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

Abstract

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.

Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungusPeltigera

“…In these examples, however, we are unable to distinguish inter-locus recombination between trnL and the other loci from intra-locus recombination within trnL between the P6b stem-loop and the rest of the intron. It has been shown that these two stem-loop types have a punctate distribution on phylogenies inferred from the remainder of the trnL locus (Oksanen et al, 2004). The two stem-loop types are also spread across our trnL phylogeny (Fig.…”

PHYLOGENETIC PATTERNS AMONG NOSTOC CYANOBIONTS WITHIN BI‐ AND TRIPARTITE LICHENS OF THE GENUS PANNARIA1

“…The data on Pseudocyphellaria cyanobionts from New Zealand (Summerfield et al 2002, Rikkinen 2004) pose interesting, but uncertain interpretations. Although Rikkinen (2004) in his tRNA analysis avoided the P6b stem loop shown to be unsuitable for phylogenetic analysis (Oksanen et al 2004), tRNA data are less precise than 16S rRNA data. Still, the data indicate that Pseudocyphellaria may have a wider cyanobiont selectivity than realized today.…”

“…2002, Rikkinen 2004) pose interesting, but uncertain interpretations. Although Rikkinen (2004) in his tRNA analysis avoided the P6b stem loop shown to be unsuitable for phylogenetic analysis (Oksanen et al. 2004), tRNA data are less precise than 16S rRNA data.…”

High selectivity in symbiotic associations of lichenized ascomycetes and cyanobacteria

“…The most commonly used gene locus in the earlier studies has been the group I intron in the tRNA Leu gene. This locus has been used to distinguish different strains of both symbiotic and free‐living Nostoc (e.g., Paulsrud and Lindblad, 1998; Paulsrud et al., 1998, 2000; Costa et al., 1999, 2001; Oksanen et al., 2002; Summerfield et al., 2002; Linke et al., 2003; Oksanen et al., 2003; Wirtz et al., 2003). Some other loci have also been utilized for cyanobacterial studies.…”