Analysis of transcriptome profiles of two Pyrus pyrifolia cultivars reveals genes associated with stone cell development

•The stone cells content in GTC with more exquisite flesh was significantly lower than TC especially in 60 days after flowering.•The hemicellulose metabolic process (GO: 0010410) and lignin catabolic process (GO: 0046274) were highly active in stone cell development.•The glucosyltransferase [EC:2.4.1.111] and peroxidase [EC:1.11.1.7]) could be important factors of lower lignin content in GTC than TC .•Several genes like peroxidase 42-like gene, vinorine synthase-like gene, and Myb4-like TFs, are likely associated with stone cell development.