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Evolution of the tRNALeu (UAA) Intron and Congruence of Genetic Markers in Lichen-Symbiotic Nostoc.

Kaasalainen U, Olsson S, Rikkinen J - PLoS ONE (2015)

Bottom Line: The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants.Here we attempt to resolve the complex evolution of the two different trnL P6b region types.Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly.

View Article: PubMed Central - PubMed

Affiliation: Department of Geobiology, University of Göttingen, Göttingen, Germany.

ABSTRACT
The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic relationships of the selected lichen cyanobionts.The phylogeny is based on 16S rRNA gene and trnL intron sequences (P6b region omitted). The posterior probability values (PP) equal or greater than 0.75 and bootstrap values (BS) equal or greater than 75 are shown on branches (just PP or PP/BS). Thick branches have PP equal or greater than 0.95. Specimens having a Class II-type trnL P6b region are marked black, a Collema-type Class I P6b region red, and a Nephroma-type Class I P6b region white on red background.
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pone.0131223.g001: Phylogenetic relationships of the selected lichen cyanobionts.The phylogeny is based on 16S rRNA gene and trnL intron sequences (P6b region omitted). The posterior probability values (PP) equal or greater than 0.75 and bootstrap values (BS) equal or greater than 75 are shown on branches (just PP or PP/BS). Thick branches have PP equal or greater than 0.95. Specimens having a Class II-type trnL P6b region are marked black, a Collema-type Class I P6b region red, and a Nephroma-type Class I P6b region white on red background.

Mentions: The separate Bayesian analyses of the 16S rRNA gene and trnL sequences resulted in trees with relatively poor resolution (S1 Fig). Visual comparison of the resolved parts of the trees revealed very little conflict between the two loci on the inspection threshold of Posterior Probability (PP) 0.8. In addition, when the regions were combined for Bayesian analysis, it resulted in a tree with higher resolution and more supported clades than either of the two individual analyses. This suggested that the phylogenetic signals from the 16S rRNA gene and trnL are not in conflict, and the combined data set could be subjected for further analyses. The Bayesian analysis of the combined 16S rRNA gene–trnL data set identified altogether 30 well supported (PP ≥ 0.95) clades among the lichen-symbiotic Nostoc (Fig 1). The ML analysis found the best tree with identical topologies 22 times, and the topology was mostly congruent with the final tree obtained by Bayesian analysis. The crown group of the Bayesian tree consisted of the Nostoc cyanobionts of Nephroma guild lichens that have Nephroma-type Class I trnL P6b regions (PP 1 / BS 87). Conversely, the Nostoc cyanobionts with Collema-type P6b regions are dispersed over ten different clades, and frequently occur mixed with Nostoc genotypes with Class II P6b regions.


Evolution of the tRNALeu (UAA) Intron and Congruence of Genetic Markers in Lichen-Symbiotic Nostoc.

Kaasalainen U, Olsson S, Rikkinen J - PLoS ONE (2015)

Phylogenetic relationships of the selected lichen cyanobionts.The phylogeny is based on 16S rRNA gene and trnL intron sequences (P6b region omitted). The posterior probability values (PP) equal or greater than 0.75 and bootstrap values (BS) equal or greater than 75 are shown on branches (just PP or PP/BS). Thick branches have PP equal or greater than 0.95. Specimens having a Class II-type trnL P6b region are marked black, a Collema-type Class I P6b region red, and a Nephroma-type Class I P6b region white on red background.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4476775&req=5

pone.0131223.g001: Phylogenetic relationships of the selected lichen cyanobionts.The phylogeny is based on 16S rRNA gene and trnL intron sequences (P6b region omitted). The posterior probability values (PP) equal or greater than 0.75 and bootstrap values (BS) equal or greater than 75 are shown on branches (just PP or PP/BS). Thick branches have PP equal or greater than 0.95. Specimens having a Class II-type trnL P6b region are marked black, a Collema-type Class I P6b region red, and a Nephroma-type Class I P6b region white on red background.
Mentions: The separate Bayesian analyses of the 16S rRNA gene and trnL sequences resulted in trees with relatively poor resolution (S1 Fig). Visual comparison of the resolved parts of the trees revealed very little conflict between the two loci on the inspection threshold of Posterior Probability (PP) 0.8. In addition, when the regions were combined for Bayesian analysis, it resulted in a tree with higher resolution and more supported clades than either of the two individual analyses. This suggested that the phylogenetic signals from the 16S rRNA gene and trnL are not in conflict, and the combined data set could be subjected for further analyses. The Bayesian analysis of the combined 16S rRNA gene–trnL data set identified altogether 30 well supported (PP ≥ 0.95) clades among the lichen-symbiotic Nostoc (Fig 1). The ML analysis found the best tree with identical topologies 22 times, and the topology was mostly congruent with the final tree obtained by Bayesian analysis. The crown group of the Bayesian tree consisted of the Nostoc cyanobionts of Nephroma guild lichens that have Nephroma-type Class I trnL P6b regions (PP 1 / BS 87). Conversely, the Nostoc cyanobionts with Collema-type P6b regions are dispersed over ten different clades, and frequently occur mixed with Nostoc genotypes with Class II P6b regions.

Bottom Line: The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants.Here we attempt to resolve the complex evolution of the two different trnL P6b region types.Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly.

View Article: PubMed Central - PubMed

Affiliation: Department of Geobiology, University of Göttingen, Göttingen, Germany.

ABSTRACT
The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.

No MeSH data available.


Related in: MedlinePlus