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Background  Multidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean.    Results  A total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean ( Glycine max ), which were denominated as  GmMATE1  -  GmMATE117 . These 117  GmMATE  genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive  cis -elements such as ABRE, ARE, HSE, LTR, MBS, as well as a  cis -element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight  GmMATE  genes. Differential gene expression analysis of these eight  GmMATE  genes in response to Al stress helps us identify  GmMATE75  as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related  MATE  genes.    Conclusions  A total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The  cis -elements and expression patterns of eight soybean  MATE  genes related to Al detoxification/iron translocation were analyzed, and  GmMATE75  was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2559-8) contains supplementary material, which is available to authorized users.

Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean