Indigenous species barcode database improves the identification of zooplankton

<div><p>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 <i>cytochrome c oxidase I</i> (<i>COI</i>) 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 <i>Branchionus leydign</i> (Rotifer, 14.3%), <i>Trichocerca elongate</i> (Rotifer, 11.5%), <i>Lecane bulla</i> (Rotifer, 15.9%), <i>Synchaeta oblonga</i> (Rotifer, 5.95%) and <i>Schmackeria forbesi</i> (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.</p>