| Summary: | We used next-generation sequencing analysis of the 3′-part of 18S rDNA, ITS1, and a 5′-part of the 5.8S rDNA region to understand genetic variation among seven diploid A-genome <i>Avena</i> species. We used 4–49 accessions per species that represented the As genome (<i>A. atlantica</i>, <i>A. hirtula</i>, and <i>wiestii</i>), Ac genome (<i>A.</i> <i>canariensis</i>), Ad genome (<i>A. damascena</i>), Al genome (<i>A. longiglumis</i>), and Ap genome (<i>A. prostrata</i>). We also took into our analysis one C-genome species, <i>A. clauda</i>, which previously was found to be related to A-genome species. The sequences of 169 accessions revealed 156 haplotypes of which seven haplotypes were shared by two to five species. We found 16 ribotypes that consisted of a unique sequence with a characteristic pattern of single nucleotide polymorphisms and deletions. The number of ribotypes per species varied from one in <i>A. longiglumis</i> to four in <i>A. wiestii</i>. Although most ribotypes were species-specific, we found two ribotypes shared by three species (one for <i>A. damascena</i>, <i>A. hirtula</i>, and <i>A. wiestii</i>, and the second for <i>A. longiglumis</i>, <i>A. atlantica</i>, and <i>A. wiestii</i>), and a third ribotype shared between <i>A. atlantica</i> and <i>A. wiestii</i>. A characteristic feature of the <i>A. clauda</i> ribotype, a diploid C-genome species, is that two different families of ribotypes have been found in this species. Some of these ribotypes are characteristic of Cc-genome species, whereas others are closely related to As-genome ribotypes. This means that <i>A. clauda</i> can be a hybrid between As- and C-genome oats.
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