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

Creators: Sperling, Alexis L.; Fabian, Daniel K.; Garrison, Erik; Glover, David M.¹

1. California Institute of Technology

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

Copyright and License

Acknowledgement

The genomics analysis was supported by NIH/NIDA U01DA047638 and NIH/NIGMS R01GM123489 to E.G. The biological work was supported by the Leverhulme Trust Project Grant RPG-2018-229 and the Wellcome Trust Institutional Strategic Support Fund (RG89305) to D.M.G. and A.L.S.

Contributions

A.L.S. designed this study, performed all biological experiments, and wrote the first draft of the original manuscript and this protocol. D.K.F. performed all genome annotations. E.G. performed all genomics-related analyses. A.L.S., D.K.F., E.G., and D.M.G. contributed to choices in methodology and experimental design. Funding for the genomics analysis was obtained by E.G. The funding for all biological experiments was obtained by A.L.S. and D.M.G.

Data Availability

All code is publicly available. The genome assembly, analysis, and quality control code are on https://github.com/ekg/drosophila. The annotation, transcriptomics analysis, and quality control code are on https://github.com/FabianDK/Dmerc. All raw and analyzed D. mercatorum genomic data is on the European Nucleotide Archive (ENA): PRJEB64421. The transcriptomics data is on ENA: PRJEB43100.

This study did not generate new unique reagents.

Conflict of Interest

The authors declare no competing interests.

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