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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

Secondary structure reconstruction of the Collema-type P6b regions 5 and 13–15 and 16.The folding of the P6b region sequences of specimens (A) 5 and 13–15, and (B) 16 were folded with NUPACK at 20°C. Beneath each structure is the calculated Gibbs free energy (ΔG). Color of each position reflects the stability of the structure, dark red being the most stable. The blue arrows in (B) show the single nucleotide polymorphism present in the analyzed data (bigger arrow indicates three possible character states and the smaller two).
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pone.0131223.g005: Secondary structure reconstruction of the Collema-type P6b regions 5 and 13–15 and 16.The folding of the P6b region sequences of specimens (A) 5 and 13–15, and (B) 16 were folded with NUPACK at 20°C. Beneath each structure is the calculated Gibbs free energy (ΔG). Color of each position reflects the stability of the structure, dark red being the most stable. The blue arrows in (B) show the single nucleotide polymorphism present in the analyzed data (bigger arrow indicates three possible character states and the smaller two).

Mentions: If the phylogenetic groups that have Collema-type P6b regions are inspected individually, adding an insertion normally lowers the overall free energy, also when calculated per nucleotide, hence stabilizing the structure (Fig 4, S4 Table). Also, most of the indel events happen in the same position of the folded structure causing an emergence of a side stem-loop structure(s) (Fig 4). Only in the Peltigera aphthosa group (sequences 13–16) the indel events have happened in different parts of the structure and included two separate 14 nt insertions of the basic Class I repeat motif, this resulting in a long stem-structure without side stem-loops (Fig 5).


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

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

Secondary structure reconstruction of the Collema-type P6b regions 5 and 13–15 and 16.The folding of the P6b region sequences of specimens (A) 5 and 13–15, and (B) 16 were folded with NUPACK at 20°C. Beneath each structure is the calculated Gibbs free energy (ΔG). Color of each position reflects the stability of the structure, dark red being the most stable. The blue arrows in (B) show the single nucleotide polymorphism present in the analyzed data (bigger arrow indicates three possible character states and the smaller two).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131223.g005: Secondary structure reconstruction of the Collema-type P6b regions 5 and 13–15 and 16.The folding of the P6b region sequences of specimens (A) 5 and 13–15, and (B) 16 were folded with NUPACK at 20°C. Beneath each structure is the calculated Gibbs free energy (ΔG). Color of each position reflects the stability of the structure, dark red being the most stable. The blue arrows in (B) show the single nucleotide polymorphism present in the analyzed data (bigger arrow indicates three possible character states and the smaller two).
Mentions: If the phylogenetic groups that have Collema-type P6b regions are inspected individually, adding an insertion normally lowers the overall free energy, also when calculated per nucleotide, hence stabilizing the structure (Fig 4, S4 Table). Also, most of the indel events happen in the same position of the folded structure causing an emergence of a side stem-loop structure(s) (Fig 4). Only in the Peltigera aphthosa group (sequences 13–16) the indel events have happened in different parts of the structure and included two separate 14 nt insertions of the basic Class I repeat motif, this resulting in a long stem-structure without side stem-loops (Fig 5).

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