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Repeat-type distribution in trnL intron does not correspond with species phylogeny: comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria

¹ Department of Applied Chemistry and Microbiology, University of Helsinki, 00014 University of Helsinki, Finland
² Department of Ecology and Systematics, University of Helsinki, 00014 University of Helsinki, Finland
³ Department of Applied Biology, University of Helsinki, 00014 University of Helsinki, Finland

Correspondence
Ilona Oksanen
ilona.oksanen{at}helsinki.fi

tRNA^Leu UAA (trnL) intron sequences are used as genetic markers for differentiating cyanobacteria and for constructing phylogenies, since the introns are thought to be more variable among close relatives than is the 16S rRNA gene, the conventional phylogenetic marker. The evolution of trnL intron sequences and their utility as a phylogenetic marker were analysed among heterocystous cyanobacteria with maximum-parsimony, maximum-likelihood and Bayesian inference by comparing their evolutionary information to that of the 16S rRNA gene. Trees inferred from the 16S rRNA gene and the distribution of two repeat classes in the P6b stem–loop of the trnL intron were in clear conflict. The results show that, while similar heptanucleotide repeat classes I and II in the P6b stem–loop of the trnL intron could be found among distant relatives, some close relatives harboured different repeat classes with a high sequence difference. Moreover, heptanucleotide repeat class II and other sequences from the P6b stem–loop of the trnL intron interrupted several other intergenic regions in the genomes of heterocystous cyanobacteria. Cluster analyses based on conserved intron sequences without loops P6b, P9 and parts of P5 corresponded in most clades to the 16S rRNA gene phylogeny, although the relationships were not resolved well, according to low bootstrap support. Thus, the hypervariable loop sequences of the trnL intron, especially the P6b stem–loop, cannot be used for phylogenetic analysis and conclusions cannot be drawn about species relationships on the basis of these elements. Evolutionary scenarios are discussed considering the origin of the repeats.

Published online ahead of print on 14 November 2003 as DOI 10.1099/ijs.0.02928-0.

Database accession numbers for the new 16S rRNA gene sequences are AY112693, AY112694, AY328896–AY328900 (GenBank) and for the trnL intron AY112695 (GenBank), AJ571702–AJ571720 (EMBL).

Bayesian tree of the 16S and trnL intron sequences, the origin of the strains studied and the list of the strains with no intron PCR products are available as supplementary material in IJSEM Online.

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