Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress

• A total of 56,932 unigenes with an average length of 817.4 bp was assembled.
• Expression analyses reveal that 155 genes were regulated expression by cadmium stress.
• Up-regulated expression of two GA2ox genes possibly related with the growth inhibition of CdS ramie.

Cadmium (Cd) contamination in agricultural soils has become a major environmental problem in China. Ramie, a fiber crop, has frequently been proposed for use as a phytoremediation crop for the restoration of Cd-contaminated farmlands. However, high levels of Cd can greatly inhibit stem growth in ramie, which reduces its economic value as a crop. To understand the potential mechanisms behind this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing on two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2). Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequence reads were generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, and de novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels in CO and CdS ramie revealed 155 differentially expressed genes (DEGs) between treatment and control conditions. Sixteen DEGs were further analyzed for expression differences by using real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase (a major enzyme for deactivating bioactive gibberellins [GAs]) showed markedly up-regulated expression in Cd stressed ramie. This might be responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that the cutin, suberine and wax biosynthesis pathway was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful in further understanding the mechanism of Cd-stress response and improving Cd stress tolerance in ramie.