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TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations

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Abstract

Seven hundred fifty-two to one thousand ninety-seven base pairs of the trnL intron and trnL–trnF intergenic spacer of the chloroplast DNA of 55 Juncaceae taxa (Juncus, Luzula, Rostkovia, and Oxychloë) was sequenced. Seventeen structural mutations (13 indels marked A to M, 3 parts of the trnF pseudogene, and insertion “o” within a pseudogene) within the chloroplast trnL–trnF region were examined as possible indicators for phylogenetic relationships in Juncaceae. Juncus trifidus (section Steirochloa) was clearly separated from the other taxa by two large (>80 bp) indels. The “Southern Hemisphere clade” was strongly supported by a unique insertion (334 bp) in the trnL intron. The monophyly of Luzula was supported by three small (<10 bp) indels in the trnL-F spacer. They were found in all 22 examined members that represent the taxonomic and geographical diversity of the genus Luzula. A tandemly duplicated tRNA pseudogene was found in the Juncus subgenus Juncus species and is supported by four small unique indels too. The acceptor stem and D-domain-encoding regions are separated by a unique 8-bp insertion. The T-domain and acceptor stem-encoding regions were not found in the pseudogene repeats. Only the Juncus sections Ozophyllum and Iridifolii contain the 5′ acceptor stem, D-domain, and anticodon domain of the tRNAF encoding DNA. The structural mutations in the trnL intron and the trnL–trnF intergenic spacer are useful for phylogenetic reconstruction in the Juncaceae.

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Acknowledgments

We would like to thank the curators of herbariums AAU, BM, C, and K, where many Juncaceae DNA samples were collected, for their great hospitality. J.K. and L.D. thank T.H.M. Mes and J. Fehrer for fruitful comments on the manuscript. We are grateful to John Novotney for improving the English. The study was done at the DNA Laboratory, Institute of Botany, ASCR, and Laboratory of the Centre for Integrated Genomics and Institute of Molecular Genetics, ASCR, and was supported in part by Grants GACR 206/02/035, GAUK 109/2002/B/BIO, and AVOZ 6005908.

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Authors and Affiliations

  1. Institute of Botany, Department of Taxonomy, Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic

    Lenka Drábková & Jan Kirschner

  2. Centre for Integrated Genomics and Institute of Molecular Genetics, Academy of Sciences, Flemingovo nám. 2, 166 37, Prague 6, Czech Republic

    Čestmír Vlček & Václav Pačes

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  1. Lenka Drábková
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  2. Jan Kirschner
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  3. Čestmír Vlček
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  4. Václav Pačes
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Correspondence to Lenka Drábková.

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Drábková, L., Kirschner, J., Vlček, Č. et al. TrnL–trnF Intergenic Spacer and trnL Intron Define Major Clades Within Luzula and Juncus (Juncaceae): Importance of Structural Mutations. J Mol Evol 59, 1–10 (2004). https://doi.org/10.1007/s00239-004-2598-7

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  • DOI: https://doi.org/10.1007/s00239-004-2598-7

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