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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.


Schematic representation of the network of Baikal oilfish obtained by Teterina et al. [15]. Dark circle diameters are proportional to the frequencies of the main haplotypes of Cytb within the groups and grey circle diameters are proportional to the respective values of nucleotide diversity (π).
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fig1: Schematic representation of the network of Baikal oilfish obtained by Teterina et al. [15]. Dark circle diameters are proportional to the frequencies of the main haplotypes of Cytb within the groups and grey circle diameters are proportional to the respective values of nucleotide diversity (π).

Mentions: As previously demonstrated, there are two genetic groups of BG that differ by two nucleotide substitutions in the mitochondrial cytochrome b gene (Cytb) [15]. One group is represented by the line of ancestral haplotypes (BGa) while another is paraphyletically related to BGa (BGp); BGp and SG are derived from the central haplotype of BGa (Figure 1). Nuclear DNA analysis and morphological data revealed no differences between BGa and BGp. It was suggested that these groups correspond to the two peaks of BG spawning. It was also assumed that the differences in mitochondrial DNA are the result of differences in female breeding timing, and nuclear genome panmixia is the result of independent mating of males with females from both genetic groups.


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)

Schematic representation of the network of Baikal oilfish obtained by Teterina et al. [15]. Dark circle diameters are proportional to the frequencies of the main haplotypes of Cytb within the groups and grey circle diameters are proportional to the respective values of nucleotide diversity (π).
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Schematic representation of the network of Baikal oilfish obtained by Teterina et al. [15]. Dark circle diameters are proportional to the frequencies of the main haplotypes of Cytb within the groups and grey circle diameters are proportional to the respective values of nucleotide diversity (π).
Mentions: As previously demonstrated, there are two genetic groups of BG that differ by two nucleotide substitutions in the mitochondrial cytochrome b gene (Cytb) [15]. One group is represented by the line of ancestral haplotypes (BGa) while another is paraphyletically related to BGa (BGp); BGp and SG are derived from the central haplotype of BGa (Figure 1). Nuclear DNA analysis and morphological data revealed no differences between BGa and BGp. It was suggested that these groups correspond to the two peaks of BG spawning. It was also assumed that the differences in mitochondrial DNA are the result of differences in female breeding timing, and nuclear genome panmixia is the result of independent mating of males with females from both genetic groups.

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.