The 5S rRNA gene units in the native New World annual Hordeum species (Triticeae : Poaceae)

We have employed a polymerase chain reaction (PCR) based approach to amplif y 5S rDNA sequences from 20 accessions representing five Hordeum species na tive to the Americas. Sequence analysis of 88 clones revealed three sets of orthologous sequences in Hordeum pusillum Nutt. and two sets in the other four species. The long H1 unit class, previously known in Hordeum bulbosum L., Hordeum marinum L. s.l., Hordeum murinum L. s.l., Hordeum spontaneum Bo iss., and Hordeum vulgare L., was found also in Hordeum depressum (Scribner & Smith) Rydberg and in H. pusillum; however, the majority of the sequence s fell within two new classes of orthologous sequences. Sequences of the lo ng H2 unit class were found in four species but not in H. depressum. Sequen ces of the long Y2 unit class were found in all five species. The long H2 a nd long Y2 unit classes appear to be unique to this group of five, mostly a nnual, North and South American species. Cladistic analysis of the ortholog ous sequences from the species with the long H1 unit class places the long H1 sequence of Hordeum flexuosum Steudel in the same clade with H. murinum, whereas H. depressum is more closely related to the perennial species, Hor deum bogdanii Wilenski and H. bulbosum. This association differs from previ ously described species relationships and it may be that the gene tree diff ers from the species tree. A cladistic analysis of paralogous sequences of the two new unit classes defined in this study together with the long H1, t he long Y1 and the long X2 unit classes uncovered in previous work in Horde um, was performed. Based upon these analyses, we hypothesize that the possi ble order of divergence was first the division into two branches leading to the long H1 unit class and the long H2 unit class; the lineage leading to the long H2 class was further divided to give rise to branches leading to t he long Y1, the long Y2 and the long X2 classes.