europaea  at various time points after these materials were treated with NaCl. We also quantified ion uptakes. Gene functional enrichment analysis was performed to determine the important pathways involved in this process.    Results  A total of 57,151 unigenes with lengths of >300 bp were assembled, in which 57.5% of these unigenes were functionally annotated. Differentially expressed genes indicated that cell wall metabolism and lignin biosynthetic pathways were significantly enriched in  S. europaea  to promote the development of the xylem under saline conditions. This result is consistent with the increase in sodium uptake as ions pass through the xylem. Given that PSII efficiency remained unaltered, salt treatment activated the expression of electron transfer-related genes encoded by the chloroplast chromosome. Chlorophyll biosynthesis was also inhibited, indicating the energy-efficient state of the electron transfer system of  S. europaea .    Conclusions  The key function of adjusting important primary metabolic pathways in salt adaption was identified by analyzing the changes in the transcriptome of  S. europaea . These pathways could involve unique salt tolerance mechanisms in halophytes. This study also provided information as the basis of future investigations on salt response genes in  S. europaea . Ample gene resources were also provided to improve the genes responsible for the salt tolerance ability of crops.

plos one

Transcriptome Analysis of Salicornia europaea under Saline Conditions Revealed the Adaptive Primary Metabolic Pathways as Early Events to Facilitate Salt Adaptation