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Title: soil metagenome : A quantitative protocol for DNA metabarcoding of springtails (Collembola)      
keywords:
Targeted Locus (Loci)
ID:
PRJDB4645
description:
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 90% operational taxonomic units of 32 and 36 collembolans were from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 almost identical morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities after normalization showed good correlation with the number of individuals in the samples (R = 0.91-0.99). Thus, this protocol is suitable for surveying collembolan biodiversity.
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJDB4645
authentication:
none
authorization:
none
dateReleased:
03-29-2016
name:
soil metagenome
ncbiID:
ncbitax:410658
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject

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