Indigenous species barcode database improves the identification of zooplankton

Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here m...

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Bibliographic Details
Published in:PloS one 2017-10, Vol.12 (10), p.e0185697
Main Authors: Yang, Jianghua, Zhang, Xiaowei, Zhang, Wanwan, Sun, Jingying, Xie, Yuwei, Zhang, Yimin, Burton, Jr, G Allen, Yu, Hongxia
Format: Article
Language:English
Subjects:
Animals
Bar codes
Biodiversity
Biology
Biology and Life Sciences
Brachionus calyciflorus
Brachionus plicatilis
Computer and Information Sciences
Copepoda
Cytochrome
Cytochrome-c oxidase
Databases, Genetic
Deoxyribonucleic acid
Divergence
DNA
DNA barcoding
DNA Barcoding, Taxonomic
Earth Sciences
Ecology
Ecology and Environmental Sciences
Ecosystem biology
Ecosystems
Elongation
Environmental monitoring
Evolution
Gene sequencing
Identification
Indigenous species
Laboratories
Mitochondria
Morphology
Next-generation sequencing
Organisms
Oxidase
Phylogenetics
Polymerase Chain Reaction
Research and Analysis Methods
Rotifera
Taxonomy
Wolbachia
Zooplankton
Zooplankton - genetics
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Summary:Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies) were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%), Trichocerca elongate (Rotifer, 11.5%), Lecane bulla (Rotifer, 15.9%), Synchaeta oblonga (Rotifer, 5.95%) and Schmackeria forbesi (Copepod, 6.5%). Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81%) with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0185697