Abstract
BackgroundEvolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. By contrast, 45% of the human genome is composed of retroposed elements, many of which were inserted in the primate lineage. A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes.ResultsTo identify and analyze the relatively recently evolved retrogenes, we carried out BLASTZ alignments of all human mRNAs against the human genome and scored a set of features indicative of retroposition. Of over 12,000 putative retrocopy-derived genes that arose mainly in the primate lineage, 726 with strong evidence of transcript expression were examined in detail. These mRNA retroposition events fall into three categories: I) 34 retrocopies and antisense retrocopies that added potential protein coding space and UTRs to existing genes; II) 682 complete retrocopy duplications inserted into new loci; and III) an unexpected set of 13 retrocopies that contributed out-of-frame, or antisense sequences in combination with other types of transposed elements (SINEs, LINEs, LTRs), even unannotated sequence to form potentially novel genes with no homologs outside primates. In addition to their presence in human, several of the gene candidates also had potentially viable ORFs in chimpanzee, orangutan, and rhesus macaque, underscoring their potential of function.ConclusionmRNA-derived retrocopies provide raw material for the evolution of genes in a wide variety of ways, duplicating and amending the protein coding region of existing genes as well as generating the potential for new protein coding space, or non-protein coding RNAs, by unexpected contributions out of frame, in reverse orientation, or from previously non-protein coding sequence.
Highlights
Evolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals
Point mutations in combination with selection can explain changes in transcriptomes and proteomes, the high number of retroposition events along the primate lineage must be considered to understand the phenotypic difference between primates and other mammals
In order to determine if the retrocopies are expressed, we looked for overlap with mRNA or EST evidence
Summary
Evolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. While it is said that the human and chimpanzee genomes share anywhere from 95 to 98.5% similarity in their DNA sequences, base exchanges and small indels alone are unlikely to completely explain the differences among diverging primates and between other mammals. Discernible retrocopies contribute only about 1% of the human genome, yet they have a much more varied protein coding space than other more numerous types of retroposed elements, including the long interspersed elements (LINEs, 21%) and short interspersed elements (SINEs, 13%). The latter lack protein coding regions altogether. Part of Alu and MIR SINEs contributed to newly evolved exons [8,9,10,11,12]
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