title: Open questions in the study of de novo genes: what, how and why.
abstract: The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes.
authors.affiliation: The Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
authors.forename: Aoife
authors.initials: A
authors.lastname: McLysaght
authors.affiliation: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, Somerset BA2 7AY, UK.
authors.forename: Laurence D
authors.initials: LD
authors.lastname: Hurst
mesh_terms: D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D011506:Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D011506:Proteins