Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Gigascience. 2022 Aug 10;11:giac068. doi: 10.1093/gigascience/giac068.

Abstract

Background: 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.

Results: We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield.

Conclusion: 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, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.

Keywords: HMW DNA extraction; genome assembly; long-read sequencing; tissue preservation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Benchmarking*
  • DNA / genetics
  • Dimethyl Sulfoxide*
  • Edetic Acid
  • High-Throughput Nucleotide Sequencing / methods
  • Molecular Weight
  • Sequence Analysis, DNA / methods

Substances

  • DNA
  • Edetic Acid
  • Dimethyl Sulfoxide