Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance

Chagas, Aline Torres de Azevedo; Ludwig, Sandra; Pimentel, Juliana da Silva Martins; Abreu, Nazaré Lúcio de; Núñez-Rodriguez, Daniela; Leal, Hortênsia Gomes; Kalapothakis, Evanguedes

doi:10.1080/24701394.2020.1748609

Cited by 9 publications

(11 citation statements)

References 41 publications

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“…Thus, the high degree of genetic homology among fish species of the same family may cause limitations to providing adequate resolution for a correct identification, since species are differentiated by point mutations. Currently, mitochondrial genomes can be rapidly obtained from genome or transcriptome datasets [ 27 ], but comparative mitogenomics has been barely used for the discovery of new specific genes useful as markers for species and strain recognition [ 19 , 53 , 54 ].…”

Section: Discussionmentioning

confidence: 99%

“…The limitation of providing adequate resolution at deep nodes emerges especially when fish species have a high degree of genetic homology. Traditional markers are inadequate, especially when they amplify for fragments that differentiate species by point mutations [ 19 ]. We have recently shown that the analysis of the complete mtDNA (mitogenomics) provides a useful approach for identifying fast and adequate barcoding markers.…”

Section: Introductionmentioning

confidence: 99%

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A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Ceruso

Mascolo

Luca

et al. 2020

Foods

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The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Ceruso

Mascolo

Luca

et al. 2020

Foods

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“…A recent molecular phylogeny revealed that P. vimboides from coastal Brazilian rivers is sister to all remaining Prochilodus , and the other four species were placed in two well‐supported clades: one composed by P. argenteus (Rio São Francisco) sister to P. harttii (Rio Pardo and Rio Jequitinhonha), and another composed by P. lineatus (Paraná‐Paraguay system and Rio Paraíba do Sul) nested within the paraphyletic P. costatus (Rio São Francisco) (Melo et al, 2016). Further analyses using a mtDNA dataset and a larger taxon sampling supported the non‐monophyly of P. costatus and P. lineatus (Melo et al, 2018), but a recent study using the mitochondrial control region obtained the monophyly of these two species (Chagas et al, 2020). However, all these studies used a single or few loci resulting in low node support in many instances along the topologies (Chagas et al, 2020; Melo et al,2016, 2018), and thus some clades in the phylogeny of Prochilodus remain to be explored by a large‐scale molecular analysis.…”

Section: Introductionmentioning

confidence: 96%

“…Further analyses using a mtDNA dataset and a larger taxon sampling supported the non‐monophyly of P. costatus and P. lineatus (Melo et al, 2018), but a recent study using the mitochondrial control region obtained the monophyly of these two species (Chagas et al, 2020). However, all these studies used a single or few loci resulting in low node support in many instances along the topologies (Chagas et al, 2020; Melo et al,2016, 2018), and thus some clades in the phylogeny of Prochilodus remain to be explored by a large‐scale molecular analysis.…”

Section: Introductionmentioning

confidence: 96%

“…Although recent advances have been achieved in understanding the evolutionary relationships of Prochilodus (Chagas et al, 2020; Melo et al, 2016, 2018), the biogeographic history of the genus remains uncertain, especially in the eastern Brazilian Shield. A large‐scale phylogeographic analysis among Prochilodus species from three hydrographic basins using mtDNA data showed that the phylogenetic structure is not associated with geography (Sivasundar et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

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Diversification of Prochilodus in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae)

Santos

Melo

Yazbeck

et al. 2021

J. Zool. Syst. Evol. Res.

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The Neotropical fish genus Prochilodus includes five species occurring in the main drainages of the eastern Brazilian Shield: P. argenteus, P. costatus, P. lineatus, P. harttii, and P. vimboides. Multi and single locus phylogenies have questioned the monophyly of P. costatus and P. lineatus, and the biogeographic history of these species in the Brazilian Shield has never been explored. We characterized new mitogenomes for these species to reconstruct their evolutionary history, estimated the timing of Prochilodus cladogenesis, and discussed the implications of past geologic events on species diversification. The phylogeny supports the monophyly of both P. costatus and P. lineatus, and indicates a Miocene divergence of P. vimboides, much earlier than subsequent species diversification. The Early Pleistocene split of P. argenteus and P. harttii (~2.1 million years ago—MYA) is hypothesized to be related to recent Quaternary reactivations of the Rio Araçuaí Fault that promoted river captures between the eastern tributaries of the São Francisco basin and the upper Rio Jequitinhonha in the Serra do Espinhaço mountain range. The time‐calibrated phylogeny also indicated a subsequent split of P. costatus and P. lineatus (~1.1 MYA) likely due to Quaternary activities of the Upper Rio São Francisco crustal discontinuity and Estrela Fault that catalyzed river captures between the upper Rio São Francisco and the Rio Grande of the Paraná basin in the Serra da Canastra mountain range. These results provide a temporal context for the diversification of Prochilodus and bring new insights to further study the historical biogeography of other riverine fish groups along the upland basins of the eastern Brazilian Shield.

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High genetic diversity in anguillid glass eels across three Southeast Asian countries revealed through mitochondrial DNA D-loop sequences, with notes on population structure

Marini,

Pedrosa-Gerasmio,

Santos

et al. 2024

Ecological Genetics and Genomics

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Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance

Cited by 9 publications

References 41 publications

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Diversification of Prochilodus in the eastern Brazilian Shield: Evidence from complete mitochondrial genomes (Teleostei, Prochilodontidae)

High genetic diversity in anguillid glass eels across three Southeast Asian countries revealed through mitochondrial DNA D-loop sequences, with notes on population structure

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