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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 rbcLX–nifV1–rpoC2–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 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 arrow points the position of the recombination breakpoint detected in rbcLX. (B) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology. (C) The two most supported topologies.
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pone.0131223.g008: The results of the rbcLX–nifV1–rpoC2–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 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 arrow points the position of the recombination breakpoint detected in rbcLX. (B) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology. (C) The two most supported topologies.

Mentions: In the Saguaro analysis of the rbcLX–nifV1–rpoC2–trnL data set, three separate supported topologies were detected, of which two, cacti 1 and 3, were by far the most strongly supported (Fig 8). The third topology, cactus 34, was only supported by six variable positions in the intergenic spacer region of the rbcLX. The topologies produced by Saguaro did not show any conflict between the most supported cacti 1 and 3, but also very little resolution. When separate ML trees were constructed from the segments supporting the different topologies, all three trees showed some topological incongruence between the segments supporting different cacti and noticeably more resolution than the topologies provided by Saguaro (S2B–S2D Fig).


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 rbcLX–nifV1–rpoC2–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 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 arrow points the position of the recombination breakpoint detected in rbcLX. (B) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology. (C) The two most supported topologies.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131223.g008: The results of the rbcLX–nifV1–rpoC2–trnL Saguaro analysis.(A) Segments supporting different topologies mapped on the analyzed 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 arrow points the position of the recombination breakpoint detected in rbcLX. (B) Relations between the different topologies. Following each name is the number of variable nucleotides supporting the topology. (C) The two most supported topologies.
Mentions: In the Saguaro analysis of the rbcLX–nifV1–rpoC2–trnL data set, three separate supported topologies were detected, of which two, cacti 1 and 3, were by far the most strongly supported (Fig 8). The third topology, cactus 34, was only supported by six variable positions in the intergenic spacer region of the rbcLX. The topologies produced by Saguaro did not show any conflict between the most supported cacti 1 and 3, but also very little resolution. When separate ML trees were constructed from the segments supporting the different topologies, all three trees showed some topological incongruence between the segments supporting different cacti and noticeably more resolution than the topologies provided by Saguaro (S2B–S2D Fig).

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