The role of taxonomic expertise in interpretation of metabarcoding studies

dc.contributor.authorPappalardo, Paula
dc.contributor.authorCollins, Allen G.
dc.contributor.authorPagenkopp Lohan, Katrina M.
dc.contributor.authorHanson, Kate M.
dc.contributor.authorTruskey, Sarit B.
dc.contributor.authorJaeckle, William
dc.contributor.authorAmes, Cheryl Lewis
dc.contributor.authorGoodheart, Jessica A.
dc.contributor.authorBush, Stephanie L.
dc.contributor.authorBiancani, Leann M.
dc.contributor.authorStrong, Ellen E.
dc.contributor.authorVecchione, Michael
dc.contributor.authorHarasewych, M. G.
dc.contributor.authorReed, Karen
dc.contributor.authorLin, Chan
dc.contributor.authorHartil, Elise C.
dc.contributor.authorWhelpley, Jessica
dc.contributor.authorBlumberg, Jamie
dc.contributor.authorMatterson, Kenan
dc.contributor.authorRedmond, Niamh E.
dc.contributor.authorBecker, Allison
dc.contributor.authorBoyle, Michael J.
dc.contributor.authorOsborn, Karen J.
dc.date.accessioned2021-05-25T02:04:16Z
dc.date.available2021-05-25T02:04:16Z
dc.date.issued2021
dc.description.abstractAbstract The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1–2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between a genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys.
dc.format.extent3397–3410
dc.identifier1054-3139
dc.identifier.citationPappalardo, Paula, Collins, Allen G., Pagenkopp Lohan, Katrina M., Hanson, Kate M., Truskey, Sarit B., Jaeckle, William, Ames, Cheryl Lewis, Goodheart, Jessica A., Bush, Stephanie L., Biancani, Leann M., Strong, Ellen E., Vecchione, Michael, Harasewych, M. G., Reed, Karen, Lin, Chan, Hartil, Elise C., Whelpley, Jessica, Blumberg, Jamie, Matterson, Kenan, Redmond, Niamh E., Becker, Allison, Boyle, Michael J., and Osborn, Karen J. 2021. "<a href="https://repository.si.edu/handle/10088/110372">The role of taxonomic expertise in interpretation of metabarcoding studies</a>." <em>ICES Journal of Marine Science</em>, 78, (9) 3397–3410. <a href="https://doi.org/10.1093/icesjms/fsab082">https://doi.org/10.1093/icesjms/fsab082</a>.
dc.identifier.issn1054-3139
dc.identifier.urihttps://hdl.handle.net/10088/110372
dc.publisherOxford University Press
dc.relation.ispartofICES Journal of Marine Science 78 (9)
dc.titleThe role of taxonomic expertise in interpretation of metabarcoding studies
dc.typearticle
sro.description.unitNMNH
sro.description.unitNH-Invertebrate Zoology
sro.description.unitSERC
sro.description.unitNH-SMS
sro.description.unitNH-Other
sro.identifier.doi10.1093/icesjms/fsab082
sro.identifier.itemID159477
sro.identifier.refworksID67815
sro.identifier.urlhttps://repository.si.edu/handle/10088/110372
sro.publicationPlaceOxford, England

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Allen Collins - Pappalardo-etal_2021_Metabarcoding Gulf Stream Plankton.pdf
Size:
1.94 MB
Format:
Adobe Portable Document Format
Description: