Watercore is a physiological disorder in pineapples, which is expressed as fluid deposition in intercellular spaces and presents as water soaked. This disorder affects the fruit quality and decreases storage life, resulting in enormous commercial losses to growers and restricting the development of the pineapple industry in China. However, the molecular mechanism of watercore remains unclear. In order to elucidate the molecular mechanism of pineapple watercore, the transcriptome analyses of watercored and normal fruits were carried out in pineapples for the first time using de novo RNA-seq technology. High-quality reads of 46.66 and 43.71 M were obtained in the transcriptomes of normal and mildly watercored fruits, respectively. Clean reads of 45.50 and 42.79 M were obtained after filtering the original data. These genes are useful resources in subsequent pineapple watercore research. Fifty genes in phenylpropanoid biosynthesis, glucose metabolism, calcium transport, and cell wall metabolism were considerably different between normal and watercored fruits. Among them, the expressions of the AcPME, AcBGLU43, Ac4CL5, AcPER1, and AcPOD genes were upregulated by 7–21 times in watercored fruit, while the expressions of AcSUS7 were downregulated by 16.61 times, and the expressions of other differential genes were upregulated or downregulated by more than 2 times. A total of 38 differentially expressed transcription factors were obtained by screening. Among these transcription factors, WRKY was the most abundant, followed by MYB. The acquisition of these genes is important for the first understanding of the molecular mechanism of this physiological disorder.
