Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large M...
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Veröffentlicht in: | Molecular ecology resources 2021-10, Vol.21 (7), p.2546-2564 |
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creator | Gold, Zachary Curd, Emily E. Goodwin, Kelly D. Choi, Emma S. Frable, Benjamin W. Thompson, Andrew R. Walker, Harold J. Burton, Ronald S. Kacev, Dovi Martz, Lucas D. Barber, Paul H. |
description | DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus‐specific validation efforts. |
doi_str_mv | 10.1111/1755-0998.13450 |
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However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus‐specific validation efforts.</description><identifier>ISSN: 1755-098X</identifier><identifier>EISSN: 1755-0998</identifier><identifier>DOI: 10.1111/1755-0998.13450</identifier><language>eng</language><publisher>Oxford: Wiley Subscription Services, Inc</publisher><subject>Accuracy ; Best practice ; California Current Large Marine Ecosystem ; Case studies ; Chemical analysis ; Classification ; Deoxyribonucleic acid ; DNA ; Ecological effects ; Ecosystems ; eDNA ; Environmental DNA ; Marine ecosystems ; Marine environment ; Marine fish ; metabarcoding ; MiFish primers ; Parameters ; Performance evaluation ; reference database ; Seawater ; Species ; Taxonomy ; Water analysis</subject><ispartof>Molecular ecology resources, 2021-10, Vol.21 (7), p.2546-2564</ispartof><rights>2021 John Wiley & Sons Ltd</rights><rights>Copyright © 2021 John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3890-d8a804841c54672f41524b7b2e3403d99616bc3ef36fa3d910c1fa8144f00de43</citedby><cites>FETCH-LOGICAL-c3890-d8a804841c54672f41524b7b2e3403d99616bc3ef36fa3d910c1fa8144f00de43</cites><orcidid>0000-0003-4525-0671 ; 0000-0001-7769-5558 ; 0000-0001-7671-7487 ; 0000-0002-6995-5329 ; 0000-0003-0490-7630 ; 0000-0001-9583-8073 ; 0000-0003-0336-6852</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2F1755-0998.13450$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1755-0998.13450$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27922,27923,45572,45573</link.rule.ids></links><search><creatorcontrib>Gold, Zachary</creatorcontrib><creatorcontrib>Curd, Emily E.</creatorcontrib><creatorcontrib>Goodwin, Kelly D.</creatorcontrib><creatorcontrib>Choi, Emma S.</creatorcontrib><creatorcontrib>Frable, Benjamin W.</creatorcontrib><creatorcontrib>Thompson, Andrew R.</creatorcontrib><creatorcontrib>Walker, Harold J.</creatorcontrib><creatorcontrib>Burton, Ronald S.</creatorcontrib><creatorcontrib>Kacev, Dovi</creatorcontrib><creatorcontrib>Martz, Lucas D.</creatorcontrib><creatorcontrib>Barber, Paul H.</creatorcontrib><title>Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem</title><title>Molecular ecology resources</title><description>DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus‐specific validation efforts.</description><subject>Accuracy</subject><subject>Best practice</subject><subject>California Current Large Marine Ecosystem</subject><subject>Case studies</subject><subject>Chemical analysis</subject><subject>Classification</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecological effects</subject><subject>Ecosystems</subject><subject>eDNA</subject><subject>Environmental DNA</subject><subject>Marine ecosystems</subject><subject>Marine environment</subject><subject>Marine fish</subject><subject>metabarcoding</subject><subject>MiFish primers</subject><subject>Parameters</subject><subject>Performance evaluation</subject><subject>reference database</subject><subject>Seawater</subject><subject>Species</subject><subject>Taxonomy</subject><subject>Water analysis</subject><issn>1755-098X</issn><issn>1755-0998</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNqFkD1PwzAQhiMEEqUws1piYUlrJ05is1VVgUoFFpDYjOOci6skLnEC5N_jEMTAwi33oec93b1BcE7wjPiYkyxJQsw5m5GYJvggmPxODn9r9nwcnDi3wzjFPKOT4GVd7Rv7buotqqCVuWyULYaulZ-2tpVRSDpntnUFdXuFFkhJB8i1XdEjq5E27hUcMjWSqJTNFlAlG1MDAmVd71qoToMjLUsHZz95Gjxdrx6Xt-Hm4Wa9XGxCFTOOw4JJhimjRCU0zSJNSRLRPMsjiCmOC85TkuYqBh2nWvqeYEW0ZIRSjXEBNJ4Gl-Ne_85bB64VlXEKylLWYDsnooTylEcRwx69-IPubNfU_jpPZThK44RxT81HSjXWuQa02DfGf9cLgsXguBg8FYO_4ttxr0hGxYcpof8PF3er-1H3BSiegfY</recordid><startdate>202110</startdate><enddate>202110</enddate><creator>Gold, Zachary</creator><creator>Curd, Emily E.</creator><creator>Goodwin, Kelly D.</creator><creator>Choi, Emma S.</creator><creator>Frable, Benjamin W.</creator><creator>Thompson, Andrew R.</creator><creator>Walker, Harold J.</creator><creator>Burton, Ronald S.</creator><creator>Kacev, Dovi</creator><creator>Martz, Lucas D.</creator><creator>Barber, Paul H.</creator><general>Wiley Subscription Services, Inc</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-4525-0671</orcidid><orcidid>https://orcid.org/0000-0001-7769-5558</orcidid><orcidid>https://orcid.org/0000-0001-7671-7487</orcidid><orcidid>https://orcid.org/0000-0002-6995-5329</orcidid><orcidid>https://orcid.org/0000-0003-0490-7630</orcidid><orcidid>https://orcid.org/0000-0001-9583-8073</orcidid><orcidid>https://orcid.org/0000-0003-0336-6852</orcidid></search><sort><creationdate>202110</creationdate><title>Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem</title><author>Gold, Zachary ; Curd, Emily E. ; Goodwin, Kelly D. ; Choi, Emma S. ; Frable, Benjamin W. ; Thompson, Andrew R. ; Walker, Harold J. ; Burton, Ronald S. ; Kacev, Dovi ; Martz, Lucas D. ; Barber, Paul H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3890-d8a804841c54672f41524b7b2e3403d99616bc3ef36fa3d910c1fa8144f00de43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Accuracy</topic><topic>Best practice</topic><topic>California Current Large Marine Ecosystem</topic><topic>Case studies</topic><topic>Chemical analysis</topic><topic>Classification</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Ecological effects</topic><topic>Ecosystems</topic><topic>eDNA</topic><topic>Environmental DNA</topic><topic>Marine ecosystems</topic><topic>Marine environment</topic><topic>Marine fish</topic><topic>metabarcoding</topic><topic>MiFish primers</topic><topic>Parameters</topic><topic>Performance evaluation</topic><topic>reference database</topic><topic>Seawater</topic><topic>Species</topic><topic>Taxonomy</topic><topic>Water analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gold, Zachary</creatorcontrib><creatorcontrib>Curd, Emily E.</creatorcontrib><creatorcontrib>Goodwin, Kelly D.</creatorcontrib><creatorcontrib>Choi, Emma S.</creatorcontrib><creatorcontrib>Frable, Benjamin W.</creatorcontrib><creatorcontrib>Thompson, Andrew R.</creatorcontrib><creatorcontrib>Walker, Harold J.</creatorcontrib><creatorcontrib>Burton, Ronald S.</creatorcontrib><creatorcontrib>Kacev, Dovi</creatorcontrib><creatorcontrib>Martz, Lucas D.</creatorcontrib><creatorcontrib>Barber, Paul H.</creatorcontrib><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular ecology resources</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gold, Zachary</au><au>Curd, Emily E.</au><au>Goodwin, Kelly D.</au><au>Choi, Emma S.</au><au>Frable, Benjamin W.</au><au>Thompson, Andrew R.</au><au>Walker, Harold J.</au><au>Burton, Ronald S.</au><au>Kacev, Dovi</au><au>Martz, Lucas D.</au><au>Barber, Paul H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem</atitle><jtitle>Molecular ecology resources</jtitle><date>2021-10</date><risdate>2021</risdate><volume>21</volume><issue>7</issue><spage>2546</spage><epage>2564</epage><pages>2546-2564</pages><issn>1755-098X</issn><eissn>1755-0998</eissn><abstract>DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross‐validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. 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subjects | Accuracy Best practice California Current Large Marine Ecosystem Case studies Chemical analysis Classification Deoxyribonucleic acid DNA Ecological effects Ecosystems eDNA Environmental DNA Marine ecosystems Marine environment Marine fish metabarcoding MiFish primers Parameters Performance evaluation reference database Seawater Species Taxonomy Water analysis |
title | Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem |
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