Phylogenetic analysis revealed reticulate evolution of allotetraploid Elymus ciliaris

•Both RPB2 and PGK1 data supported that E. ciliairs has multiple origins.•The St genome in E. ciliaris species has a complex evolutionary history.•Both RPB2 and PGK1 data suggested the absence of St genome in accession PI 377532.•cpDNA RPS16 clearly indicated St species as maternal of the accession PI 377532.•Two lineages of St genome present in E. ciliaris species.

Increasing evidence has shown the complex and dynamic nature of polyploids. Two single copy nuclear genes were used to explore genome evolutionary dynamics and the origin of tetraploid E. ciliaris: the phosphoglycerate kinase (PGK1) and the second largest subunit of RNA polymerase II (RPB2) together with a chloroplast gene encoding ribosomal protein S16 (RPS16). RPS16 data confirmed that the maternal origin of E. ciliaris is the St genome species. Both RPB2 and PGK1 data supported that E. ciliairs has multiple origins, and originated from the Pseudorogneria (St) and unknown donor (Y) diploids. The St genome in E. ciliaris species has a complex evolutionary history. Both RPB2 and PGK1 data suggested the absence of St genome in accession PI 377532 of E. ciliaris. However, cpDNA RPS16 clearly indicated that its maternal origin is the same as other E. ciliaris accessions, and is St genomic diploid species. Results suggest that there are two lineages of St genome present in E. ciliaris species; one is grouped with Pseudoroegneria diploid species, the other is grouped with Hordeum (H) species (named St?). The Japanese accession PI 377532 might have introgression either from Hordeum H genome species or from Elymus StH genome species with replacement of at least some nuclear St-loci by H-loci. The correlation between genome differentiation and geographical distribution is also discussed.

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