RT Journal Article
SR Electronic
T1 Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.07.13.451380
DO 10.1101/2021.07.13.451380
A1 Hollis A. Dahn
A1 Jacquelyn Mountcastle
A1 Jennifer Balacco
A1 Sylke Winkler
A1 Iliana Bista
A1 Anthony D. Schmitt
A1 Olga Vinnere Pettersson
A1 Giulio Formenti
A1 Karen Oliver
A1 Michelle Smith
A1 Wenhua Tan
A1 Anne Kraus
A1 Stephen Mac
A1 Lisa M. Komoroske
A1 Tanya Lama
A1 Andrew J. Crawford
A1 Robert W. Murphy
A1 Samara Brown
A1 Alan F. Scott
A1 Phillip A. Morin
A1 Erich D. Jarvis
A1 Olivier Fedrigo
YR 2021
UL http://biorxiv.org/content/early/2021/07/20/2021.07.13.451380.abstract
AB Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.Competing Interest StatementThe authors have declared no competing interest.