DNA barcoding, an effective tool for species identification: a review

Antil, Sandeep; Abraham, Jeeva Susan; Somasundaram, Sripoorna; Maurya, Swati; Dagar, Jyoti; Makhija, Seema; Bhagat, Pooja; Gupta, Renu; Sood, Utkarsh; Lal, Rup; Toteja, Ravi

doi:10.1007/s11033-022-08015-7

Cited by 85 publications

(50 citation statements)

References 97 publications

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“…Authors have suggested one way to circumvent these issues is to be selective in the public data used for specimen identification (Diaz et al, 2016; Cariani et al, 2017; Oliveira et al, 2016). Building barcode reference libraries for a group or region of interest has become increasingly popular where authors create protocols for exhaustively analyzing public data to include the best public data available (ex ELASMOMED DNA Barcode Reference Library from Cariani et al (2017)) (Diaz et al, 2016; Cariani et al, 2017; Oliveira et al, 2016; Fort et al, 2021; Antil et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…DNA barcoding is a technique for identifying specimens through the use of standardized genomic regions, called ‘barcoding genes’ (Ward et al, 2009). The mitochondrial gene Cytochrome Oxidase Subunit I ( coI ) is conventionally used for animals (Antil et al, 2022). Many studies have shown that coI sequences differ among closely related species to an extent that species identity can be established by comparing their sequences, even discriminating recently diverged cryptic species (Castresana et al, 1994; Hebert et al, 2003; Hubert et al, 2008; Ward et al, 2009; Lara et al, 2010; Pires & Marinoni, 2010; Kress et al, 2015; Creer et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

Perez,

Fontenelle,

Kolmann

et al. 2023

Preprint

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As global biodiversity declines continue, conservation efforts are increasingly important in megadiverse areas such as the Neotropics where biodiversity is especially imperiled. The accurate identification of specimens is critical to successful conservation plans. However, in groups such as freshwater fishes, different identification methodologies have documented challenges. Using a biodiversity survey of fishes from the Barra del Colorado Wildlife Refuge in northeastern Costa Rica, we compared: (1) morphological identifications in the field, (2) morphological identifications in the lab by experts, (3) DNA barcode-based identifications, and (4) identifications based on an integrative approach. Our results suggest that both barcode-based identifications and field morphological identifications provided fewer correct species identifications than lab identifications performed by experts using morphology. We attribute shortfalls of DNA barcoding in this case to the misidentification of reference material, the use of outdated taxonomy for references sequences, and the non-uniform representation of groups in public databases across taxa. We suggest the use of an integrative approach to identify freshwater fishes in Costa Rica and other megadiverse areas of the Neotropics where similar issues with public barcode reference libraries exist. We also recommend the creation of regional curated barcode reference libraries to aid in the identification of traditionally difficult to identify species/specimens. We also provide the most up to date species list for the ichthyofauna of the Barra del Colorado Wildlife Refuge identifying 51 species from 42 genera, 21 families, and 17 orders. Generating accurate species lists for protected areas and areas of importance will provide conservation practitioners with effective tools for tracking diversity changes over time.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

Perez,

Fontenelle,

Kolmann

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The majority of records in our BOLD search were for the mitochondrial cytochrome c oxidase subunit I gene (COI). DNA metabarcoding of COI is presently the best tool available to collect data on both species identification and intraspecific genetic diversity (Antil et al, 2022;Hebert et al, 2004).…”

Section: Opportunities For Edna Metabarcoding For Biomonitoring and C...mentioning

confidence: 99%

Prioritizing taxa for genetic reference database development to advance inland water conservation

Monchamp

Taranu

Garner

et al. 2023

Biological Conservation

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“…The "DNA barcode" is based on a standardized short sequence of DNA within a small region of one species' genome, which can quickly and accurately distinguish diverse species (Antil et al, 2023). As a representative marker, the region of the internal transcriptional spacer 2 (ITS2) locates at the position of nuclear RNA cistron rapid evolution, is not only very different in the sequence, but also has the characteristics of easy ampli cation and strong generality, therefore it is very suitable reference as the "DNA barcode" (Schultz et al, 2005).…”

Section: Identi Cation Of Leonurus Species By Using the Its2 Sequencesmentioning

confidence: 99%

Appearance, molecule identification, and phylogenetic analysis of the three Leonurus species used for the treatment of gynecological diseases

Rong

Zhang

et al. 2023

Preprint

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We analyzed and compared the three Leonurus species from appearance characteristics, intrinsic gene contents and functions, gene transcribed spacer regions (ITS2) in the nuclear genome, and the process of evolutionary development. The chloroplast genomes of them were found to be common circular structures with the four regions, the length range from 151236bp to 151689bp including the identical number of 37 tRNA and 8 rRNA. The special trans-spliced rps12 genes with two introns and three exons can be caught sight of L. sibiricus. The isoleucine (AUU) and cysteine (UGC) was the most and least abundant amino acid with the codons ending with most bases of A/U. The eleven hotspot divergent regions and four specific CDS genes were systematically counted with the highest nucleotide diversity. We cloned the DNA sequences of the two chosen IGS regions (atpH-atpI and rps15-ycf1) to develop the DNA barcodes, thus found that sixteen specific variable SNP sites and two Indel sites within the three Leonurus species. Furthermore, the ITS2 DNA sequences of 7 Leonurus species were varied after the 57th base in a total of 221 bases. In the aftermath of evolutional analysis, the three Leonurus species were significantly clustered into one great clade, while they were located at the different sub-branch with similar topology and close relationship of Phlomoides rotata based on the sequences of 64 shared nucleotide and ITS2 DNA. Thus above results can directly offer various evidence to better clarify the specific distinction among the three Leonurus species and their evolutionary history.

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DNA barcoding, an effective tool for species identification: a review

Cited by 85 publications

References 97 publications

Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

Comparing Approaches to Specimen Identification using Neotropical Freshwater Fishes in the Barra del Colorado Wildlife Refuge, Costa Rica

Prioritizing taxa for genetic reference database development to advance inland water conservation

Appearance, molecule identification, and phylogenetic analysis of the three Leonurus species used for the treatment of gynecological diseases

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