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Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.

Brbić M, Warnecke T, Kriško A, Supek F - Genome Biol Evol (2015)

Bottom Line: Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions.Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome.Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome.

View Article: PubMed Central - PubMed

Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.

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Distributions of selected dinucleotide frequencies at 1st, 2nd, and 3rd codon positions of protein-coding genes. (A–D) Ellipses show nine-number summaries of distributions, with borders indicating (in the increasing intensity of coloration) the minimum–maximum, 1st–7th octile, 2nd–6th octile, and 3rd–5th octile. Dinucleotide frequencies are normalized to the expected frequency given the G + C content. Plotted separately for thermophiles (A), halophiles (B), aerotolerant organisms (C), and psychrophiles (D). Letters in center of ellipse denote the environmental preference (t, thermophile; h, halophile; a, aerotolerant; p, psychrophile), and the number indicates the 1st, 2nd, or 3rd codon position this repeats.
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evv088-F7: Distributions of selected dinucleotide frequencies at 1st, 2nd, and 3rd codon positions of protein-coding genes. (A–D) Ellipses show nine-number summaries of distributions, with borders indicating (in the increasing intensity of coloration) the minimum–maximum, 1st–7th octile, 2nd–6th octile, and 3rd–5th octile. Dinucleotide frequencies are normalized to the expected frequency given the G + C content. Plotted separately for thermophiles (A), halophiles (B), aerotolerant organisms (C), and psychrophiles (D). Letters in center of ellipse denote the environmental preference (t, thermophile; h, halophile; a, aerotolerant; p, psychrophile), and the number indicates the 1st, 2nd, or 3rd codon position this repeats.

Mentions: Next, we visualize the distributions of selected dinucleotide frequencies of thermophilic and mesophilic protein-coding genes in all three codon positions (fig. 7). Here, the codon positions and can be compared qualitatively, in terms of direction and magnitude of change. Indeed, differences between the codon positions can be observed, where, for instance, the second codon position shifts toward higher GpA/TpC values in thermophiles, whereas this trend is reversed in the third codon position. These differences are not evident in randomized data (supplementary fig. S7, Supplementary Material online). Similar visualizations reveal significant differences between codon positions in dinucleotide frequency shifts between halophiles and non-halophiles (fig. 7B), strict anaerobes and aerotolerant organisms (fig. 7C), psychrophiles and non-psychrophiles (fig. 7D), and other niches (not shown).Fig. 7.—


Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.

Brbić M, Warnecke T, Kriško A, Supek F - Genome Biol Evol (2015)

Distributions of selected dinucleotide frequencies at 1st, 2nd, and 3rd codon positions of protein-coding genes. (A–D) Ellipses show nine-number summaries of distributions, with borders indicating (in the increasing intensity of coloration) the minimum–maximum, 1st–7th octile, 2nd–6th octile, and 3rd–5th octile. Dinucleotide frequencies are normalized to the expected frequency given the G + C content. Plotted separately for thermophiles (A), halophiles (B), aerotolerant organisms (C), and psychrophiles (D). Letters in center of ellipse denote the environmental preference (t, thermophile; h, halophile; a, aerotolerant; p, psychrophile), and the number indicates the 1st, 2nd, or 3rd codon position this repeats.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494046&req=5

evv088-F7: Distributions of selected dinucleotide frequencies at 1st, 2nd, and 3rd codon positions of protein-coding genes. (A–D) Ellipses show nine-number summaries of distributions, with borders indicating (in the increasing intensity of coloration) the minimum–maximum, 1st–7th octile, 2nd–6th octile, and 3rd–5th octile. Dinucleotide frequencies are normalized to the expected frequency given the G + C content. Plotted separately for thermophiles (A), halophiles (B), aerotolerant organisms (C), and psychrophiles (D). Letters in center of ellipse denote the environmental preference (t, thermophile; h, halophile; a, aerotolerant; p, psychrophile), and the number indicates the 1st, 2nd, or 3rd codon position this repeats.
Mentions: Next, we visualize the distributions of selected dinucleotide frequencies of thermophilic and mesophilic protein-coding genes in all three codon positions (fig. 7). Here, the codon positions and can be compared qualitatively, in terms of direction and magnitude of change. Indeed, differences between the codon positions can be observed, where, for instance, the second codon position shifts toward higher GpA/TpC values in thermophiles, whereas this trend is reversed in the third codon position. These differences are not evident in randomized data (supplementary fig. S7, Supplementary Material online). Similar visualizations reveal significant differences between codon positions in dinucleotide frequency shifts between halophiles and non-halophiles (fig. 7B), strict anaerobes and aerotolerant organisms (fig. 7C), psychrophiles and non-psychrophiles (fig. 7D), and other niches (not shown).Fig. 7.—

Bottom Line: Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions.Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome.Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome.

View Article: PubMed Central - PubMed

Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.

Show MeSH