The Recent De Novo Origin of Protein C-Termini.
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.
Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.Show MeSH
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Mentions: Nonsingleton SCP gene sequences were then realigned with their monomorphic sister reference sequences and reanalyzed for SCP. Genes were excluded if the stop codon position in the monomorphic sister species was not shared with any of the focal species alleles, reducing the number of genes to 817. The remaining genes were then classified as additions, subtractions, or ambiguous events (fig. 1). Alignments of genes that were classified as additions were manually checked for quality and poorly aligned sequences were removed. The remaining sequences were then realigned and edges were cleaned using the extend and prune algorithm described above.Fig. 1.—
Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.