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SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.

Yinqiu JiTea HuotariTomas V RoslinNiels Martin SchmidtJiaxin WangDouglas W YuOtso Ovaskainen
Published in: Molecular ecology resources (2019)
The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (a) a percent-coverage threshold to filter out false positives, (b) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (c) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPE pipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2  = .93, mitogenomes R2  = .95) and a high repeatability across environmental-sample replicates (barcodes R2  = .94, mitogenomes R2  = .93). As proof of concept, we sequence arthropod samples from the High Arctic, systematically collected over 17 years, detecting changes in species richness, species-specific abundances, and phenology. SPIKEPIPE provides cost-efficient and reliable quantification of eukaryotic communities.
Keyphrases
  • circulating tumor
  • cell free
  • single molecule
  • high resolution
  • single cell
  • antibiotic resistance genes
  • nucleic acid
  • healthcare
  • climate change
  • human health
  • risk assessment
  • amino acid