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The Recent De Novo Origin of Protein C-Termini.

Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MH, Masel J - Genome Biol Evol (2015)

Bottom Line: Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes.We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic.Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.

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Related in: MedlinePlus

Distribution of addition allele across strains in S. paradoxus (A) and S. cerevisiae (B). Unrooted phylogenetic trees were taken from Liti et al. (2009). As is well-known, S. paradoxus shows more population structure (appearing here as dark blue monophyletic blocks or pale blue “coherent” near-monophyletic blocks) than S. cerevisiae. The strong phylogenetic pattern further demonstrates that these additions are not mere sequencing errors. A number of additions have risen to high frequency.
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evv098-F2: Distribution of addition allele across strains in S. paradoxus (A) and S. cerevisiae (B). Unrooted phylogenetic trees were taken from Liti et al. (2009). As is well-known, S. paradoxus shows more population structure (appearing here as dark blue monophyletic blocks or pale blue “coherent” near-monophyletic blocks) than S. cerevisiae. The strong phylogenetic pattern further demonstrates that these additions are not mere sequencing errors. A number of additions have risen to high frequency.

Mentions: The distributions of additions across strains of S. cerevisiae and S. paradoxus are shown in figure 2. A significant number of addition alleles have risen to high frequency. Forty-eight percent (12 out of 25) addition alleles sit neatly on monophyletic clades within the tree of strains in S. paradoxus (Fig. 2A), whereas only 34% (11 out of 32) are found to be monophyletic in S. cerevisiae (fig. 2B). Those additions that are not monophyletic are widely dispersed across our sampled populations, especially in S. cerevisiae (fig. 2B). This is consistent with previous observations of greater population structure in S. paradoxus (Liti et al. 2009).Fig. 2.—


The Recent De Novo Origin of Protein C-Termini.

Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MH, Masel J - Genome Biol Evol (2015)

Distribution of addition allele across strains in S. paradoxus (A) and S. cerevisiae (B). Unrooted phylogenetic trees were taken from Liti et al. (2009). As is well-known, S. paradoxus shows more population structure (appearing here as dark blue monophyletic blocks or pale blue “coherent” near-monophyletic blocks) than S. cerevisiae. The strong phylogenetic pattern further demonstrates that these additions are not mere sequencing errors. A number of additions have risen to high frequency.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494051&req=5

evv098-F2: Distribution of addition allele across strains in S. paradoxus (A) and S. cerevisiae (B). Unrooted phylogenetic trees were taken from Liti et al. (2009). As is well-known, S. paradoxus shows more population structure (appearing here as dark blue monophyletic blocks or pale blue “coherent” near-monophyletic blocks) than S. cerevisiae. The strong phylogenetic pattern further demonstrates that these additions are not mere sequencing errors. A number of additions have risen to high frequency.
Mentions: The distributions of additions across strains of S. cerevisiae and S. paradoxus are shown in figure 2. A significant number of addition alleles have risen to high frequency. Forty-eight percent (12 out of 25) addition alleles sit neatly on monophyletic clades within the tree of strains in S. paradoxus (Fig. 2A), whereas only 34% (11 out of 32) are found to be monophyletic in S. cerevisiae (fig. 2B). Those additions that are not monophyletic are widely dispersed across our sampled populations, especially in S. cerevisiae (fig. 2B). This is consistent with previous observations of greater population structure in S. paradoxus (Liti et al. 2009).Fig. 2.—

Bottom Line: Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes.We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic.Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.

Show MeSH
Related in: MedlinePlus