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Albuminoid genes: evolving at the interface of dispensability and selection.

Mozzi A, Forni D, Cagliani R, Pozzoli U, Vertemara J, Bresolin N, Sironi M - Genome Biol Evol (2014)

Bottom Line: Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations.A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration.Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy manuela.sironi@bp.lnf.it.

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Analysis of selective pressure in the human and chimpanzee lineages. (A) Violin plot of selection coefficients (median, white dot; interquartile range, black bar). Selection coefficients (γ) are classified as strongly beneficial (100, 50), moderately beneficial (10, 5), weakly beneficial (1), neutral (0), weakly deleterious (−1), moderately deleterious (−5, −10), strongly deleterious (−50, −100), and inviable (−500). (B) Multiple alignment of human ALB, AFM, and AFP. Positively selected sites in the human (cyan) and chimpanzee (orange) lineages are highlighted. Sites selected in whole phylogeny are reported in red. Protein domains are indicated below the alignment: Signal peptide in yellow, domain I in magenta, and domain II in green.
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evu235-F3: Analysis of selective pressure in the human and chimpanzee lineages. (A) Violin plot of selection coefficients (median, white dot; interquartile range, black bar). Selection coefficients (γ) are classified as strongly beneficial (100, 50), moderately beneficial (10, 5), weakly beneficial (1), neutral (0), weakly deleterious (−1), moderately deleterious (−5, −10), strongly deleterious (−50, −100), and inviable (−500). (B) Multiple alignment of human ALB, AFM, and AFP. Positively selected sites in the human (cyan) and chimpanzee (orange) lineages are highlighted. Sites selected in whole phylogeny are reported in red. Protein domains are indicated below the alignment: Signal peptide in yellow, domain I in magenta, and domain II in green.

Mentions: In both humans and chimpanzees, we observed a general preponderance of codons evolving under negative selection (γ < 0) in all genes. The most striking difference was observed for GC, which showed stronger purifying selection compared with the other three genes in humans but not in chimpanzees (fig. 3A).Fig. 3.—


Albuminoid genes: evolving at the interface of dispensability and selection.

Mozzi A, Forni D, Cagliani R, Pozzoli U, Vertemara J, Bresolin N, Sironi M - Genome Biol Evol (2014)

Analysis of selective pressure in the human and chimpanzee lineages. (A) Violin plot of selection coefficients (median, white dot; interquartile range, black bar). Selection coefficients (γ) are classified as strongly beneficial (100, 50), moderately beneficial (10, 5), weakly beneficial (1), neutral (0), weakly deleterious (−1), moderately deleterious (−5, −10), strongly deleterious (−50, −100), and inviable (−500). (B) Multiple alignment of human ALB, AFM, and AFP. Positively selected sites in the human (cyan) and chimpanzee (orange) lineages are highlighted. Sites selected in whole phylogeny are reported in red. Protein domains are indicated below the alignment: Signal peptide in yellow, domain I in magenta, and domain II in green.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255767&req=5

evu235-F3: Analysis of selective pressure in the human and chimpanzee lineages. (A) Violin plot of selection coefficients (median, white dot; interquartile range, black bar). Selection coefficients (γ) are classified as strongly beneficial (100, 50), moderately beneficial (10, 5), weakly beneficial (1), neutral (0), weakly deleterious (−1), moderately deleterious (−5, −10), strongly deleterious (−50, −100), and inviable (−500). (B) Multiple alignment of human ALB, AFM, and AFP. Positively selected sites in the human (cyan) and chimpanzee (orange) lineages are highlighted. Sites selected in whole phylogeny are reported in red. Protein domains are indicated below the alignment: Signal peptide in yellow, domain I in magenta, and domain II in green.
Mentions: In both humans and chimpanzees, we observed a general preponderance of codons evolving under negative selection (γ < 0) in all genes. The most striking difference was observed for GC, which showed stronger purifying selection compared with the other three genes in humans but not in chimpanzees (fig. 3A).Fig. 3.—

Bottom Line: Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations.A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration.Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics, Scientific Institute IRCCS E.MEDEA, Bosisio Parini, Italy manuela.sironi@bp.lnf.it.

Show MeSH