title: TrnL- trnF intergenic spacer and trnL intron define major clades within Luzula and Juncus (Juncaceae): importance of structural mutations.
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.
authors.affiliation: Institute of Botany, Department of Taxonomy, Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic. drabkova@ibot.cas.cz
authors.forename: Lenka
authors.initials: L
authors.lastname: Drábková
authors.forename: Jan
authors.initials: J
authors.lastname: Kirschner
authors.forename: Cestmír
authors.initials: C
authors.lastname: Vlcek
authors.forename: Václav
authors.initials: V
authors.lastname: Paces
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D017931:DNA Primers; D018742:DNA, Chloroplast / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D005843:Geography; D019684:Magnoliopsida / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011544:Pseudogenes / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D018742:DNA, Chloroplast; D021901:DNA, Intergenic