Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

Cawthorn, Donna‐Mareè; Steinman, Harris; Witthuhn, R. Corli

doi:10.1016/j.gene.2011.09.009

Cited by 69 publications

(46 citation statements)

References 52 publications

(65 reference statements)

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“…The mean genetic K2P genetic distances of COI were similar between intraspecific and interspecific species but different at the confamilial taxonomic level suggesting the absence of a barcoding gap, an observation also made by Zou et al , 32 . A study on publicly available sequences of marine and freshwater fishes available from the Barcoding of Life Database also reported a paucity of barcoding gap in COI 1, 20 .…”

Section: Discussionsupporting

confidence: 79%

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

2016

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DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.

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Section: Discussionsupporting

confidence: 79%

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

2016

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“…Mitochondrial 12S and 16S rRNA partial sequences were evaluated as universal makers for the identification of fish at the species level, and it is recommended that 1 or more faster-evolving DNA regions be analyzed to confirm the identities of closely-related fish species (Cawthorn et al 2012). It has been suggested that 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians, and 16S fragment is superior to COI in some respects (Vences et al 2005).…”

Section: Dna Extraction Polymerase Chain Reaction and Sequencingmentioning

confidence: 99%

Integrative taxonomy helps to reveal the mask of the genusGynandropaa(Amphibia: Anura: Dicroglossidae)

Huang

Wang

et al. 2016

Integrative Zoology

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Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs. Zoobank registration: urn:lsid:zoobank.org:pub:0772D78D-E5C4-4D05-9154-38B155C09948

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“…A range of other markers are also used for DNA barcoding of animals. For instance, 16S (a mitochondrial ribosomal RNA [rRNA] gene) has been used for amphibians (Vences, Thomas, Meijden, Chiari, & Vieites, ); 16S, 12S (another mitochondrial rRNA gene) or cytochrome b (CytB; a protein‐coding mitochondrial gene) for fishes (Cawthorn, Steinman, & Witthuhn, ; Sevilla et al, ); and more recently, an unexplored region at the 3′ end of the COI gene for odonates (dragonflies and damselflies) (Rach et al, ). However, the reference libraries for these alternative markers are small in comparison with those for COI.…”

Section: Introductionmentioning

confidence: 99%

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

Marquina

Andersson

Ronquist

2018

Molecular Ecology Resources

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Insect metabarcoding has been mainly based on PCR amplification of short fragments within the "barcoding region" of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein-coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon-based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.

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Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa

Cited by 69 publications

References 52 publications

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

DNA barcoding of Clarias gariepinus, Coptodon zillii and Sarotherodon melanotheron from Southwestern Nigeria

Integrative taxonomy helps to reveal the mask of the genusGynandropaa(Amphibia: Anura: Dicroglossidae)

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

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