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Background  Arabidopsis has 5 paralogs of the  S -adenosylmethionine decarboxylase ( SAMDC ) gene. Neither their specific role in development nor the role of positive/purifying selection in genetic divergence of this gene family is known. While some data are available on organ-specific expression of  AtSAMDC 1,  AtSAMDC 2,  AtSAMDC 3 and  AtSAMDC 4, not much is known about their promoters including  AtSAMDC 5, which is believed to be non-functional.    Results  (1) Phylogenetic analysis of the five  AtSAMDC  genes shows similar divergence pattern for promoters and coding sequences (CDSs), whereas, genetic divergence of 5’UTRs and 3’UTRs was independent of the promoters and CDSs; (2) while  AtSAMDC 1 and  AtSAMDC 4 promoters exhibit high activity (constitutive in the former), promoter activities of  AtSAMDC 2,  AtSAMDC 3 and  AtSAMDC 5 are moderate to low in seedlings (depending upon translational or transcriptional fusions), and are localized mainly in the vascular tissues and reproductive organs in mature plants; (3) based on promoter activity, it appears that  AtSAMDC 5 is both transcriptionally and translationally active, but based on it’s coding sequence it seems to produce a non-functional protein; (4) though 5’-UTR based regulation of  AtSAMDC  expression through upstream open reading frames (uORFs) in the 5’UTR is well known, no such uORFs are present in  AtSAMDC 4 and  AtSAMDC 5; (5) the promoter regions of all five  AtSAMDC  genes contain common stress-responsive elements and hormone-responsive elements; (6) at the organ level, the activity of  At SAMDC enzyme does not correlate with the expression of specific  AtSAMDC  genes or with the contents of spermidine and spermine.    Conclusions  Differential roles of positive/purifying selection were observed in genetic divergence of the  AtSAMDC  gene family. All tissues express one or more  AtSAMDC  gene with significant redundancy, and concurrently, there is cell/tissue-specificity of gene expression, particularly in mature organs. This study provides valuable information about  AtSAMDC  promoters, which could be useful in future manipulation of crop plants for nutritive purposes, stress tolerance or bioenergy needs. The  AtSAMDC 1 core promoter might serve the need of a strong constitutive promoter, and its high expression in the gametophytic cells could be exploited, where strong male/female gametophyte-specific expression is desired; e.g. in transgenic modification of crop varieties.    Electronic supplementary material  The online version of this article (10.1186/s12870-017-1208-y) contains supplementary material, which is available to authorized users.

Polyamines in the life of Arabidopsis: profiling the expression of S-adenosylmethionine decarboxylase (SAMDC) gene family during its life cycle