Why genome skimming?

Genome skimming is the process of conducting shallow shotgun sequencing across all DNA in a sample. It generally involves cutting the DNA into smaller fragments, then sequencing millions of these pieces and putting them together like a puzzle using bioinformatic assembly tools. Imagine cutting the same quilt (the genome) up many, many times (because 100s-1000s of copies of the genome are present in any tissue sample), and then putting those pieces back together. 

In contrast, Sanger dideoxy sequencing relies on identifying a particular gene or region of the genome (a “barcode”), making copies of this region using special primers and polymerase chain reaction (PCR), and then sequencing only this region. Commonly sequenced barcode gene regions include cytochrome oxidase I (COI), or ribosomal subunit genes (16S, 18S, etc). Genome skimming provides a multitude of benefits beyond traditional barcode sequencing: 

• Greater taxonomic resolution: Barcode regions useful for identifying many species do not evolve quickly enough in other groups to be useful. For example, COI barcodes cannot distinguish ecologically significant species in benthic or deep-sea habitat resources (e.g., corals, sponges). Genome skimming provides multiple barcode markers, giving much stronger resolution for species identification and evolutionary studies.

• Genome skimming works when Sanger sequencing does not: Standard Sanger barcoding workflows will not work if primers don’t match the DNA, or if the sample has a mixture of DNA from multiple organisms (e.g. symbionts, gut contents, epibionts - think corals, filter feeders, small individuals) that is hard to separate and may co-amplify, creating indecipherable data. Genome skimming can provide the individual key markers, PLUS the off-target ones, providing more information about species-species interactions and microbiomes.

• Unlocking Collections: DNA from older and degraded samples (often from museum and deep-sea specimens) is often fragmented in smaller pieces, making Sanger processes impractical. Genome skimming succeeds because it involves stitching together many shorter pieces of DNA. This unlocks collections, linking previously inaccessible samples such as type specimens to modern biodiversity and conservation studies.

• Better archival material: Tissue sampling and DNA extraction for genome skimming workflows results in greater quantities of DNA, and therefore leaves a more permanent record for future use and reuse of physical samples. 

• More data per specimen: Genome skimming recovers DNA from all parts of an organisms’ genome and can generate full mitochondrial genomes and nuclear repeat markers, providing many potential taxonomically informative gene regions from a single sample instead of just one (e.g. COI). This information can be used to design species or group specific molecular assays, and allows evaluation of false positive and false negative potential. 

• Cost-effective and efficient: Because genome skimming creates orders of magnitude greater sequence data (millions of base pairs vs. hundreds), the cost per specimen is lower than doing multiple traditional barcodes one-by-one, especially when accounting for failed barcode sequencing.

• Future-ready data: Data can be reanalyzed to answer new questions, facilitate discovery (e.g. natural products) and support emerging biodiversity tools, making it a long-term investment rather than a one-time test.

• Broad scientific value: The multiple types of data produced by genome skimming can support a wide range of research — from systematics and biodiversity surveys to eDNA reference databases to population connectivity and microbiome studies.