ArticleMolecular ecology2020
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.
Article in Molecular ecology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 118 citations in OpenAlex.
- Plant species identification by genome skimming across the vascular plant tree of life.The New phytologist · 2026Article
- DipSkmer: Reference-free population genomics with diploid genome skims.bioRxiv : the preprint server for biology · 2026Article
- ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distances.Genome biology · 2026Article
- DNA barcodes analyses provide insights into species delineation and possible cryptic species in Amentotaxus (Taxaceae).BMC plant biology · 2026Article
- Evidence of a putative new species Haemagogus 'Trinidad sp. A' from the Caribbean sharing mitogenome lineages with species endemic to the Amazon.Scientific reports · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Mapping the Genetic Relatedness of Outdoor-BitingInsects · 2025Article
- Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.Molecular ecology resources · 2025Article
- A composite universal DNA signature for the tree of life.Nature ecology & evolution · 2025Article
- Identification of herbal medicine species of Lysimachia L. (Primulaceae) in Southern China using genome skimming.BMC plant biology · 2025Article
- Exploring genetic diversity and genomic insights of Bacillus subtilis isolates from cassava rhizosphere using molecular barcoding and whole genome sequencing.Scientific reports · 2025Article
- Phylogenetic taxonomy of the Zambian Anopheles coustani group using a mitogenomics approach.Malaria journal · 2025Article
- Mitogenomes of mosquito species of Harris County in Texas.Scientific reports · 2025Article
- A curated benchmark dataset for molecular identification based on genome skimming.Scientific data · 2025Article
- Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).Plant diversity · 2025Article
- A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.Molecular ecology resources · 2025Article
- Skmer approach improves species discrimination in taxonomically problematic genusPlant diversity · 2024Article
- Skimming genomes for systematics and DNA barcodes of corals.Ecology and evolution · 2024Article
- Analyses of Nuclear Reads Obtained Using Genome Skimming.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution.Communications biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.
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Registered trials
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