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...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5627919?pdf=render |
| _version_ | 1828859720015806464 |
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| author | Jianghua Yang Xiaowei Zhang Wanwan Zhang Jingying Sun Yuwei Xie Yimin Zhang G Allen Burton Hongxia Yu |
| author_facet | Jianghua Yang Xiaowei Zhang Wanwan Zhang Jingying Sun Yuwei Xie Yimin Zhang G Allen Burton Hongxia Yu |
| author_sort | Jianghua Yang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T02:24:09Z |
| format | Article |
| id | doaj.art-59570d77805447e0b283f6d965f20c98 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T02:24:09Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-59570d77805447e0b283f6d965f20c982022-12-22T00:02:41ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-011210e018569710.1371/journal.pone.0185697Indigenous species barcode database improves the identification of zooplankton.Jianghua YangXiaowei ZhangWanwan ZhangJingying SunYuwei XieYimin ZhangG Allen BurtonHongxia YuIncompleteness 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.http://europepmc.org/articles/PMC5627919?pdf=render |
| spellingShingle | Jianghua Yang Xiaowei Zhang Wanwan Zhang Jingying Sun Yuwei Xie Yimin Zhang G Allen Burton Hongxia Yu Indigenous species barcode database improves the identification of zooplankton. PLoS ONE |
| title | Indigenous species barcode database improves the identification of zooplankton. |
| title_full | Indigenous species barcode database improves the identification of zooplankton. |
| title_fullStr | Indigenous species barcode database improves the identification of zooplankton. |
| title_full_unstemmed | Indigenous species barcode database improves the identification of zooplankton. |
| title_short | Indigenous species barcode database improves the identification of zooplankton. |
| title_sort | indigenous species barcode database improves the identification of zooplankton |
| url | http://europepmc.org/articles/PMC5627919?pdf=render |
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