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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

Haplotype networks showing the differences in the Collema-type trnL P6b regions.(A) Haplotype network constructed from the Collema-type trnL P6b regions with the program Network. (B) Haplotype network modified to reflect the possible evolutionary events in the Collema-type P6b region. One sequence from each clade present in the phylogenetic tree (Fig 1) was put together with the program Network (grey background and connecting lines). These connections reflect the overall similarity of the sequences and the different P6b types are probably results of independent adoption events. The rest of the P6b sequences were connected to their above mentioned phylogenetic relatives with the least amount of changes (black lines; each indel event or single nucleotide mutation equals one change), and the probable actual indel events and single nucleotide mutations are also marked with black.
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pone.0131223.g003: Haplotype networks showing the differences in the Collema-type trnL P6b regions.(A) Haplotype network constructed from the Collema-type trnL P6b regions with the program Network. (B) Haplotype network modified to reflect the possible evolutionary events in the Collema-type P6b region. One sequence from each clade present in the phylogenetic tree (Fig 1) was put together with the program Network (grey background and connecting lines). These connections reflect the overall similarity of the sequences and the different P6b types are probably results of independent adoption events. The rest of the P6b sequences were connected to their above mentioned phylogenetic relatives with the least amount of changes (black lines; each indel event or single nucleotide mutation equals one change), and the probable actual indel events and single nucleotide mutations are also marked with black.

Mentions: The single nucleotide similarity based relations between the Collema-type Nostoc trnL P6b regions do not follow the phylogenetic reconstruction of the group (Fig 3A). However, if each indel event is only counted as one change and the haplotype network modified according to the obtained phylogeny, a simpler network is obtained (Fig 3B): the latter network is 15 changes shorter (altogether 40 changes) than the network constructed by the program (altogether 55 changes). The only major change seen in the latter network is represented by the long branch between Nostoc sequence 16 and the rest of the Peltigera aphthosa group Nostoc sequences (13–15).


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

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

Haplotype networks showing the differences in the Collema-type trnL P6b regions.(A) Haplotype network constructed from the Collema-type trnL P6b regions with the program Network. (B) Haplotype network modified to reflect the possible evolutionary events in the Collema-type P6b region. One sequence from each clade present in the phylogenetic tree (Fig 1) was put together with the program Network (grey background and connecting lines). These connections reflect the overall similarity of the sequences and the different P6b types are probably results of independent adoption events. The rest of the P6b sequences were connected to their above mentioned phylogenetic relatives with the least amount of changes (black lines; each indel event or single nucleotide mutation equals one change), and the probable actual indel events and single nucleotide mutations are also marked with black.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131223.g003: Haplotype networks showing the differences in the Collema-type trnL P6b regions.(A) Haplotype network constructed from the Collema-type trnL P6b regions with the program Network. (B) Haplotype network modified to reflect the possible evolutionary events in the Collema-type P6b region. One sequence from each clade present in the phylogenetic tree (Fig 1) was put together with the program Network (grey background and connecting lines). These connections reflect the overall similarity of the sequences and the different P6b types are probably results of independent adoption events. The rest of the P6b sequences were connected to their above mentioned phylogenetic relatives with the least amount of changes (black lines; each indel event or single nucleotide mutation equals one change), and the probable actual indel events and single nucleotide mutations are also marked with black.
Mentions: The single nucleotide similarity based relations between the Collema-type Nostoc trnL P6b regions do not follow the phylogenetic reconstruction of the group (Fig 3A). However, if each indel event is only counted as one change and the haplotype network modified according to the obtained phylogeny, a simpler network is obtained (Fig 3B): the latter network is 15 changes shorter (altogether 40 changes) than the network constructed by the program (altogether 55 changes). The only major change seen in the latter network is represented by the long branch between Nostoc sequence 16 and the rest of the Peltigera aphthosa group Nostoc sequences (13–15).

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