It is generally considered that in prokaryotes and in some species of early diverging eukaryote groups e.g. yeast, Saccharomyces cerevisiae, rRNA genes are organised in a single operon, clustered in tandem and transcribed by the same RNA polymerase. In eukaryotes, the 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are transcribed by different polymerases, RNA polymerase I and III, respectively. Independent control of transcription probably enabled physical separation of both loci in chromosomes, an arrangement that is typical for most eukaryotic organisms. Nevertheless, it seems that there are several exceptions to this rule. For example, 5S genes linkage to other repetitive sequences including 35S, histone genes or the trans-spliced leader has been demonstrated . These linked arrangements are found among diverse biological taxa including nematodes , fungi , crustaceans , slime moulds  or mosses [6, 7], and they are believed to represent transition states between linked (prokaryotic) and unlinked (eukaryotic) arrangements. However, our recent observations in a group of angiosperms (genus Artemisia, Asteraceae)  clearly point to the possibility that linked arrangements might not be restricted to prokaryotes and primitive eukaryotes but may occur throughout the tree of life.
The Asteraceae, also named Compositae, is the largest family of the angiosperms in terms of numbers of species, with 1,620 genera and 23,600 species , constituting approximately 8-10% of all flowering plants. Although many trees and shrubs exist, a majority of species of Asteraceae are herbaceous, and they are easily recognizable by a suite of characters including fused anthers, a fruit with a single ovule, and a specialized inflorescence termed the capitulum. The family occurs in all continents of the world except Antarctica  and includes many edible, medicinal, noxious, invasive or endangered species. Estimates indicate that the Asteraceae originated in the mid Eocene (45-49 Mya) and that most tribal splits occurred during the Oligocene (28-36 Mya). The family has been the subject of intensive phylogenetic analyses using all kinds of molecular and morphological data [9, 11] and it is currently considered to hold 12 major lineages , four of which (Asteroideae, Carduoideae, Cichorioideae and Mutisioideae) comprise 99% of its species diversity. Considering the size and importance of this family, however, relatively little has been published about rDNA position, organisation and structure in this group as a whole. In the past, the 5S and 35S genes have been mapped on chromosomes in some Asteraceae genera, e.g. Tragopogon , Centaurea , Helianthus , and Hypochaeris [16, 17] among others, showing one or several separate loci of each, mostly in different chromosomes. In contrast, initial FISH mapping on Artemisia showed colocalised 35S and 5S signals [18–20]. Employing molecular methods we have recently demonstrated that several Artemisia species have evolved unusual ribosomal units resembling the arrangement in yeast: the 5S genes locate within the 26S-18S intergenic spacer and are transcribed from the opposite strand of the 35S rDNA operon . In species displaying linked arrangement the homogenisation of linked rRNA genes most likely went to completion, since no unlinked genes were detected by FISH or Southern blot hybridisation. Taking into account the large size of the family it is not known how frequently such arrangement occurs, whether it is conserved in related species, its chromosomal dynamics and evolutionary success. With these issues in mind, we examined ribosomal DNA structure and organisation in selected representatives of the Asteraceae using molecular and cytogenetic methods. In addition, we searched for any nodes in extant Asteraceae phylogeny [21, 22] that mark a switch in the organisation of rDNA.