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Background  Hybridization and polyploidization can be major mechanisms for plant evolution and speciation. Thus, the process of polyploidization and evolutionary history of polyploids is of widespread interest. The species in  Elymus  L. sensu lato are allopolyploids that share a common St genome from  Pseudoroegneria  in different combinations with H, Y, P, and W genomes. But how the St genome evolved in the  Elymus  s. l. during the hybridization and polyploidization events remains unclear. We used nuclear and chloroplast DNA-based phylogenetic analyses to shed some light on this process.    Results  The Maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) data showed that the  Pseudoroegneria ,  Hordeum  and  Agropyron  species served as the St, H and P genome diploid ancestors, respectively, for the  Elymus  s. l. polyploids. The ML tree for the chloroplast genes ( mat K and the intergenic region of  trn H- psb A) suggests that the  Pseudoroegneria  served as the maternal donor of the St genome for  Elymus  s. l. Furthermore, it suggested that  Pseudoroegneria  species from Central Asia and Europe were more ancient than those from North America. The molecular evolution in the St genome appeared to be non-random following the polyploidy event with a departure from the equilibrium neutral model due to a genetic bottleneck caused by recent polyploidization.    Conclusion  Our results suggest the ancient common maternal ancestral genome in  Elymus  s. l. is the St genome from  Pseudoroegneria . The evolutionary differentiation of the St genome in  Elymus  s. l. after rise of this group may have multiple causes, including hybridization and polyploidization. They also suggest that  E. tangutorum  should be treated as  C. dahurica  var.  tangutorum , and  E. breviaristatus  should be transferred into  Campeiostachys . We hypothesized that the  Elymus  s. l. species origined in Central Asia and Europe, then spread to North America. Further study of intraspecific variation may help us evaluate our phylogenetic results in greater detail and with more certainty.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-015-0517-2) contains supplementary material, which is available to authorized users.

Phylogeny and differentiation of the St genome in Elymus L. sensu lato (Triticeae; Poaceae) based on one nuclear DNA and two chloroplast genes