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The Future of DNA Barcoding: Reflections from Early Career Researchers

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diversity Opinion The Future of DNA Barcoding: Reflections from Early Career Researchers Danielle M. Grant 1,2,3 , Ole Bjørn Brodnicke 4, Ann M. Evankow 5 , André O. Ferreira 6,7 , João T. Fontes 6,7 , Aslak Kappel Hansen 8,9,10 , Mads Reinholdt Jensen 8 , Tu˘gbaErgül Kalaycı 11 , Alexandra Leeper 12,13, Shalaka Kiran Patil 3, Sebastian Prati 14,15 , Anna Reunamo 16, Aradhana J. Roberts 17, Rajesh Shigdel 18, Valentina Tyukosova 19, Mika Bendiksby 5,19, Rakel Blaalid 20, Filipe O. Costa 6,7 , Peter M. Hollingsworth 21, Elisabeth Stur 19 and Torbjørn Ekrem 19,* 1 NORCE Norwegian Research Centre, NO-5012 Bergen, Norway; [email protected] 2 Bjerknes Centre for Climate Research, NO-5007 Bergen, Norway 3 Department of Biological Sciences, University of Bergen, NO-5020 Bergen, Norway; [email protected] 4 Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark; [email protected] 5 Natural History Museum, University of Oslo, NO-0318 Oslo, Norway; [email protected] (A.M.E.); [email protected] (M.B.) 6 CBMA—Centre of Molecular and Environmental Biology, University of Minho, 4710-057 Braga, Portugal; [email protected] (A.O.F.); [email protected] (J.T.F.); [email protected] (F.O.C.) 7 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal 8 Department of Biology, Aarhus University, DK-8000 Aarhus, Denmark; [email protected] (A.K.H.); [email protected] (M.R.J.) 9 Natural History Museum of Denmark, DK-1350 Copenhagen, Denmark 10 Citation: Grant, D.M.; Brodnicke, Natural History Museum Aarhus, DK-8000 Aarhus, Denmark 11 O.B.; Evankow, A.M.; Ferreira, A.O.; Department of Biology, University of RTE, 53100 Rize, Turkey; [email protected] 12 Fontes, J.T.; Hansen, A.K.; Jensen, Aquaculture Department, Matís ohf. Food and Biotechnology, 113 Reykjavík, Iceland; [email protected] 13 Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life M.R.; Kalaycı, T.E.; Leeper, A.; Patil, Sciences, NO-1432 Aas, Norway S.K.; et al. The Future of DNA 14 Department of Arctic and Marine Biology, University of Tromsø, NO-9019 Tromsø, Norway; Barcoding: Reflections from Early [email protected] Career Researchers. Diversity 2021, 13, 15 Department of Aquatic Ecology, University of Duisburg-Essen, D-45141 Essen, Germany 313. https://doi.org/10.3390/ 16 Finnish Environment Institute SYKE, 00790 Helsinki, Finland; anna.reunamo@syke.fi d13070313 17 Department of Physical Geography and Ecosystem Science, Lund University, S-223 62 Lund, Sweden; [email protected] 18 Academic Editor: Stephan Department of Clinical Science, University of Bergen, NO-5020 Bergen, Norway; [email protected] 19 Koblmüller Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; [email protected] (V.T.); [email protected] (E.S.) 20 Department of Natural History, University Museum of Bergen, NO-5020 Bergen, Norway; Received: 14 June 2021 [email protected] Accepted: 5 July 2021 21 Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK; [email protected] Published: 9 July 2021 * Correspondence: [email protected]; Tel.: +47-73597812 Publisher’s Note: MDPI stays neutral Abstract: Over the last two decades, the use of DNA barcodes has transformed our ability to identify with regard to jurisdictional claims in and assess life on our planet. Both strengths and weaknesses of the method have been exemplified published maps and institutional affil- through thousands of peer-reviewed scientific articles. Given the novel sequencing approaches, iations. currently capable of generating millions of reads at low cost, we reflect on the questions: What will the future bring for DNA barcoding? Will identification of species using short, standardized fragments of DNA stand the test of time? We present reflected opinions of early career biodiversity researchers in the form of a SWOT analysis and discuss answers to these questions. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. Keywords: biodiversity; cryptic species; metabarcoding; reference libraries; high-throughput This article is an open access article sequencing; biomonitoring distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). Diversity 2021, 13, 313. https://doi.org/10.3390/d13070313 https://www.mdpi.com/journal/diversity Diversity 2021, 13, x FOR PEER REVIEW 2 of 11 Diversity 2021, 13, 313 2 of 11 1. Introduction The use of short, standardized DNA sequences to identify species (i.e., DNA 1.barcoding Introduction [1]) has considerably changed how we assess, analyze, and monitor biodiversityThe use ofwithin short, all standardized ecosystems DNA (e.g., sequences [2,3]). Since to identifyits initiation, species DNA (i.e., barcoding DNA barcod- has ingsignificantly [1]) has considerably contributed changed to our understanding how we assess, of analyze, species andboundaries monitor and biodiversity the composition within allof ecosystemsbiological (e.g.,communities [2,3]). Since across its initiation,the world DNA [4]. barcodingIn addition, has it significantly has paved contributedthe way for tonational our understanding and international of species biodiversity boundaries research and the compositionprograms. Notable of biological examples communities include acrossbiodiversity the world biomonitoring [4]. In addition, [5], food it has industry paved the surveillance way for national [6], and and detecting international substitution biodi- versityin the researchherbal medicine programs. industry Notable [7]. examples include biodiversity biomonitoring [5], food industryThe surveillance foundation [6of], andspecies detecting identification substitution by DNA in the barcoding herbal medicine is a curated industry barcode [7]. referenceThe foundation library, enabling of species comparisons identification of DNA by sequences DNA barcoding from unidentified is a curated organisms barcode referenceto sequences library, from enabling previously comparisons identified of taxa. DNA The sequences largest database from unidentified for this purpose organisms is the toBarcode sequences of Life from Data previously Systems identified (BOLD taxa.[8]) containing The largest more database than fornine this million purpose DNA is thebarcodes Barcode (Figure of Life 1). Data The Systemsreference (BOLD library [ 8is]) continuously containing more expanding, than nine with million ~60% DNAof the barcodesentries published (Figure1). during The reference the last decade. library This is continuously effort has been expanding, primarily with driven ~60% by research of the entriesprojects published promoted during by the lastInternational decade. This Barc effortode hasof beenLife primarilyconsortium driven (iBOL), by research such as projectsBarcode promoted 500K (completed by the International in 2015) Barcodeand BIOSCAN, of Life consortium launched (iBOL),June 2019 such [9,10]. as Barcode Other 500Kinitiatives, (completed such inas 2015)the Earth and BIOSCAN,Biogenome launched Project, aim June to 2019 genome [9,10]. sequence Other initiatives, all eukaryotic such asbiodiversity the Earth Biogenome in the upcoming Project, decade, aim to genomewhich will sequence further all expand eukaryotic DNA biodiversity barcode coverage. in the upcomingThe vast majority decade, which of organisms will further still expandlack DNA DNA barcodes, barcode coverage.and much Theof the vast current majority work of organismshas been carried still lack out DNA in Europe barcodes, and and North much America, of the current resulting work in a has bias been in barcoded carried out biota in Europe(Figure and 1). North America, resulting in a bias in barcoded biota (Figure1). FigureFigure 1. 1.Number Number ofof publicpublic DNADNA barcodes available in Barcode Barcode of of Life Life Data Data Systems Systems (BOLD) (BOLD) by by countrycountry (obtained (obtained 1 1 January, January, 2021). 2021). AA review review by by DeSalle DeSalle and and Goldstein Goldstein [ 4[4]] highlighted highlighted that that DNA DNA barcoding barcoding is is a a widely widely appliedapplied contemporary contemporary tool tool that that has has diversified diversified paradigms paradigms and and practices. practices. The The adoption adoption of of high-throughputhigh-throughput sequencing sequencing (HTS) (HTS) technologies technologies has further has further decreased decreased costs and increasedcosts and theincreased range of the applications range of applications for DNA barcoding for DNA [barcoding5,11]. Despite [5,11]. differences Despite differences in the choice in ofthe targetchoice DNA of target marker DNA and marker challenges and challenges with generating with generating barcodes barcodes for some for taxa some [12 taxa], DNA [12], barcodingDNA barcoding is now is routinely now routinely used across used across the tree the of tree life of and life functions and functions as an integratedas an integrated and standardand standard methodology methodology in biodiversity in biodiversity studies. studies. The essential The essential value ofvalue DNA of barcodingDNA barcoding as an identificationas an identification tool is obvious:tool is obvious: many species many wouldspecies remainwould unidentified,remain unidentified, hidden, orhidden, cryptic or by other means of identification. The added value of DNA barcodes for
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  • DNA Barcoding for Species Identification and Discovery in Diatoms

    DNA Barcoding for Species Identification and Discovery in Diatoms

    557_578_MANN.fm Page 557 Mercredi, 8. décembre 2010 8:58 08 Cryptogamie, Algologie, 2010, 31 (4): 557-577 © 2010 Adac. Tous droits réservés DNA barcoding for species identification and discovery in diatoms David G. MANN a* , Shinya SATO a, Rosa TROBAJO b, Pieter VANORMELINGEN c & Caroline SOUFFREAU c a Royal Botanic Garden Edinburgh, Inverleith Row, Edinburgh EH3 5LR, Scotland, UK b Aquatic Ecosystems, Institute for Food and Agricultural Research and Technology (IRTA), Ctra Poble Nou Km 5.5, Sant Carles de la Ràpita, Catalunya, E-43540, Spain c Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281-S8, B-9000 Gent, Belgium Abstract – Diatoms are the largest group of microalgae, play an enormous role in the biosphere, and have major significance as bioindicators. Traditional identification requires inter alia long training, considerable microscopical skill, and use of a vast and scattered literature. During the life cycle, diatom cells change in size and pattern, often also shape, but the full cycle is known in <1% of described species. Recent evidence shows that there are many pseudocryptic and cryptic species of diatoms, requiring molecular methods for discovery and recognition. These and other factors argue that DNA barcoding would be highly beneficial. It could be ‘strong’, resolving nearly all species, or ‘weak’, resolving mostly species already recognized from light microscopy. Attempts have already been made to identify suitable genes and we evaluate these on the basis of universality and practicality, and ability to discriminate between species in the very few ‘model’ systems offering likely examples of sister-species-pairs. No candidate marker is ideal but LSU rDNA and rbcL may be acceptable, though their discriminatory power is lower than that of some other markers.