Universal primer cocktails for fish DNA barcoding

By Natalia N. Ivanova, Tyler S. Zemlak, Robert H. Hanner, Paul D. N. Hebert. 2007

1,443 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/d4fa2d300c2b74ddbb4d2fa27e12fd3eebfd734e

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Citations in the corpus

DNA barcoding detects market substitution in North American seafood (2008, methodology): “A 652 bp fragment from the 50region of COI was PCR amplified using a forward and reverse primer cocktail (Table 2), C_FishF1t1 and C_FishR1t1 (Ivanova et al., 2007), appended with M13 tails to aid in sequencing (Messing, 1983).”
DNA barcoding is a useful tool for the identification of marine fishes from Japan (2011, methodology): “PCR amplification Fragments of the 50 region of mitochondrial COI gene were initially amplified with VF2_t1/FR1d_t1 primers (Ivanova et al., 2007), and the failed ones were tried again with primers FishF2_t1/FR1d_t1.”
DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus (2008, methodology): “A 631–645 bp fragment of the cytochrome oxidase I (COI) gene was amplified following the fish DNA barcoding protocol developed by Ivanova et al. (2007), with some adjustments.”
Use of DNA barcoding to detect invertebrate invasive species from diapausing eggs (2011, background): “As universal COI and 16S primers amplify products of similar size, they can be considered a positive control for each other (Ivanova et al. 2007).”
DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species (2008, methodology): “Specimens were sequenced for an approximately 650 bp region of the mitochondrial gene cytochrome c oxidase following Ward et al. (2005) or Ivanova et al. (2007).”
The campaign to DNA barcode all fishes, FISH-BOL. (2009, background): “Barcoding typically uses inexpensive high-throughput extraction (Ivanova et al., 2006), and sequencing (Hajibabaei et al., 2005) protocols coupled with primers and primer cocktails developed for fishes (Ward et al., 2005; Ivanova et al., 2007).”
Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates (2010, methodology): “The 50 Folmer region of the mitochondrial (mtDNA) cytochrome c oxidase I (COX1) gene has been recommend as a standard for DNA barcoding (Folmer et al. 1994; Hebert et al. 2003a, b; Ivanova et al. 2007).”
Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols (2011, methodology): “The M13 tails were used as universal sequencing primers (Ivanova et al. 2007), which contributed to the high sequencing success.”
Identification of shark and ray fins using DNA barcoding (2009, methodology): “…10× PCR buffer [200 mM Tris–HCl (pH 8.4), 500 mM Cl], 0.625 L MgCl2 (50 mM), 0.125 L of each primer cocktail 0.01 mM, using primer cocktails C FishF1t1 and C FishR1t1 from vanova et al., 2007), 0.062 L of each dNTP (10 mM), 0.060 L f Platinum® Taq Polymerase (Invitrogen), and 2.0 L of DNA emplate.”
Comparative analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene in ciliates (Alveolata, Ciliophora) and evaluation of its suitability as a biodiversity marker (2010, methodology): “, 2006 ), we designed several degenerate primers and additionally tagged them with the M13 Forward and M13 Reverse primers, respectively, to enable PCR runs with multiple primer pairs ( Ivanova et al. , 2007 ).”