Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies
Summary: 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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2024-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724001394 |
| _version_ | 1797220444148858880 |
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| author | Alexis L. Sperling Daniel K. Fabian Erik Garrison David M. Glover |
| author_facet | Alexis L. Sperling Daniel K. Fabian Erik Garrison David M. Glover |
| author_sort | Alexis L. Sperling |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-24T12:49:38Z |
| format | Article |
| id | doaj.art-10a3372f5e72476b9c9f9ee364953e9e |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-24T12:49:38Z |
| publishDate | 2024-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-10a3372f5e72476b9c9f9ee364953e9e2024-04-06T04:40:35ZengElsevierSTAR Protocols2666-16672024-06-0152102974Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assembliesAlexis L. Sperling0Daniel K. Fabian1Erik Garrison2David M. Glover3University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK; Corresponding authorUniversity of Cambridge; Department of Genetics, Cambridge CB2 3EH, UKUniversity of Tennessee Health Science Center, Memphis, TN 38163, USAUniversity of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166724001394BioinformaticsGeneticsGenomics |
| spellingShingle | Alexis L. Sperling Daniel K. Fabian Erik Garrison David M. Glover Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies STAR Protocols Bioinformatics Genetics Genomics |
| title | Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies |
| title_full | Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies |
| title_fullStr | Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies |
| title_full_unstemmed | Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies |
| title_short | Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies |
| title_sort | protocol for preparing drosophila genomic dna to create chromosome level de novo genome assemblies |
| topic | Bioinformatics Genetics Genomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724001394 |
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