title: Using pseudogene database to identify lineage-specific genes and pseudogenes in humans and chimpanzees.
abstract: It has been revealed that gene content changes, or gene gains or losses, have played an important role in the evolution of modern humans. As one of the major players accounting for gene content changes, gene pseudogenization is abundant in mammalian genomes, and approximately 20000 pseudogenes have been identified in ape genomes. Therefore, it is an interesting question how to exploit rich information embedded in pseudogenes. Here, I present a bioinformatic pipeline that utilizes a pseudogene database to identify both lineage-specific genes and pseudogenes in humans and chimpanzees. I found 6 human-specific gene gains (HSGs), 1 chimpanzee-specific gene gain, and 4 chimpanzee-specific pseudogenes, most not discovered in previous studies. Further analysis showed that HSGs have been evolving under strong purifying selection and are broadly expressed, indicating strong functional constraint. This study demonstrates the usage of pseudogene information in comparative genomics and suggests that new genes during primate evolution may acquire essential functions in a short time. The pipeline developed here could also be applied to other species.
authors.affiliation: the Department of Human Evolutionary Biology, Graduate School of Art and Science, Harvard University, 11 Divinity Avenue, Cambridge, MA 02138.
authors.forename: Qu
authors.initials: Q
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D006801:Humans; D002679:Pan troglodytes / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*
keywords: adaptive evolution; comparative genomics; lineage-specific gene; lineage-specific pseudogene; primates; purifying selection