Sanger Tree of Life HMW DNA Extraction: Automated MagAttract for Small Arthropods v1

This protocol describes the automated extraction and SPRI of HMW DNA from small arthropod samples intended for long-read sequencing using the Qiagen MagAttract HMW DNA extraction kit and the Thermo Fisher KingFisher™ Apex. This protocol is primarily effective for the class Arachnida and order Isopoda within Arthropoda covered by the Tree of Life Programme. This protocol has resulted in successful extractions for a number of species including Linyphia triangularis, Anilocra frontalis, Lekanesphaera levii, Cymodoce truncata, Porcellio scaber, Idotea baltica and Ligia oceanica, as well as a reference genome generation for Troglohyphantes excavatus. The output of this protocol is HMW DNA, which depending upon yield and genome size of the species, can be directed towards either HMW DNA Pooling, HMW DNA Fragmentation: Diagenode Megaruptor®3 for LI PacBio or HMW DNA Fragmentation: g-Tube for ULI PacBio. This protocol was primarily adapted from the 'HMW DNA Extraction of Jumping Spiders v.4' protocol; this was developed through R&D by the Meier/Jiggin group for jumping spider tissue, which uses elements of the Qiagen MagAttract protocol and the Lawniczak Lab extraction v.6 for small insects. This protocol also incorporates the pre-shear SPRI element of the 'Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2' protocol. Acronyms HMW: high molecular weight SPRI: solid-phase reversible immobilisation LI: low input ULI: ultra-low input