DNA barcoding of fish fauna from low order streams of Tapajós River basin

Guimarães, Karen Larissa Auzier; Sousa, Marcos Paulo Alho de; Ribeiro, Frank Raynner Vasconcelos; Porto, Jorge Ivan Rebelo; Rodrigues, Luís Reginaldo Ribeiro

doi:10.1371/journal.pone.0209430

Cited by 8 publications

(10 citation statements)

References 37 publications

(41 reference statements)

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“…In the last decades, the field of molecular systematics experienced remarkable progress that led to the development of standardized DNA sequences used for taxonomy (e.g., Koroiva et al, 2017 ; Guimarães et al, 2018 ). Among these genetic tools, we found the mitochondrial gene Cytochrome Oxidase I (mtCOI, Cox 1 or COI), which was first suggested by Hebert and colleagues, as a basis for creating a global species identification system, especially for animals ( Hebert et al, 2003 ; Hebert, Ratnasingham & de Waard, 2003 ).…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding for identification of anuran species in the central region of South America

Koroiva

Rodrigues

Santana

2020

PeerJ

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The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.

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Section: Introductionmentioning

confidence: 99%

DNA barcoding for identification of anuran species in the central region of South America

Koroiva

Rodrigues

Santana

2020

PeerJ

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“…OTUs alignment against a custom COI fish database was performed by blastn (version 2.8.1). This local database was built with fish COI sequences mined from GenBank and Bold and also implemented with published sequences [ 41 ], but not yet available under GenBank ( S2 Table ). This final database has 160,944 entries representing 3,480 genera and 15,429 fish species distributed worldwide.…”

Section: Methodsmentioning

confidence: 99%

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

et al. 2022

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To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.

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“…The reactions were performed according to Guimarães et al . (2018). The DNA barcoding sequences were obtained through the capillary sequencing by di‐desoxiterminal reaction (Sanger method) using a ABI PRISM BigDye Terminator V.3 Cycle Sequencing kit and the genetic analyser ABI3500 (Applied Biosystems, Nijmegen, The Netherlands).…”

Section: Methodsmentioning

confidence: 99%

A new species of Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the Crepori River, Amazon basin, Brazil

Guimarães

Rosso

González‐Castro

et al. 2021

Journal of Fish Biology

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A new species belonging to the Hoplias malabaricus complex from the Amazon basin, Brazil, is described. The new species is characterized by 15–16 predorsal scales, 37–39 lateral‐line scales, 5 scales from dorsal fin to lateral line, 38–39 vertebrae, iii‐iv, 7–8 anal‐fin rays, ii‐iv, 12–15 caudal‐fin rays, last vertical series of scales on the base of caudal‐fin rays forming a straight line, 6–7 dark bands in anal fin and no distinctive dark bands or blotches on flanks. The new species is also distinguished from other congeners of the H. malabaricus species‐group by means of landmark‐based morphometrics and DNA Barcoding (Cytochrome c Oxidase I gene). An identification key to species of the H. malabaricus species complex is provided.

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DNA barcoding of fish fauna from low order streams of Tapajós River basin

Cited by 8 publications

References 37 publications

DNA barcoding for identification of anuran species in the central region of South America

DNA barcoding for identification of anuran species in the central region of South America

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

A new species of Hoplias malabaricus species complex (Characiformes: Erythrinidae) from the Crepori River, Amazon basin, Brazil

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