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Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms

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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.

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Acknowledgements

The authors wish to thank technical support and fruitful discussion to Sonja Siljak-Yakovlev (CNRS, Paris), Oriane Hidalgo (Institut Botànic de Barcelona, CSIC-ICUB), Roman Matyasek (Academy of Sciences of the Czech Republic) and Elizabeth McCarthy (University of London). Dr. E. Durant McArthur (Shrub Sciences Laboratory, USDA) is also acknowledged for providing seed material of the Artemisia tridentata populations used in this study, as all people who helped us in plant collection (mentioned in Supplementary Table S1) and also the Botanical Gardens of Brno and Barcelona for providing seed or leaf material of the specimens studied. This research was funded by the Grant Agency of the Czech Republic (521/07/0116), the Academy of Sciences of the Czech Republic (AVOZ50040507 and AVOZ50040702), NERC (UK), the Ministry of Science and Innovation of the Spanish government (CGL 2004-04563-C02-02/BOS, and two pre-doctoral grants for two of the authors, S. G. and J. P.) and by the CSIC (through a JAE-Doc contract for S. G.).

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Authors and Affiliations

  1. Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Catalonia, Spain

    Sònia Garcia, Jaume Pellicer & Joan Vallès

  2. Institut Botànic de Barcelona(CSIC-ICUB), Catalonia, Spain

    Sònia Garcia & Teresa Garnatje

  3. School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK

    K. Yoong Lim, Michael Chester & Andrew R. Leitch

  4. Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic

    Aleš Kovařík

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  1. Sònia Garcia
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  2. K. Yoong Lim
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Correspondence to Aleš Kovařík.

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Communicated by I. Schubert

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Table S1

Origin and collection data of the specimens studied (DOC 50.0 KB).

Fig. S1

Sequencing of the IGS clones (Fig. 1) from A. absinthium and A. tridentata. Alignment of the IGS1 (between the 26S and 5S genes) clones was carried out using Clustal X program. The characteristic sequence features are indicated in colours. Blue—26S and 18S rDNA genes; red—5S rDNA genes; dark green—102-bp sub-repeats; light green—248-bp sub-repeats; grey shading—imperfect 5′ inverted repeat from a putative Cassandra element; yellow shading—imperfect (−) strand priming site (DOC 106 KB).

Fig. S2

Southern blot hybridisation of A. tridentata ssp. wyomingensis genomic DNA digested with different restriction enzymes and hybridised with the 26S and 5S rDNA probes. Note that both probes co-hybridised to the most of the fragments (arrows). The hybridisation of the upper ∼6 kb EcoRV was stronger with the 5S probe than to the 26S probe which can be explained by the presence of 5S tandem repeat (double 5S) in the gene family corresponding to upper band (DOC 638 KB).

Fig. S3

Dot matrix self comparison of the IGS from A. absinthium clone 8 (window = 21; stringency = 14). TIS, transcription initiation site (DOC 411 KB).

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Garcia, S., Lim, K.Y., Chester, M. et al. Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms. Chromosoma 118, 85–97 (2009). https://doi.org/10.1007/s00412-008-0179-z

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