RT Journal Article SR Electronic T1 Extensive hidden genetic variation shapes the structure of functional elements in Drosophila JF bioRxiv FD Cold Spring Harbor Laboratory SP 114967 DO 10.1101/114967 A1 Chakraborty, Mahul A1 Zhao, Roy A1 Zhang, Xinwen A1 Kalsow, Shannon A1 Emerson, J.J. YR 2017 UL http://biorxiv.org/content/early/2017/03/08/114967.abstract AB Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, though the fragmented nature of most contemporary assemblies obscure them. To discover such mutations, we assembled the first reference quality genome of Drosophila melanogaster since its initial sequencing. By comparing this genome to the existing D. melanogaster assembly, we create a structural variant map of unprecedented resolution, revealing extensive genetic variation that has remained hidden until now. Many of these variants constitute strong candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that dramatically amplifies the expression of detoxification genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high quality references are to deciphering phenotypes.