RESEARCH ARTICLE Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms Sònia Garcia & K. Yoong Lim & Michael Chester & Teresa Garnatje & Jaume Pellicer & Joan Vallès & Andrew R. Leitch & Aleš Kovařík Received: 4 June 2008 / Revised: 22 July 2008 / Accepted: 20 August 2008 / Published online: 9 September 2008 # Springer-Verlag 2008 Abstract Typically in plants, the 5S and 35S ribosomal DNA (rDNA) encoding two major ribosomal RNA species occur at separate loci. However, in some algae, bryophytes and ferns, they are at the same locus (linked arranged). Southern blot hybridisation, polymerase chain reactions (PCR), fluorescent in situ hybridisation, cloning and sequencing were used to reveal 5S and 35S rDNA genomic organisation in Artemisia. We observed thousands of rDNA units at two–three loci containing 5S rDNA in an inverted orientation within the inter-genic spacer (IGS) of 35S rDNA. The sequenced clones of 26–18S IGS from Artemisia absinthium appeared to contain a conserved 5S gene insertion proximal to the 26S gene terminus (5S rDNA-1) and a second less conserved 5S insertion (5S rDNA-2) further downstream. Whilst the 5S rDNA-1 showed all the structural features of a functional gene, the 5S-rDNA-2 had a deletion in the internal promoter and probably represents a pseudogene. The linked arrangement probably evolved before the divergence of Artemisia from the rest of Asteraceae (>10 Myrs). This arrangement may have involved retrotransposons and once formed spread via mechanisms of concerted evolution. Heterogeneity in unit structure may reflect ongoing homogenisation of variant unit types without fixation for any particular variant. Introduction The nuclear genes encoding rRNA have been the subject of much research amongst molecular biologists and cytogene- ticists, particularly for inferring evolutionary relationships between species. In most eukaryotes, 5S rRNA and 35S rRNA genes are usually clustered in separate tandem arrays and are transcribed by RNA polymerase III and RNA polymerase I, respectively (Grummt and Pikaard 2003). Each 35S rDNA unit carries the 18S, 5.8S and 26S genes, transcribed in this order as a single operon. However, there are notable exceptions to this organisa- tion of rRNA genes in some eukaryotes. For example, 5S rRNA genes do not occur in tandem arrays in some fungi but instead are dispersed across the genome (Goyon et al. 1996). Several studies have shown that both 35S and 5S rRNA genes can be linked to other repeats (Drouin and Moniz de Sá 1995). Furthermore, there are reports from organisms scattered across the tree of life (e.g. fungi, amoebas, nematodes, earthworms, arthropods and fishes) that there is a physical linkage of 35S and 5S rRNA units (Vahidi et al. 1988; Belkhiri et al. 1992; Drouin and Moniz Chromosoma (2009) 118:85–97 DOI 10.1007/s00412-008-0179-z Communicated by I. Schubert Electronic supplementary material The online version of this article (doi:10.1007/s00412-008-0179-z) contains supplementary material, which is available to authorized users. S. Garcia : J. Pellicer : J. Vallès Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Catalonia, Spain S. Garcia : T. Garnatje Institut Botànic de Barcelona(CSIC-ICUB), Catalonia, Spain K. Y. Lim : M. Chester : A. R. Leitch School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK A. Kovařík (*) Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic e-mail: kovarik@ibp.cz