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Background  Waterlogging or flooding is one of the most challenging abiotic stresses experienced by plants. Unlike many flooding-tolerant plants, floating-leaved aquatic plants respond actively to flooding stress by fast growth and elongation of its petioles to make leaves re-floating. However, the molecular mechanisms of this plant group responding to flood have not been investigated before. Here, we investigated the genetic basis of this adaptive response by characterizing the petiole transcriptomes of a floating-leaved species  Nymphoides peltata  under normal and flooding conditions.    Results  Clean reads under normal and flooding conditions with pooled sampling strategy were assembled into 124,302 unigenes. A total of 8883 unigenes were revealed to be differentially expressed between normal and flooding conditions. Among them, top ranked differentially expressed genes were mainly involved in antioxidant process, photosynthesis process and carbohydrate metabolism, including the glycolysis and a modified tricarboxylic acid cycle – alanine metabolism. Eight selected unigenes with significantly differentiated expression changes between normal and flooding conditions were validated by qRT-PCR.    Conclusions  Among these processes, antioxidant process and glycolysis are commonly induced by waterlogging or flooding environment in plants, whereas photosynthesis and alanine metabolism are rarely occurred in other flooding-tolerant plants, suggesting the significant contributions of the two processes in the active response of  N. peltata  to flooding stress. Our results provide a valuable genomic resource for future studies on  N. peltata  and deepen our understanding of the genetic basis underlying the response to flooding stress in aquatic plants.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3515-y) contains supplementary material, which is available to authorized users.

Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress