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Background   Elytrigia lolioides  (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into  Elytrigia ,  Elymus , and  Lophopyrum  genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of  E. lolioides  is still unknown. To identify the genome constitution and evolution of  E. lolioides , we used single-copy nuclear genes acetyl-CoA carboxylase ( Acc1 ) and elongation factor G  (EF-G ), multi-copy nuclear gene internal transcribed space ( ITS ), chloroplast gene  trnL-F  together with fluorescence and genomic in situ hybridization.    Results  Despite the widespread homogenization of  ITS  sequences, two distinct lineages (genera  Pseudoroegneria  and  Hordeum ) were identified.  Acc1  and  EF-G  sequences suggested that in addition to  Pseudoroegneria  and  Hordeum , unknown genome was the third potential donor of  E .  lolioides . Data from chloroplast DNA showed that  Pseudoroegneria  is the maternal donor of  E .  lolioides . Data from specific FISH marker for St genome indicated that  E .  lolioides  has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of  Hordeum  genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of  Acc1  sequences was detected in  E .  lolioides  possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6–26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH.    Conclusions  Phylogenetic and in situ hybridization indicated the presence of two sets of  Pseudoroegneria  and one set of  Hordeum  genome in  E .  lolioides . The genome formula of  E .  lolioides  was designed as StStStStHH.  E. lolioides  may have originated through the hybridization between tetraploid  Elymus  (StH) and diploid  Pseudoroegneria  species. E and unknown genomes may participate in the speciation of  E .  lolioides  through introgression. According to the genome classification system,  E .  lolioides  should be transferred into  Elymus  L. and renamed as  Elymus lolioidus  (Kar. er Kir.) Meld.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1779-x) contains supplementary material, which is available to authorized users.

Genome constitution and evolution of Elytrigia lolioides inferred from Acc1, EF-G, ITS, TrnL-F sequences and GISH