Genome-wide identification and expression pattern analysis of the MATE gene family in carmine radish (Raphanus sativus L.)

•A total of 85 candidate MATE gene family members were identified in the radish genome and comprised 4 groups by phylogenetic analysis of MATE genes in carmine radish with relation to other species.•In all of the examined tissues, the expression levels of 4 RsMATE genes (e.g. RsMATE31-b, RsMATE37-a, RsMATE13-c and RsMATE42-b) accumulated (RPKM > 5), suggesting that these genes are crucial for tissue development in radish.•The expression patterns of fifteen key RsMATE genes were investigated in 'XCB' (Xichangbai) and ‘HX’ (Hongxin) roots under Cd stress for different treatment times using quantitative real-time polymerase chain reaction (qRT-PCR), which showed compared to HX, RsMATE49-b, RsMATE33 and RsMATE26 transcripts were strongly altered at different time points in XCB responsive to Cd stress. Subsequently, RsMATE40-b, RsMATE16-b and RsMATE13-a genes were significantly expressed under ABA and NaCl stress treatments. Carmine radish (Raphanus sativus L.) is famousforcontaininganaturalredpigment(redradishpigment) that grown in Fuling, Chongqing City, China. MATE (multidrug and toxic compound extrusion), as an integral member of the multidrug efflux transporter family, has various functions in plants. However, noinformationhasbeenavailableaboutcharacteristicsoftheMATEgenefamily in carmine radish. In this study, total of 85 candidate MATE gene family members classifiedinto 4 groups were identified and foundtobewidelyandrandomlydistributedindifferent genome. Synteny analysis revealed that twenty-one segmental and ten tandem duplications acted as important regulators for the expansion of RsMATE genes. The Ka/Ks ratios of RsMATE indicated that RsMATE may have undergone intense purification in the radish genome. Cis-acting element analysis of RsMATE in the promoter region indicated that RsMATE were mainly related to the abiotic stress response and phytohormone. Quantitative real-time polymerase chain reaction (qRT-PCR) showed that RsMATE40-b, RsMATE16-b and RsMATE13-a genes were significantly expressed under ABA (abscisic acid) and NaCl stress treatments respectively. In addition, the expression patterns of fifteen key RsMATE genes were investigated in 'XCB' (Xichangbai) and ‘HX’ (Hongxin) roots under Cadmium (Cd) stress for different treatment times using qRT-PCR, of those, RsMATE49-b, RsMATE33 and RsMATE26 transcripts were strongly altered at different time points in XCB responsive to Cd stress,compared to HX. This study will provide valuable insights for stu