title: Population diversity of ORFan genes in Escherichia coli.
abstract: The origin and evolution of "ORFans" (suspected genes without known relatives) remain unclear. Here, we take advantage of a unique opportunity to examine the population diversity of thousands of ORFans, based on a collection of 35 complete genomes of isolates of Escherichia coli and Shigella (which is included phylogenetically within E. coli). As expected from previous studies, ORFans are shorter and AT-richer in sequence than non-ORFans. We find that ORFans often are very narrowly distributed: the most common pattern is for an ORFan to be found in only one genome. We compared within-species population diversity of ORFan genes with those of two control groups of non-ORFan genes. Patterns of population variation suggest that most ORFans are not artifacts, but encode real genes whose protein-coding capacity is conserved, reflecting selection against nonsynonymous mutations. Nevertheless, nonsynonymous nucleotide diversity is higher than for non-ORFans, whereas synonymous diversity is roughly the same. In particular, there is a several-fold excess of ORFans in the highest decile of diversity relative to controls, which might be due to weaker purifying selection, positive selection, or a subclass of ORFans that are decaying.
authors.affiliation: Institute for Bioscience and Biotechnology Research, University of Maryland, USA. yuguoqin2011@gmail.com
authors.forename: Guoqin
authors.initials: G
authors.lastname: Yu
authors.forename: Arlin
authors.initials: A
authors.lastname: Stoltzfus
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D049810:Genetic Speciation; D014644:Genetic Variation / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D011544:Pseudogenes / Q000235:genetics; D012760:Shigella / Q000235:genetics