Limits...
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

trnL P6b region ancestral character state reconstruction.A cladogram from the bayesian analysis of the combined 16S rRNA gene–trnL data set with reconstructed ancestral character states for the trnL P6b region. Black specimens have a Class II and red specimens Collema-type Class I trnL P6b region. The pie charts show the probability of the presence of Class II (white) or Class I (Collema and Nephroma types; red) trnL P6b region for the ancestral nodes. The clade formed by the cyanobionts of Nephroma guild lichens has been collapsed to a single branch for the figure.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4476775&req=5

pone.0131223.g002: trnL P6b region ancestral character state reconstruction.A cladogram from the bayesian analysis of the combined 16S rRNA gene–trnL data set with reconstructed ancestral character states for the trnL P6b region. Black specimens have a Class II and red specimens Collema-type Class I trnL P6b region. The pie charts show the probability of the presence of Class II (white) or Class I (Collema and Nephroma types; red) trnL P6b region for the ancestral nodes. The clade formed by the cyanobionts of Nephroma guild lichens has been collapsed to a single branch for the figure.

Mentions: The ancestral character reconstruction analysis estimates that the probability of the common ancestor of the Nostoc clade having a Class II p6b region is more than 99% (Fig 2). The probability of the other analyzed ancestral nodes having a Class II P6b region varied from 93 to over 99%, except for the final 17th node. The 17th node is the common ancestor of the Nephroma guild Nostoc cyanobionts with Nephroma-type Class I P6b regions and their sister group with Collema-type Nostoc P6b regions, and it was the most probable analyzed ancestor with a Class I P6b region with a probability of 79%.


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

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

trnL P6b region ancestral character state reconstruction.A cladogram from the bayesian analysis of the combined 16S rRNA gene–trnL data set with reconstructed ancestral character states for the trnL P6b region. Black specimens have a Class II and red specimens Collema-type Class I trnL P6b region. The pie charts show the probability of the presence of Class II (white) or Class I (Collema and Nephroma types; red) trnL P6b region for the ancestral nodes. The clade formed by the cyanobionts of Nephroma guild lichens has been collapsed to a single branch for the figure.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131223.g002: trnL P6b region ancestral character state reconstruction.A cladogram from the bayesian analysis of the combined 16S rRNA gene–trnL data set with reconstructed ancestral character states for the trnL P6b region. Black specimens have a Class II and red specimens Collema-type Class I trnL P6b region. The pie charts show the probability of the presence of Class II (white) or Class I (Collema and Nephroma types; red) trnL P6b region for the ancestral nodes. The clade formed by the cyanobionts of Nephroma guild lichens has been collapsed to a single branch for the figure.
Mentions: The ancestral character reconstruction analysis estimates that the probability of the common ancestor of the Nostoc clade having a Class II p6b region is more than 99% (Fig 2). The probability of the other analyzed ancestral nodes having a Class II P6b region varied from 93 to over 99%, except for the final 17th node. The 17th node is the common ancestor of the Nephroma guild Nostoc cyanobionts with Nephroma-type Class I P6b regions and their sister group with Collema-type Nostoc P6b regions, and it was the most probable analyzed ancestor with a Class I P6b region with a probability of 79%.

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