Genome-wide identification and characterization of SPX domain-containing proteins and their responses to phosphorus and/or nitrogen deficiency in apple (Malus domestica Borkh.)

•25 MdSPXs, belong to four subfamilies, were identified and characterised in Malus domestica, specific PSR element P1BS were found in the promoter of 16 MdSPXs.•15 and 13 MdSPX2 responded to P and N deficiency, respectively, and the response exhibited apparent tissue-specificity.•The PSR involved in MdSPX1, MdSPX2, and MdSPX5 depended on nitrogen availability.•MdSPXs were predicted to interact with multiple nitrate and phosphate signaling response proteins and transcription factors.•The expression of six MdSPX2 were affected by bZIP transcription factor MdTGA4.