Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

Background
White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.

Results
We created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.

Conclusions
The work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.