PT  - JOURNAL ARTICLE
AU  - Chakraborty, Mahul
AU  - Zhao, Roy
AU  - Zhang, Xinwen
AU  - Kalsow, Shannon
AU  - Emerson, J.J.
TI  - Extensive hidden genetic variation shapes the structure of functional elements in <em>Drosophila</em>
AID  - 10.1101/114967
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 114967
4099  - http://biorxiv.org/content/early/2017/03/08/114967.short
4100  - http://biorxiv.org/content/early/2017/03/08/114967.full
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.