In what way a crop wild relative (CWR) of tomato, salt-tolerant halophytic vegetable fruit crop, Solanum chilense L., deal with salinity: a transcriptome analysis and De novo assembly.. Solanum chilense and Solanum lycopersicum

Soil salinity affects the plant growth and productivity detrimentally, but Solanum chilense L., a wild relative of cultivated tomato (Solanum lycopersicum L.), reveals exceptional salt tolerance. It has precise adaptations against direct exposure to salt stress conditions. Hence, a better understanding of the tolerance mechanism to salinity by the comprehensive study on S. chilense can help us to answer many questions regarding the salt stress. Using one-month-old seedlings of S. chilense and S. lycopersicum exposed to NaCl treatment, we summarized changes in the gene expression patterns in leaves by RNA-sequencing. A total of 386 million clean reads were produced via an Illumina HiSeqTM 2000 sequencing platform. Clean reads further de novo assembled into a transcriptome dataset comprising of 5,14,747 unigenes with N50 length of 578 bp and could be aligned in the public databases. Genebank non-redundant (Nr), Viridiplantae, Gene Ontology (GO), KOG, and KEGG databases classification suggested that the enrichment of these unigenes in 30 GO categories, 26 KOG, and 127 pathways, respectively. Out of 2,65,158 genes that were differentially expressed contrary to salt treatment, 1,34,566 and 1,30,592 genes were significantly up and down-regulated, respectively. All differentially expressed genes (DEGs) aligned to known signaling pathways. The outcomes revealed that most of the DEGs involved in cytokinin, ethylene, auxin, abscisic acid, gibberellin, and Ca2+ mediated signaling pathways were up-regulated. Furthermore, GO enrichment analysis was performed using REVIGO and the DEGs between Chilense_Treated vs. DVRT-1_Treated group suggested that the oxidation-reduction process is important for salt tolerance in S. chilense. Through pathway analysis of DEGs, “Wnt signaling pathway” was identified as a novel pathway for the response to the salinity. Moreover, key genes for salinity tolerance, such as genes encoding proline and arginine metabolism, ROS scavenging system, transport mechanism, osmotic regulation, defense and stress response, homeostasis and transcription factors not only salt-induced in S. chilense but also showed higher expression in salt-treated S. chilense as compared to salt-treated S. lycopersicum, specifying that these genes may possess significant parts in salinity tolerance in S. chilense. Overall, our findings would help in better understanding and provide new insights into the molecular mechanism essential for salt tolerance environments in plants.