DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent
Abstract The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost‐effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain signi...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-10-01
|
| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.10649 |
| _version_ | 1827782298780565504 |
|---|---|
| author | Daniel Fonseca Teixeira Heron Oliveira Hilário Gilmar Bastos Santos Daniel Cardoso Carvalho |
| author_facet | Daniel Fonseca Teixeira Heron Oliveira Hilário Gilmar Bastos Santos Daniel Cardoso Carvalho |
| author_sort | Daniel Fonseca Teixeira |
| collection | DOAJ |
| description | Abstract The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost‐effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp – NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%–87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker‐dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR‐dependent protocols. |
| first_indexed | 2024-03-11T15:30:14Z |
| format | Article |
| id | doaj.art-92cb2316b2054ef9a1043cce55e58a0c |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-03-11T15:30:14Z |
| publishDate | 2023-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-92cb2316b2054ef9a1043cce55e58a0c2023-10-27T04:40:51ZengWileyEcology and Evolution2045-77582023-10-011310n/an/a10.1002/ece3.10649DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependentDaniel Fonseca Teixeira0Heron Oliveira Hilário1Gilmar Bastos Santos2Daniel Cardoso Carvalho3Post‐Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte BrazilPost‐Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte BrazilPost‐Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte BrazilPost‐Graduate Program in Vertebrate Biology Pontifical Catholic University of Minas Gerais, PUC Minas Belo Horizonte BrazilAbstract The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost‐effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp – NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%–87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker‐dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR‐dependent protocols.https://doi.org/10.1002/ece3.1064912S rRNACOIhigh‐throughput DNA sequencingmolecular taxonomy |
| spellingShingle | Daniel Fonseca Teixeira Heron Oliveira Hilário Gilmar Bastos Santos Daniel Cardoso Carvalho DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent Ecology and Evolution 12S rRNA COI high‐throughput DNA sequencing molecular taxonomy |
| title | DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent |
| title_full | DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent |
| title_fullStr | DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent |
| title_full_unstemmed | DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent |
| title_short | DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker‐dependent |
| title_sort | dna metabarcoding assessment of neotropical ichthyoplankton communities is marker dependent |
| topic | 12S rRNA COI high‐throughput DNA sequencing molecular taxonomy |
| url | https://doi.org/10.1002/ece3.10649 |
| work_keys_str_mv | AT danielfonsecateixeira dnametabarcodingassessmentofneotropicalichthyoplanktoncommunitiesismarkerdependent AT heronoliveirahilario dnametabarcodingassessmentofneotropicalichthyoplanktoncommunitiesismarkerdependent AT gilmarbastossantos dnametabarcodingassessmentofneotropicalichthyoplanktoncommunitiesismarkerdependent AT danielcardosocarvalho dnametabarcodingassessmentofneotropicalichthyoplanktoncommunitiesismarkerdependent |