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

	SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
	Ji, YQ; Huotari, T; Roslin, T; Schmidt, NM; Wang, JX; Yu, DW; Ovaskainen, O
	2020
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	20 期号:1 页码:256-267
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: (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 R-2 = .93, mitogenomes R-2 = .95) and a high repeatability across environmental-sample replicates (barcodes R-2 = .94, mitogenomes R-2 = .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.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/12995
专题	科研部门_生态学与环境保护中心（俞维理）
推荐引用方式 GB/T 7714	Ji, YQ,Huotari, T,Roslin, T,et al. SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes[J]. MOLECULAR ECOLOGY RESOURCES,2020,20(1):256-267.
APA	Ji, YQ.,Huotari, T.,Roslin, T.,Schmidt, NM.,Wang, JX.,...&Ovaskainen, O.(2020).SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes.MOLECULAR ECOLOGY RESOURCES,20(1),256-267.
MLA	Ji, YQ,et al."SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes".MOLECULAR ECOLOGY RESOURCES 20.1(2020):256-267.

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2020110416.pdf（766KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文