de novo Transcriptome Assembly and Analysis of the Halophyte Suaeda fruticosa

Major efforts to improve salt tolerance in agricultural crops have been attempted to address problems with increasing soil salinity due to irrigation. Conventional crops have been used to breed salt tolerance through genetic engineering, in which genes for salt tolerance were introduced directly to plants. Most of these traditional cash crops can only endure relatively low concentrations of salt; therefore, it may be reasonable to study and domesticate a native, salt tolerant plant. We sequenced a cDNA library using Illumina platform from shoots and roots of a perennial salt-tolerant plant Suaeda fruticosa. The reads were quality assessed, filtered and digitally normalized to 30X coverage totaling to 99,577,045 paired-end reads. We assembled the transcriptome of this species using Oases, Trinity, Trans-Abyss, SOAPdenovo and MIRA. We have compared results from the different assemblers and assessed the contigs based on predicted protein coding regions and on the percentage of reads mapped back to the assembly using GSNAP. Our results shows the best de-novo assembly of the transcriptome of non-conventional crop plants comparing no salt and optimal salt concentration. This project aims to study the adaptation of halophytes to salt tolerance and identify genes that are involved in this response mechanism.