Abiotic stress is the negative effe

Abiotic stress is the negative effect on living organisms of nonliving factors such as high temperature, drought and salinity. Abiotic stress affects normal plant growth and development and severely reduces agricultural productivity. Abiotic stressors, especially salinity and drought, are the primary cause of crop loss worldwide, leading to 50% average yield reductions per year for major crops [1,2]. Due to the important role of the Solanaceae family in agronomic and ornamental crops, holistic-scale approaches have been used to examine salt tolerance in this family. Root proteomic profiling in four tomato (Solanum lycopersicum) accessions (Roma, Super Marmande, Cervil and Levovil) was conducted in response to short-term stress by exposing hydroponically grown plants to 100 mM NaCl [3], and a cDNA microarray was used on two cultivated tomato genotypes (LA2711 and ZS-5) growing hydroponically under 150 mM NaCl to study gene expression in early stages of development in tomato plants [4]. RNA-seq offers several advantages over existing technologies; it requires neither previous genome annotation nor pre-synthesized nucleotide as probes and it is not limited by Expressed SequenceTag (EST) availability [5]. Transcriptome sequences can be reconstructed by de novo assembling millions of short DNA sequences (reads) [6] enabling downstream analysis such as novel gene discovery or expression profile analysis [7,8]. The assembly of DNA reads into a meaningful transcriptome can be performed with different de novo assemblers such as Trinity [9], Trans-ABySS [10], and SOAPdenovo-trans [11]. Thus, RNA-seq has become the method of choice to carry out transcriptomic analysis in both model and non-model organisms [12].