Redesign of <scp>PCR</scp> primers for mitochondrial cytochrome <i>c</i> oxidase subunit <scp>I</scp> for marine invertebrates and application in all‐taxa biotic surveys

Geller, Jonathan B.; Meyer, Christopher P.; Parker, Meaghan; Hawk, Heather

doi:10.1111/1755-0998.12138

Cited by 833 publications

(606 citation statements)

References 19 publications

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“…For barcoding, tissue was subsampled from each specimen and placed individually in 96-well Costar plates (Corning) for phenol DNA extraction. DNA amplification and Sanger sequencing used standard protocols (SI Text, section V.A) and previously published primers (19,20). For metabarcoding, DNA was extracted from 10 g of homogenized sessile tissue and the crushed half of the 2-mm to 500-μm and 500-to 106-μm samples using the MO-BIO Powermax Soil DNA Isolation Kit (SI Text, section V.B).…”

Section: Methodsmentioning

confidence: 99%

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Leray

Knowlton

2015

Proc. Natl. Acad. Sci. U.S.A.

464

503

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Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic organisms that colonized multilayered settlement surfaces (autonomous reef monitoring structures) over a 6-mo period were identified by cytochrome c oxidase subunit I barcoding (>2-mm mobile organisms) and metabarcoding (sessile and smaller mobile organisms). In a total area of ∼15.64 m 2 and volume of ∼0.09 m 3 , 2,179 operational taxonomic units (OTUs) were recorded from 983,056 sequences. However, only 10.9% could be matched to reference barcodes in public databases, with only 8.2% matching barcodes with both genus and species names. Taxonomic coverage was broad, particularly for animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding could not be confidently assigned to a taxonomic group. The smallest size fraction (500 to 106 μm) was the most diverse (more than two-thirds of OTUs). There was little taxonomic overlap between VA and FL, and samples separated by ∼2 m were significantly more similar than samples separated by ∼100 m. Ground-truthing with independent assessments of taxonomic composition indicated that both presence-absence information and relative abundance information are captured by metabarcoding data, suggesting considerable potential for ecological studies and environmental monitoring. U nderstanding the diversity of life in the sea continues to challenge marine scientists because samples typically contain many rare species, most of them small and difficult to identify (1). Moreover, recent estimates suggest that between 33% and 91% of all marine species have never been named (2, 3). These constraints have limited our ability to investigate patterns of diversity beyond a few indicator groups (4), most often conspicuous macroinvertebrates and fish. For this reason, molecular methods, particularly high-throughput sequencing (HTS) approaches, hold considerable promise not only for fundamental understanding of diversity but also for biodiversity monitoring in the context of global change (5).Molecular methods are particularly powerful when combined with standardized sampling, allowing for direct comparisons across space and through time. In the ocean, analyzing standard volumes of readily sampled material (e.g., seawater, sediments) has a long tradition, and, increasingly, HTS approaches are being applied to these samples (6). Complex hard substrates provide greater challenges for consistent sampling, which can be met either by collecting approximately standard volumes (e.g., of rubble) or by deploying settlement structures (e.g., ref. 7).Here, we combin...

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Section: Methodsmentioning

confidence: 99%

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Leray

Knowlton

2015

Proc. Natl. Acad. Sci. U.S.A.

464

503

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“…DNA processing DNA was extracted from 10 g of each homogenized sample using PowerMax Soil DNA Isolation Kit (www.mobio.com). Two genes were amplified: a 100-110 bp fragment in the v7 region of the 18S rRNA gene, using the 18S_allshorts primers (Guardiola et al, 2015; forward: 5'-TTTGTCTGSTTAATTSCG-3' and reverse: 5'-TCACAGACCTGTTATTGC-3), and a fragment of the COI gene, amplified with a modification of the forward miCOIintF primer (Leray et al, 2013): 5'-GGWACWRGWTGRACWITITAYCCYCC-3' and the reverse jgHCO2198 primer (Geller et al, 2013): 5'-TAIACYTCIGGRTGICCRAARAAYCA-3'. The forward primer incorporated two more wobble bases and two inosine nucleotides in the most degenerate positions, relative to the original miCOIintF.…”

Section: Samplingmentioning

confidence: 99%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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“…For most species and OTUs, we used the primers dgLCO1490/dgHCO2198 (Meyer 2003), which are slight modifications of the universal primers LCO1490/ HCO2198 (Folmer et al 1994). For one species, Polymastia corticata Rildey & Dendy, 1886, CO1 sequences of satisfactory quality could be obtained only with the primers jgLCO1490/jgHCO2198 (Geller et al 2013).…”

Section: Taxonomic Scopementioning

confidence: 99%

Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology

et al. 2016

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Polymastiidae Gray, 1867 is a worldwide distributed sponge family, which has a great significance for understanding of the demosponge deep phylogeny since the former order Hadromerida Topsent, 1894 has been recently split based on the molecular evidence and a new separate order has been established for the polymastiids. However, molecular data obtained from Polymastiidae so far are scarce, while the phylogenetic reconstruction based on morphology has faced a deficit of characters along with the vagueness of their states. The present study is a phylogenetic reconstruction of Polymastiidae based on novel data on two molecular markers, cytochrome oxidase subunit I and large subunit ribosomal DNA, obtained from a broad set of species. Monophyly of the family and nonmonophyly of four polymastiid genera are revealed, suggesting a high level of homoplasy of morphological characters, which are therefore not an appropriate base for the natural classification of Polymastiidae. Although the presented phylogenies cannot yet provide an alternative classification scheme, several strongly supported clades, which may be used as reference points in future classification, are recovered and three taxonomic actions are proposed: transfer of one species from Radiella to Polymastia Bowerbank, 1862; transfer of three species from Radiella Schmidt, 1870 to Spinularia Gray, 1867; and the consequent abandonment of Radiella.

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Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys

Cited by 833 publications

References 19 publications

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Molecular phylogenies challenge the classification of Polymastiidae (Porifera, Demospongiae) based on morphology

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