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Background  Sugarcane served as the model plant for discovery of the C 4  photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter ( MGT ) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of  MGTs  in sugarcane due to the complexity of the  Saccharum  genome.    Results  Here, we identified 10  MGTs  from the  Saccharum spontaneum  genome. Phylogenetic analysis of  MGTs  suggested that the  MGTs  contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that  MGTs  family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the  MGTs  are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that  SsMGT1/SsMGT2  originated from the recent ρWGD, and  SsMGT7/SsMGT8  originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant.  MGT6, MGT9  and  MGT10  weredominant genes in the  MGT  family and werepredicted to be located inthe chloroplast .  Of the 3 dominant  MGTs, SsMGT6  expression levels were found to be induced in the light period ,  while  SsMGT9  and  SsMTG10  displayed high expression levels in the dark period. These results suggested that  SsMGT6  may have a function complementary to  SsMGT9  and  SsMTG10  that follows thecircadian clock for MGT in the leaf tissues of  S. spontaneum .  MGT3, MGT7  and  MGT10  had higher expression levels In saccharum officinarum  than in  S. spontaneum , suggesting their functional divergence after the split of  S. spontaneum  and  S. officinarum .    Conclusions  This study of gene evolution and expression of  MGTs  in  S. spontaneum  provided basis for the comprehensive genomic study of the entire  MGT  genes family in  Saccharum . The results are valuable for further functional analyses of  MGT  genes and utilization of the MGTs for  Saccharum  genetic improvement.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5437-3) contains supplementary material, which is available to authorized users.

Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum