Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Giada Ferrari; Lore Esselens; Michelle Hart; Steven Janssens; Catherine Kidner; Maurizio Mascarello; Joshua Peñalba; Flávia Pezzini; Thomas von Rintelen; Gontran Sonet; Carl Vangestel; Massimiliano Virgilio; Peter Hollingsworth

doi:10.3897/BDJ.11.e102317

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Biodiversity Data Journal 11: e102317
https://doi.org/10.3897/BDJ.11.e102317 (27 Oct 2023)

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Introduction
- Natural history collections as a resource for genomic science
- Storage and preservation of museum specimens
- Properties of DNA in natural history collections and implications for sequencing museum specimens
- Outstanding challenges to the routine sequencing of museum specimens
Deciding when it is appropriate to sample museum specimens for DNA sequencing
Minimising the risks of contamination and generation of erroneous sequence data
- Historic DNA versus ancient DNA versus modern optimally-preserved DNA
- Current operational practices for processing hDNA
- Laboratory set-ups and workflows for hDNA sequencing
- Data verification and contamination controls
Maximising the recovery of endogenous DNA sequences
Case study overview
Case study 1: Assessing the potential of rapid shotgun sequencing for the recovery of mtDNA genomes from pinned insect specimens
- Introduction
- Materials and Methods
- Results and Discussion
Case study 2: Genomic vouchering in insect museum collections: the quest for a pragmatic approach to routine, large-scale genotyping
- Introduction
- Materials and Methods
- Results and Discussion
Case study 3: Genome skimming as a tool to recover whole plastid genomes from threatened Central African timber species
- Introduction
- Materials and Methods
- Results and Discussion
Case study 4: Comparing hybridisation capture derived sequences from herbarium specimens with data from living material of the same genetic individuals
- Introduction
- Materials and Methods
- Results and Discussion
Case study 5: Selecting samples with the greatest likelihood of success for reduced-representation sequencing from museum collections
- Introduction
- Materials and Methods
- Results and Discussion
Case study 6: Single-tube DNA library preparation for ancient bones
- Introduction
- Materials and Methods
- Results and Discussion
Concluding remarks
Acknowledgements
References
Supplementary files

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