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Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations.

Teterina VI, Mamontov AM, Sukhanova LV, Kirilchik SV - Biomed Res Int (2015)

Bottom Line: Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations.Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii).Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

View Article: PubMed Central - PubMed

Affiliation: Limnological Institute, Siberian Branch, Russian Academy of Sciences, P.O. Box 278, Irkutsk 664033, Russia.

ABSTRACT
Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

No MeSH data available.


Fitch-Margoliash consensus tree of the Cytb haplotypes of BGa, BGp, and SG based on genetic distances between mRNA secondary structures. Haplotypes are shown as GenBank Accession Numbers. Small letters represent SG; large black letters represent BGa; large white letters in black rectangles represent BGp. Asterisks indicate the main haplotypes. Numbers indicate percentage support values.
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Related In: Results  -  Collection


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fig5: Fitch-Margoliash consensus tree of the Cytb haplotypes of BGa, BGp, and SG based on genetic distances between mRNA secondary structures. Haplotypes are shown as GenBank Accession Numbers. Small letters represent SG; large black letters represent BGa; large white letters in black rectangles represent BGp. Asterisks indicate the main haplotypes. Numbers indicate percentage support values.

Mentions: According to the tree based on mRNA structures (Figure 5), BGa and SG haplotypes were largely mixed while the representatives of BGp with few exceptions were arranged in a more compact manner: 15 representatives formed one monophyletic group. Although the reliability of the tree was not evaluated in a traditional way and branch support values were not high, its pattern could serve as an additional indirect indicator of a nonrandom distribution of substitutions during the formation of genetic polymorphism of the groups (i.e., the action of selection).


Signs of Selection in Synonymous Sites of the Mitochondrial Cytochrome b Gene of Baikal Oilfish (Comephoridae) by mRNA Secondary Structure Alterations.

Teterina VI, Mamontov AM, Sukhanova LV, Kirilchik SV - Biomed Res Int (2015)

Fitch-Margoliash consensus tree of the Cytb haplotypes of BGa, BGp, and SG based on genetic distances between mRNA secondary structures. Haplotypes are shown as GenBank Accession Numbers. Small letters represent SG; large black letters represent BGa; large white letters in black rectangles represent BGp. Asterisks indicate the main haplotypes. Numbers indicate percentage support values.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4465659&req=5

fig5: Fitch-Margoliash consensus tree of the Cytb haplotypes of BGa, BGp, and SG based on genetic distances between mRNA secondary structures. Haplotypes are shown as GenBank Accession Numbers. Small letters represent SG; large black letters represent BGa; large white letters in black rectangles represent BGp. Asterisks indicate the main haplotypes. Numbers indicate percentage support values.
Mentions: According to the tree based on mRNA structures (Figure 5), BGa and SG haplotypes were largely mixed while the representatives of BGp with few exceptions were arranged in a more compact manner: 15 representatives formed one monophyletic group. Although the reliability of the tree was not evaluated in a traditional way and branch support values were not high, its pattern could serve as an additional indirect indicator of a nonrandom distribution of substitutions during the formation of genetic polymorphism of the groups (i.e., the action of selection).

Bottom Line: Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations.Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii).Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

View Article: PubMed Central - PubMed

Affiliation: Limnological Institute, Siberian Branch, Russian Academy of Sciences, P.O. Box 278, Irkutsk 664033, Russia.

ABSTRACT
Studies over the past decade have shown a significant role of synonymous mutations in posttranscriptional regulation of gene expression, which is particularly associated with messenger RNA (mRNA) secondary structure alterations. Most studies focused on prokaryote genomes and the nuclear genomes of eukaryotes while little is known about the regulation of mitochondrial DNA (mtDNA) gene expression. This paper reveals signs of selection in synonymous sites of the mitochondrial cytochrome b gene (Cytb) of Baikal oilfish or golomyankas (Comephoridae) directed towards altering the secondary structure of the mRNA and probably altering the character of mtDNA gene expression. Our findings are based on comparisons of intraspecific genetic variation patterns of small golomyanka (Comephorus dybowski) and two genetic groups of big golomyanka (Comephorus dybowskii). Two approaches were used: (i) analysis of the distribution of synonymous mutations between weak-AT (W) and strong-GC (S) nucleotides within species and groups in accordance with mutation directions from central to peripheral haplotypes and (ii) approaches based on the predicted mRNA secondary structure.

No MeSH data available.