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Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers After HotSHOT DNA Extraction.

Vivian Feng1,2, Caroline Høegh-Guldberg3,4, Rudolf Meier1,2

  • 1Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.

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|February 14, 2026
PubMed
Summary
This summary is machine-generated.

The HotSHOT DNA extraction method preserves high-quality genomic DNA (gDNA) in insect specimens for genomics. Proper pre-extraction storage is crucial for maintaining DNA integrity, especially under field conditions.

Keywords:
HotSHOTbarcodinggenomic DNA qualitygenomicsmalaise trap

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Area of Science:

  • Molecular Biology
  • Genomics
  • Entomology

Background:

  • The HotSHOT alkaline buffer system is a rapid, cost-effective DNA extraction method for specimen barcoding.
  • Uncertainty exists regarding the suitability of DNA extracted using HotSHOT from small insect vouchers for downstream genomic applications.

Purpose of the Study:

  • To evaluate the quality and quantity of genomic DNA (gDNA) in insect specimens before and after HotSHOT treatment.
  • To assess the impact of pre-extraction storage conditions (flash-frozen vs. ethanol at tropical temperatures) on gDNA integrity.

Main Methods:

  • HotSHOT DNA extraction was performed on 11 insect families from six orders.
  • Specimens were subjected to different storage conditions prior to extraction to simulate field conditions.
  • gDNA quality and quantity were assessed using genomic sequencing techniques.

Main Results:

  • Sufficient high-quality gDNA for genomic sequencing was retained after HotSHOT treatment.
  • Field storage, particularly in ethanol under tropical conditions, led to significant DNA degradation.
  • Extended HotSHOT treatment at high temperatures resulted in shorter DNA fragment lengths, influenced by specimen sclerotization.

Conclusions:

  • Optimized HotSHOT protocols and controlled pre-extraction storage can preserve voucher gDNA suitable for short-read and potentially long-read sequencing.
  • Guidelines for protocol selection are provided to enhance gDNA preservation in HotSHOT-treated samples.
  • This is vital for genomic studies of rare or limited-specimen species identified through barcoding.