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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

The results of the 16S rRNA gene–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 16S rRNA and trnL genes. Each color represents a different topology (cactus). The narrower gray areas include the positions that did not support any of the filtered cacti. The red arrows point the positions of the recombination breakpoints detected in 16S rRNA gene. (B) Two the most supported topologies, cacti 39 and 2. (C) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology.
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pone.0131223.g007: The results of the 16S rRNA gene–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 16S rRNA and trnL genes. Each color represents a different topology (cactus). The narrower gray areas include the positions that did not support any of the filtered cacti. The red arrows point the positions of the recombination breakpoints detected in 16S rRNA gene. (B) Two the most supported topologies, cacti 39 and 2. (C) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology.

Mentions: Saguaro analysis of the 16S rRNA gene and trnL identified seven different cacti supported by the data set. The alignment segments supporting the cacti included 164 of the 189 variable nucleotide positions present in the alignment (Fig 7). The most supported topology, cactus 39, was supported by 11 separate alignment segments. These segments included 71 variable positions in the 16S rDNA and 30 variable positions in the trnL region, covering 48 and 73% of all variable nucleotide positions of the regions, respectively. Also the second most supported topology, cactus 2, was supported by alignment segments present in both 16S rRNA gene and trnL regions, including altogether 38 variable positions distributed among nine separate segments. The remaining five cacti were all supported by less than ten variable nucleotide positions, and all these within the 16S rRNA gene.


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

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

The results of the 16S rRNA gene–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 16S rRNA and trnL genes. Each color represents a different topology (cactus). The narrower gray areas include the positions that did not support any of the filtered cacti. The red arrows point the positions of the recombination breakpoints detected in 16S rRNA gene. (B) Two the most supported topologies, cacti 39 and 2. (C) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131223.g007: The results of the 16S rRNA gene–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 16S rRNA and trnL genes. Each color represents a different topology (cactus). The narrower gray areas include the positions that did not support any of the filtered cacti. The red arrows point the positions of the recombination breakpoints detected in 16S rRNA gene. (B) Two the most supported topologies, cacti 39 and 2. (C) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology.
Mentions: Saguaro analysis of the 16S rRNA gene and trnL identified seven different cacti supported by the data set. The alignment segments supporting the cacti included 164 of the 189 variable nucleotide positions present in the alignment (Fig 7). The most supported topology, cactus 39, was supported by 11 separate alignment segments. These segments included 71 variable positions in the 16S rDNA and 30 variable positions in the trnL region, covering 48 and 73% of all variable nucleotide positions of the regions, respectively. Also the second most supported topology, cactus 2, was supported by alignment segments present in both 16S rRNA gene and trnL regions, including altogether 38 variable positions distributed among nine separate segments. The remaining five cacti were all supported by less than ten variable nucleotide positions, and all these within the 16S rRNA gene.

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