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Background  Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils.  Citrus  are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some  Citrus  orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ ( Citrus sinensis ) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for  Citrus  Mg-deficiency tolerance.    Results  We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of  Citrus  roots to Mg-deficiency was related to the several aspects: ( a ) inhibiting root respiration and related gene expression via inducing  miR158  and  miR2919 ; ( b ) enhancing antioxidant system by down-regulating related miRNAs ( miR780 ,  miR6190 ,  miR1044 ,  miR5261  and  miR1151 ) and the adaptation to low-phosphorus ( miR6190 ); ( c ) activating transport-related genes by altering the expression of  miR6190 ,  miR6485 ,  miR1044 ,  miR5029  and  miR3437 ; ( d ) elevating protein ubiquitination due to decreased expression levels of  miR1044 ,  miR5261 ,  miR1151  and  miR5029 ; ( e ) maintaining root growth by regulating  miR5261 ,  miR6485  and  miR158  expression; and ( f ) triggering DNA repair (transcription regulation) by regulating  miR5176  and  miR6485  ( miR6028 ,  miR6190 ,  miR6485 ,  miR5621, miR160  and  miR7708 ) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in  Citrus  Mg-deficiency tolerance.    Conclusions  We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3999-5) contains supplementary material, which is available to authorized users.

MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing