Physiological responses and transcriptome analyses of upland rice following exposure to arsenite and arsenate

•The responsive genes of upland rice exposed to As(III) and As(V) were studied.•In response to As(III) and As(V) stress, a larger number of genes were down-regulated compared to those that were up-regulated.•As(III) and As(V) treatments led to common and unique transcriptome profile changes in upland rice.•A novel set of common response genes was identified in upland rice exposed to As(III) and As(V).•The antioxidant enzyme activities were consistent with the expression of antioxidant enzyme related genes.