New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment

Milan, DT; Mendes, I; Damasceno, JS; Teixeria, DF; Guimaraes Sales, N; Carvalho, DC

Abstract

The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.

Citation

Milan, D., Mendes, I., Damasceno, J., Teixeria, D., Guimaraes Sales, N., & Carvalho, D. (2020). New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Scientific reports, 10, https://doi.org/10.1038/s41598-020-74902-3

• Journal Article Type: Article
• Online Publication Date: Oct 21, 2020
• Publication Date: Oct 21, 2020
• Deposit Date: Jan 31, 2023
• Publicly Available Date: Jan 31, 2023
• Journal: Scientific Reports
• Print ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Volume: 10
• DOI: https://doi.org/10.1038/s41598-020-74902-3
• Publisher URL: https://doi.org/10.1038/s41598-020-74902-3
• Additional Information: Funders : CEMIG;FAPEMIG;CNPq; Grant Number: P&D GT0635