Data from: Benchmarking DNA metabarcoding for biodiversity-based monitoring and assessment
| Main Authors: | Aylagas, Eva, Borja, Angel, Irigoien, Xabier, Rodriguez-Ezpeleta, Naiara |
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| Format: | info dataset Journal |
| Terbitan: |
, 2017
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4941830 |
Daftar Isi:
- Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing represents an alternative to rapidly, accurately and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.
- Taxonomic assignments using mlCOI barcodeThe file contains the taxonomic assignments for reads obtained using mlCOI barcode across all stations for each sample source, DNA type (Extracellular, Bulk or Pooled DNA) and PCR annealing temperature (46 °C, 50 °C or, TD). Ecological Group (EG) for each taxa according AMBI is detailed and number of reads transformed into relative proportions shown. Presence/absence of taxa found using traditional identification at each station is represented by x.Taxonomic_assignments_mlCOI.docTaxonomic assignments using folCOI barcodeThe file contains the taxonomic assignments for reads obtained using folCOI barcode across all stations for each sample source, DNA type (Extracellular, Bulk or Pooled DNA) and PCR annealing temperature (46 °C, 50 °C or, TD). Ecological Group (EG) for each taxa according AMBI is detailed and number of reads transformed into relative proportions shown. Presence/absence of taxa found using traditional identification at each station is represented by x.Taxonomic_assignments_folCOI.docUnique Sequences mlCOI barcodeFollowing Illumina MiSeq sequencing of the mlCOI barcode of 114 samples, 130,670 unique metazoan sequences were identified. The zip file contains a fasta file with all the unique sequences and a table showing the distribution of sequencing reads for all unique sequences across the 114 samples for each DNA type (extracellular (ext), Bulk or Pooled DNA) and PCR annealing temperature (46 °C, 50 °C or, TD).UniqueSequences_mlCOI.zipUnique Sequences folCOI barcodeFollowing Illumina MiSeq sequencing of the folCOI barcode of 110 samples, 652,356 unique metazoan sequences were identified. The zip file contains a fasta file with all the unique sequences and a table showing the distribution of sequencing reads for all unique sequences across the 110 samples for each DNA type (extracellular (ext), Bulk or Pooled DNA) and PCR annealing temperature (46, 50 or TD).UniqueSequences_folCOI.zip