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Peer-reviewedCC BYBMC genomics

Incidence and attributes of chimeric COI and 18S rDNA sequences derived from nematode-infected arthropods.

  • Jacopo D'Ercole1,2
  • Robin Floyd3
  • Sean Wj Prosser3
  • Saeideh Jafarpour3
  • Paul Dn Hebert3,4
4 affiliations
  1. 1Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada. [email protected].
  2. 2Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada. [email protected].
  3. 3Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada.
  4. 4Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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Abstract

Background

PCR amplification of mixed-template samples can generate chimeric sequences, molecules that combine partial sequences from two or more source organisms. These artefacts pose a significant challenge for high-throughput sequencing studies, generating both type I errors (true species mistakenly rejected) and type II errors (chimeras incorrectly viewed as valid species). Despite their impact, the incidence, structural properties, and factors driving chimera formation remain poorly understood.Results

Using nanopore sequencing of 531 nematode-infected arthropod specimens, chimera formation was characterized in two widely used gene regions: the 658 bp of cytochrome c oxidase subunit I (COI) barcode and a 900 bp segment of 18S ribosomal DNA (18S rDNA). Chimeras were detected for both gene regions despite the deep sequence divergences between members of these two phyla. However, the incidence of chimeric molecules was higher for 18S rDNA than COI with chimera formation correlating with local variation in DNA stability and conserved sequence tracts between parent species.Conclusions

By clarifying the associations between DNA stability, sequence conservation, and chimera formation, this study offers insights that can inform the development of more robust approaches to chimera detection.

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Cite

BibTeXRIS
BibTeX
@article{dercole2026incidence,
  title = {{Incidence and attributes of chimeric COI and 18S rDNA sequences derived from nematode-infected arthropods.}},
  author = {Jacopo D'Ercole and Robin Floyd and Sean Wj Prosser and Saeideh Jafarpour and Paul Dn Hebert},
  journal = {BMC genomics},
  year = {2026},
  month = aug,
  doi = {10.1186/s12864-026-13235-3},
  url = {https://europepmc.org/article/MED/42968010},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Incidence and attributes of chimeric COI and 18S rDNA sequences derived from nematode-infected arthropods.
AU  - Jacopo D'Ercole
AU  - Robin Floyd
AU  - Sean Wj Prosser
AU  - Saeideh Jafarpour
AU  - Paul Dn Hebert
PY  - 2026
DA  - 2026/08/05
JO  - BMC genomics
DO  - 10.1186/s12864-026-13235-3
UR  - https://europepmc.org/article/MED/42968010
AB  - Background  PCR amplification of mixed-template samples can generate chimeric sequences, molecules that combine partial sequences from two or more source organisms. These artefacts pose a significant challenge for high-throughput sequencing studies, generating both type I errors (true species mistakenly rejected) and type II errors (chimeras incorrectly viewed as valid species). Despite their impact, the incidence, structural properties, and factors driving chimera formation remain poorly understood.Results  Using nanopore sequencing of 531 nematode-infected arthropod specimens, chimera formation was characterized in two widely used gene regions: the 658 bp of cytochrome c oxidase subunit I (COI) barcode and a 900 bp segment of 18S ribosomal DNA (18S rDNA). Chimeras were detected for both gene regions despite the deep sequence divergences between members of these two phyla. However, the incidence of chimeric molecules was higher for 18S rDNA than COI with chimera formation correlating with local variation in DNA stability and conserved sequence tracts between parent species.Conclusions  By clarifying the associations between DNA stability, sequence conservation, and chimera formation, this study offers insights that can inform the development of more robust approaches to chimera detection.
SN  - 1471-2164
ER  -