Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies

Alexis L Sperling; Daniel K Fabian; Erik Garrison; David M Glover

doi:10.1016/j.xpro.2024.102974

Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies

STAR Protoc. 2024 Apr 5;5(2):102974. doi: 10.1016/j.xpro.2024.102974. Online ahead of print.

Authors

Alexis L Sperling¹, Daniel K Fabian², Erik Garrison³, David M Glover⁴

Affiliations

¹ University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK. Electronic address: alb84@cam.ac.uk.
² University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK.
³ University of Tennessee Health Science Center, Memphis, TN 38163, USA.
⁴ University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: dmglover@caltech.edu.

Abstract

De novo genome assemblies are common tools for examining novel biological phenomena in non-model organisms. Here, we present a protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies. We describe steps for high-molecular-weight DNA preparation with phenol or Genomic-tips, quality control, long-read nanopore sequencing, short-read DNA library preparation, and sequencing. We then detail procedures of genome assembly, annotation, and assessment that can be used for downstream comparison and functional analysis. For complete details on the use and execution of this protocol, please refer to Sperling et al.¹.

Keywords: Bioinformatics; Genetics; Genomics.