| 论文题目: | SPIKEPIPE: A Metagenomic Pipeline for the Accurate Quantification of Eukaryotic Species Occurrences and Intraspecific Abundance Change Using DNA Barcodes or Mitogenomes |
| 作者: | Ji Y, Huotari T, Roslin T, Schmidt NM, Wang J, Yu DW, Ovaskainen O |
| 联系作者: | dougwyu@mac.com |
| 发表年度: | 2019 |
| DOI: | doi: 10.1111/1755-0998.13057 |
| 摘要: | 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: (1) a percent-coverage threshold to filter out false positives, (2) an internal-standard DNA spike-in to correct for stochasticity during sequencing, and (3) technical replicates to correct for stochasticity across sequencing runs. The SPIKEPIPEpipeline achieves a strikingly high accuracy of intraspecific abundance estimates (in terms of DNA mass) from samples of known composition (mapping to barcodes R2 =0.93, mitogenomes R2 =0.95) and a high repeatability across environmental-sample replicates (barcodes R2=0.94, mitogenomes R2 =0.93). 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 |
| 刊物名称: | Molecular Ecology Resources |
| 论文出处: | https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13057 |
| 影响因子: | 7.046(2018年) |
