Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor®3 for PacBio HiFi v1
Maja Todorovic, Filipa Sampaio, Caroline Howard
Abstract
This protocol describes the fragmentation of HMW DNA from either the MagAttract v.1, Plant MagAttract v.1, or Plant MagAttract v.2 Sanger Tree of Life HMW DNA extraction protocols, using the Diagenode Megaruptor®3. This process is highly effective for DNA extracts from all of the taxonomic groups covered by the Tree of Life Programme, with DNA sheared into an average fragment size range of 12–20 kb. However, challenging samples include those that are highly concentrated or highly viscous, as well as samples which contain contaminants or impurities following DNA extraction. The output of this protocol is sheared DNA which can be directed towards fragmented DNA clean up, with either the Manual or Automated SPRI protocols. This protocol has since been updated to Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor® 3 for LI PacBio in order to process samples resulting from the Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2, Automated Plant MagAttract v.3 and Automated Plant MagAttract v.4 protocols. Acronyms and abbreviations HMW: high molecular weight SPRI: solid-phase reversible immobilisation HiFi: high fidelity LI: low input