Two halophytes, Dichanthium annulatum (moderately salt tolerant) and Urochondra setulosa (highly salt tolerant) were selected to generate transcriptome at different salinity levels. Sequencing of RNA samples was done on Illumina-Hi-Seq platform for de novo transcriptome assembly from the leaf tissues of D. annulatum at salinity of ECe ∼30 dS/m and of U. setulosa at three salt levels (i.e. ECe ∼30, ∼40 and ∼50 dS/m). DESeq was used for identification of differentially expressed transcripts and a total of 267,196 and 384,442 transcripts were assembled through Trinity in both the plants respectively. A total of 32,246 and 25,479 SSRs were identified respectively in both the plants using MISA perl script with mono and tri-nucleotide repeats as most common motif.
