The traditional Chinese desert shrub Lycium ruthenicum is widely distributed in arid environments such as north-west China, exhibiting ideal salt tolerance to cope with soil desertification, salinity, and alkalinity. However, the salt-tolerance mechanism of L. ruthenicum, especially of its young seedlings at early vegetative stages, remains largely unknown. In the present study, we collected whole-seedling samples from Lycium ruthenicum at a-pair-leaf stage with and without a mild salt (75 mM sodium chloride) treatment, and then performed transcriptome profiling to compare their gene expression patterns. The de novo assembly achieved 94,651 unigenes with 55,156 annotated. Among them, 199 differentially expressed genes (DEGs) were identified between salt-treated seedlings and control, with 41 up-regulated and 158 down-regulated. These DEGs were highly enriched into gene ontology (GO) classifications 'metabolic process' and 'catalytic activity', into Clusters of Orthologous Groups (COG) function classifications 'translation, ribosomal structure and biogenesis' and 'energy production and conversion', and into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways 'ribosome' and 'oxidative phosphorylation'. Specifically, genes involved in energy metabolism (oxidative phosphorylation) and related energy-consuming metabolisms, including ribosome-associated biogenesis and biosynthesis of organic nitrogen-derived compatible solutes (i.e., arginine and proline), were generally down-regulated. Specific genes involved in abscisic acid (ABA) biosynthesis and signaling pathway were simultaneously up-regulated. Changes in the transcript levels of salt-responsive DEGs selected from the transcriptomic profiling were further validated by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Based on these results, salinity-adaptive strategies for the L. ruthenicum early seedlings are discussed.
