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DNA Barcoding Botanica Marina 2020; 63(3): 253–272 Review Angela G. Bartolo*, Gabrielle Zammit, Akira F. Peters and Frithjof C. Küpper The current state of DNA barcoding of macroalgae in the Mediterranean Sea: presently lacking but urgently required https://doi.org/10.1515/bot-2019-0041 Received 12 June, 2019; accepted 18 February, 2020; online first 28 Introduction March, 2020 This review delves into the current state of DNA barcod- Abstract: This review article explores the state of DNA ing of macroalgae with a focus on the Mediterranean Sea. barcoding of macroalgae in the Mediterranean Sea. Data To this end, data from the Barcode of Life Data System from the Barcode of Life Data System (BOLD) were utilised (BOLD) were researched and a literature review was con- in conjunction with a thorough bibliographic review. Our ducted. The study concludes that there is a lack of genetic findings indicate that from around 1124 records of algae data for these organisms. This article discusses the steps in the Mediterranean Sea, only 114 species have been required for improving DNA-based methods in this region. barcoded. We thus conclude that there are insufficient Algae including macrophytes and phytoplankton are macroalgal genetic data from the Mediterranean and the base of marine food webs, provide oxygen to aquatic that this area would greatly benefit from studies involv- environments and humans, can be used as biological indi- ing DNA barcoding. Such research would contribute to cators, and are a potential food source which is underuti- resolving numerous questions about macroalgal system- lised in most parts of the world (Wolf 2012). However, in atics in the area and address queries related to biogeog- direct contrast to their importance in marine ecosystems raphy, especially those concerned with non-indigenous (Brodie et al. 2017), only 10% of algal species are believed species. It could also possibly result in the development to have been described so far (De Vargas et al. 2015). and application of better, cost-effective biodiversity moni- Macroalgae include mainly three phylogenetic line- toring programmes emanating from UN conventions and ages. Green and red algae originated about 1.5 billion EU Directives. One possible way of achieving this is to years ago after the endosymbiotic event that resulted construct DNA libraries via sequencing and barcoding, in the first photosynthetic eukaryotes (Yoon et al. 2004, subsequently enabling better cost-effective biodiversity Rodríguez-Ezpeleta et al. 2005). On the other hand, the monitoring through environmental DNA metabarcoding. brown algae evolved after a secondary endosymbiotic event that occurred around 1.3 billion years ago, involving Keywords: algae; barcoding; Chlorophyta; Phaeophyceae; a unicellular red alga engulfed by a heterokont protist that Rhodophyta. was only distantly related to the green and red algae (Yoon et al. 2004, Ševčíková et al. 2015). Complex multicellular- *Corresponding author: Angela G. Bartolo, School of Biological ity is thought to have evolved independently in the three Sciences, University of Aberdeen, Cruickshank Building, St. Machar large groups (Cock et al. 2010). Drive, Aberdeen AB24 3UU, Scotland, UK; and Laboratory of The term “seaweed” has traditionally been used to Applied Phycology, Department of Biology, Fourth Floor, Biomedical define the macroscopic, multicellular marine algae (Wolf Sciences Building, University of Malta, MSD2620, Msida, Malta, 2012). However, these may also exist as microscopic rep- e-mail: [email protected]. https://orcid.org/0000-0001-9109-8979 resentatives since all macroalgae are unicellular at some Gabrielle Zammit: Laboratory of Applied Phycology, Department of point in their life cycle, as zygotes or spores, which could Biology, Fourth Floor, Biomedical Sciences Building, University of also be temporarily planktonic (Amsler and Searles 1980). Malta, MSD2620, Msida, Malta The term Mediterranean is derived from the Latin Akira F. Peters: Bezhin Rosko, 40 rue des pêcheurs, 29250 Santec, Mare medi terraneum, meaning “sea in the middle of the Brittany, France Frithjof C. Küpper: School of Biological Sciences, University of land” (Coll et al. 2010). It is the largest and deepest semi- Aberdeen, Cruickshank Building, St. Machar Drive, Aberdeen AB24 enclosed sea in the world. The Mediterranean is connected 3UU, Scotland, UK to the Atlantic Ocean through the Strait of Gibraltar, to the 254 A.G. Bartolo et al.: The current state of DNA barcoding of macroalgae in the Mediterranean Sea Sea of Marmara and the Black Sea through the Darda- and the detection of morphologically cryptic algae at new nelles and to the Red Sea and the Indian Ocean through locations (Provan et al. 2005, Uwai et al. 2006). This is the Suez Canal (Coll et al. 2010). important since cryptic species are frequently produced The Mediterranean has a large area classified as deep by recent speciation or convergent evolution, and these sea with high salinity (37.5–39.5) and homothermy from species are impossible to differentiate morphologically; around 300 to 500 m to the bottom of 12.8–13.5°C in the however, they are genetically distinct (Cianciola et al. western basin and 13.5–15.5°C in the eastern basin (Coll 2010). Moreover, diverse genetic populations which are et al. 2010). It also has a geological history that included indistinguishable morphologically may have a different segregation from the other seas causing the Messin- invasive range (e.g. Voisin et al. 2005). Crypticisms could ian Salinity Crisis around 5.96 million years ago, which refer to cryptic size (i.e. microscopic species), cryptic brought about major changes in climate, salinity and sea stages that may be unknown microscopic forms of a level (Coll et al. 2010). known macroalgal species, cryptic morphology (i.e. where Although Mediterranean species evolved from ances- morphology is hardly discernible) or cryptic species (i.e. tors originating from the Atlantic following the Messinian different species of similar morphologies) (Peters et al. Salinity Crisis, both temperate and subtropical organisms 2015). Morphological identification is problematic in the have managed to survive in the Mediterranean’s wide case of crypticisms and thus DNA barcoding is necessary range of hydrology and climate. However, the Mediter- to reveal them. For example, as indicated in Zanolla et al. ranean Sea also has a high level of endemism (Coll et al. (2018), genetic studies have revealed two cryptic lineages 2010, Pascual et al. 2017) and is considered a biodiversity in Asparagopsis armata Harvey and six in Asparagopsis hotspot. taxiformis (Delile) Trevisan (Andreakis et al. 2004, 2016, DNA barcoding involves the identification of DNA Dijoux et al. 2014) and, due to their cryptogenic status, sequences by checking their identity against a publicly- their native ranges remain unknown (Dijoux et al. 2014). accessible database. DNA barcoding has revolutionised Cryptogenic species are species with an undefined origin classical species identification, biogeographical and pop- which are often small and/or cryptic, belong to taxonomic ulation studies. The concept of DNA barcoding is based groups which have not been studied extensively and are upon sequencing one or a few relatively short loci, which frequently described taxonomically by diverse names in are standardised among a large number of taxa, and which different new areas (Carlton 2009, Mineur et al. 2012). provide an unambiguous identification of the given taxon – DNA metabarcoding combines the concepts of DNA similar to barcoding a commercial product (Hebert et al. barcoding with that of Next Generation Sequencing (NGS) 2003). It is meant to be rapid, relatively inexpensive and and involves High-Throughput Sequencing (HTS) methods applicable using generic methodology and equipment – applied directly to an environmental sample without thus, at least in principle, empowering non-specialists the prerequisite of isolation of individuals (Porter and or even non-scientists to obtain a correct identification Hajibabaei 2018). The importance of environmental DNA of any previously identified taxon (including groups for (eDNA) metabarcoding is that it simultaneously charac- which very few taxonomic experts exist worldwide). terises the composition of species in environmental DNA, So far, barcoded taxa span across almost all known and is thus contributing significantly to taxonomic, eco- eukaryotic phyla, including groups which are morpho- logical and biogeochemical studies (Deagle et al. 2014). logically difficult to identify such as the oomycete genus eDNA consists of genetic material which is present in Pythium (Robideau et al. 2011), dinoflagellates (Stern samples such as sediment, air and water, including whole et al. 2012) or the ciliate Tetrahymena (Kher et al. 2011). cells, cell debris, different life stages such as propagules, However, large gaps in coverage still exist, both geograph- whole microorganisms and/or extracellular DNA (Ficetola ically and phylogenetically. et al. 2008). Community DNA also relies on metabarcod- DNA barcoding provides many benefits including ing; however, it is distinguished as “bulk organismal identification at a faster speed especially for routine samples”. The difference to eDNA is blurred in this case, monitoring and also for the discovery of new algal species especially when whole microorganisms are captured in which could be flagged faster (Saunders and Kucera eDNA samples (Ruppert et al. 2019). eDNA metabarcod- 2010). In addition,
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