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Updated: May 23, 2025

Metagenomic Analysis of Silage
Published on: January 13, 2017
Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies
Yiqiu Lu1, Yuran Dong1, Min Zhang1
1Co-Innovation Center for Sustainable Forestry in Southern China, Laboratory of Biodiversity and Conservation, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China.
Abstract:
Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.
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