Differential expression data
De novo transcriptome assembly of two halophytes, Dichanthium annulatum (moderately salt tolerant) and Urochondra setulosa (highly salt tolerant) were generated on Illumina- Hi Seq platform at salinity levels of ECe ~30, ~40 and ~50 dS/m. Differential expression of transcripts was analyzed using DESeq and novel gene expression patterns of the differentially expressed genes (DEGs) related to salinity/salt tolerance was identified and validated using qPCR.
Steps to reproduce
Leaves of both the plants were collected in ice and RNA was isolated with one set of control and different salinity treatments in two replications each separately for both the plants. Sequencing was performed on Illumina-HiSeq platform. The RNAseq libraries were prepared with Illumina-compatible NEBNext® Ultra™ Directional RNA Library Prep Kit. Processed reads were assembled using graph-based approach by Trinity program. Clustering of the assembled transcripts based on sequence similarity was performed using CD-HIT-EST. Processed reads were aligned back to the final assembly using Bowtie with end to end parameters. DESeq, was used for differential expression analysis.