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next-generation sequencing approach to river biomonitoring revealed a good potential in it. Many studies have shown that metabarcoding and HTS (high-throughput sequencing) can be utilized to estimate the quality status and diversity in freshwaters. As part of the
Environment Agency, Kelly et al. has developed a DNA-based metabarcoding approach to assess diatom communities in rivers for the UK. Vasselon et al. compared morphological and HTS approaches for diatoms and found that HTS gave a reliable indication of quality status for most rivers in terms of Specific Polluosensitivity Index (SPI). Vasselon et al. also applied DNA metabarcoding of diatoms communities to the monitoring network of rivers on the tropical Island Mayotte (French DOM-TOM).
458:
studies. One of the major limitation is the availability of reference barcodes for diatoms species. The reference database of bioindicator taxa is far from complete despite the constant efforts of numerous national barcoding initiatives a lot of species are still lacking barcode information. Furthermore, most existing metabarcoding data are only locally available and geographically scattered, which is hindering the development of globally useful tools. Visco et al. estimated that no more than 30% of
European diatoms species are currently represented in reference databases. For example, there is an important lack for a number of species from the Fennoscandian communities (especially acidophilic diatoms, such as
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environmental samples with HTS. and discusses its use and limitations for diatom identification. This fragment includes the V4 subunit which is the largest and most complex of the highly variable regions within the 18S locus. They highlighted that this hypervariable region of the 18S gene have great potential for studying protist diversity at large scale but has limited efficiency to identification below species level or cryptic species.
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complement or improve traditional methods. Stoeck et al. also showed that eDNA barcoding provides a more insight into diatom diversity or other protist communities and therefore could be used for ecological projection of global diversity. Other studies showed different results. For example, inventories obtained from the molecular-based method were closer to those obtained by the morphology-based method when abundant species are in focus.
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36:
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processes would be to compare the species list generated by different pipelines when using the same reference database. This has yet to be done for the variety of pipelines used in molecular assessment of diatom communities in Europe. Taxonomically validated databases, which includes accessible vouchers are also crucial for reliable taxa identification via NGS.
411:. It has been shown repeatedly that the molecular data gained by diatom eDNA metabarcoding quite faithfully reflect the morphology-based biotic diatom indices and therefore provide a similar assessment of ecosystem status. In the meantime, diatoms are routinely used for the assessment of ecological quality in other freshwater ecosystems. Together with aquatic
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stressors. Indirectly, the molecular methods can also help filling the gaps in knowledge of species ecology, by increasing the number of samples processed coupled with a decrease in processing time (cost-effectiveness), as well as by increasing the accuracy and precision of correlation between species/MOTUs occurrence and environmental factors.
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species with a success rate of 99.5%. Despite this amplification success, Zimmerman et al. criticised the use of ITS-2 due to intra-individual heterogeneity. It has been suggested that SSU or the rbcL (Mann et al., 2010) markers less heterogenous between individuals and therefore more beneficial when distinguishing between species.
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Almeida, Salomé F.P.; Elias, Carmen; Ferreira, João; Tornés, Elisabet; Puccinelli, Camilla; Delmas, François; Dörflinger, Gerald; Urbanič, Gorazd; Marcheggiani, Stefania (2014). "Water quality assessment of rivers using diatom metrics across
Mediterranean Europe: A methods intercalibration exercise".
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Several barcodes for chlorophytes have been proposed for DNA-based identification in order to bypass the problematics of the morphological one. Although the cytochrome oxidase I (COI, COX) coding gene (link) is a standard barcode for animals it proved to be unsatisfactory for chlorophytes because the
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Diatoms are used to as a diagnosis tool for drowning in forensic practices. The diatom test is based on the principle of diatom inhalation from water into the lungs and distribution and deposition around the body. DNA methods can be used to confirm if the cause of death was indeed drowning and locate
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The inference of abundance from metabarcoding data is considered as one of the most difficult issues in environmental use. The number of generated sequences by HTS does not directly correspond to the number of specimen or biomass and that different species can produce different amount of reads, (for
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Moniz and
Kaczmarska investigated the amplification success of the SSU, COI, and ITS2 markers and found that the 300 – 400 bp ITS-2 + 5.8S fragment provided the highest success rate of amplification and good species resolution. This marker was subsequently used to separate morphologically defined
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and comparability across geographic regions, which is often difficult using morphological characters only. Moreover, DNA-based identification allows extending the range of potential bioindicators, including the inconspicuous taxonomic groups that could be highly sensitive or tolerant to particular
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has a small biovolume, and thus will generate less copies of the rbcL fragment (located in the chloroplast) than larger species. This correction factor, however, requires extensive calibration with each species own biovolume and has been tested only on a few species that far. Fluctuations of gene
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Another well-known limitation of barcoding for taxonomic identification is the clustering method used before the taxonomic assignation: It often leads to massive loss of genetic information and the only reliable way to assess the effects of different clustering and different taxonomic assignation
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The rbcl gene is used for taxonomy studies (Trobajo et al. 2009) which benefits include that rarely any intragenomic variation and they are very easily aligned and compared. An open-access reference library, called R-Syst::diatom includes data for two barcodes (18S and rbcL). It is freely
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they are considered as the best indicators of disturbance related to physical, chemical or biological conditions of watercourses. Numerous studies are using benthic diatoms for biomonitoring. Because no ideal diatom DNA barcode was found, it has been proposed that different markers are used for
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Over the recent years, researchers have developed and standardised the tools for the metabarcoding and sequencing of diatoms, to complement the traditional assessment using microscopy, opening up a new avenue of biomonitoring for aquatic systems. Using benthic diatoms through a method of
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Diatoms are routinely used as part of a suite of biomonitoring tools which must be monitored as part of the
European Water Framework Directive. Diatoms are used as an indicator of ecosystem health in freshwaters because they are ubiquitous, directly affected by the changes in physico-chemical
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Currently there is no consensus concerning methods for DNA preservation and isolation, the choice of DNA barcodes and PCR primers, nor agreement concerning the parameters of MOTU clustering and their taxonomic assignment. Sampling and molecular steps need to be standardize through development
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Molecular methods based on the NGS technology almost always leads to a higher number of identified taxa whose presence could subsequently be verified by light microscopy. Results of this study provides evidence that eDNA barcoding of diatoms is suitable for water quality assessment and could
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possess an ancients and taxonomically very diverse lineage (Fang et al. 2014), including terrestrial plants too. Even though more than 14 000 species have been described based on structural and ultrastructural criteria (Hall et al. 2010) their morphological identification is often limited.
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The 18S gene region has been widely used as a marker in other protist groups and Jahn et al. were the first to test the 18S gene region for diatoms barcoding. Zimmerman et al. proposed a 390–410 bp long fragment of the 1800 bp long 18S rRNA gene locus as a barcode marker for the analysis of
622:—a morphological rather than taxonomic grouping—can be very challenging to identify because of their simple morphology, phenotypic plasticity and alternate lifecycle stages. Thus, algal systematics and identification have come to rely heavily on genetic/molecular tools such as
487:
Barcoding marker usually combine hypervariable regions of the genome (to allow the distinction between species) with very conserved region (to insure a specificity to the target organism). Several DNA markers, belonging to the nuclear, mitochondrial, and chloroplast genomes
395:. Using the V4 hypervariable region of the ribosomal small subunit DNA (SSU rDNA), DNA-based identification was found to be more efficient then the classical morphology based approach. Other conserved regions in the genomes which are frequently used as marker genes are
2837:
Valero, Myriam; KĂĽpper, Frithjof C.; Tsiamis, Konstantinos; Couceiro, LucĂa; Peters, Akira F. (2015). "Barcoding of
Cryptic Stages of Marine Brown Algae Isolated from Incubated Substratum Reveals High Diversity in Acinetosporaceae (Ectocarpales, Phaeophyceae)1".
574:
DNA barcoding and metabarcoding can be used to establish molecular metrics and indices, which potentially provide conclusions broadly similar to those of the traditional approaches about the ecological and environmental status of aquatic ecosystems.
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the origin of drowning. Diatom DNA metabarcoding, provides the opportunity to quickly analyse the diatom community present within a body and locate the origin of drowning and investigate if a body may have been moved from one place to another.
1952:
Evans, Katharine M.; Wortley, Alexandra H.; Mann, David G. (2007). "An
Assessment of Potential Diatom "Barcode" Genes (cox1, rbcL, 18S and ITS rDNA) and their Effectiveness in Determining Relationships in Sellaphora (Bacillariophyta)".
469:
Additionally, primer bias is often found to be a major source of variation in barcoding and PCR primers efficiency can differ between diatoms species, i.e. some primers lead to a preferential amplification of one taxon over another.
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Visco, Joana Amorim; Apothéloz-Perret-Gentil, Laure; Cordonier, Arielle; Esling, Philippe; Pillet, Loïc; Pawlowski, Jan (2015-07-07). "Environmental
Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data".
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Kermarrec, Lenaïg; Franc, Alain; Rimet, Frédéric; Chaumeil, Philippe; Frigerio, Jean-Marc; Humbert, Jean-François; Bouchez, Agnès (2014). "A next-generation sequencing approach to river biomonitoring using benthic diatoms".
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Kermarrec, L.; Franc, A.; Rimet, F.; Chaumeil, P.; Humbert, J. F.; Bouchez, A. (2013). "Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms".
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Apothéloz-Perret-Gentil, Laure; Cordonier, Arielle; Straub, François; Iseli, Jennifer; Esling, Philippe; Pawlowski, Jan (2017). "Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring".
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Vasselon, Valentin; Rimet, Frédéric; Tapolczai, Kálmán; Bouchez, Agnès (2017). "Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France)".
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Applying the DNA barcoding concept to diatoms promises great potential to resolve the problem of inaccurate species identification and thus facilitate analyses of the biodiversity of environmental samples.
416:
different purposes. Indeed, the highly variable cox1, ITS and 28S genes were considered more suitable for taxonomic studies, while more conserved 18S and rbcL genes seem more appropriate for biomonitoring.
570:
Rimet et al. also explored the possibility of using HTS for assessing diatom diversity and showed that diversity indices from both HTS and microscopic analysis were well correlated although not perfect.
592:
Diatom metabarcoding may help delimit cryptic species that are difficult to identify using microscopy and help complete reference databases by comparing morphological assemblages to metabarcoding data.
1446:
Martin, Gonzalo; Reyes
Fernandez, Maria de los (2012-05-16), Voudouris, Kostas (ed.), "Diatoms as Indicators of Water Quality and Ecological Status: Sampling, Analysis and Some Ecological Remarks",
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group, meaning that within the group they do not all share a recent common ancestor, making it challenging to find a gene that is conserved among all but variable enough for species identification.
1078:
Zimmermann, Jonas; Glöckner, Gernot; Jahn, Regine; Enke, Neela; Gemeinholzer, Birgit (2015). "Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies".
2758:
Harper, J.T.; Saunders, G.W. (2001). "The application of sequences of the ribosomal cistron to the systematics and classification of the florideophyte red algae (Florideophyceae, Rhodophyta)".
1827:
Edgar, Graham J.; Alexander, Timothy J.; Lefcheck, Jonathan S.; Bates, Amanda E.; Kininmonth, Stuart J.; Thomson, Russell J.; Duffy, J. Emmett; Costello, Mark J.; Stuart-Smith, Rick D. (2017).
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Rimet, Frédéric; Vasselon, Valentin; A.-Keszte, Barbara; Bouchez, Agnès (2018). "Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes".
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gene contains several introns in this algae group (Turmel et al. 2002). Nuclear marker genes have been used for chlorophytes are SSU rDNA, LSU rDNA, rDNA ITS (Leliaert et al. 2014).
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Saunders, Gary W.; McDevit, Daniel C. (2012), Kress, W. John; Erickson, David L. (eds.), "Methods for DNA Barcoding
Photosynthetic Protists Emphasizing the Macroalgae and Diatoms",
474:
example, due to differences in the chloroplast size with the rbcL marker). Vasselon et al. recently created a biovolume correction factor when using the rbcL marker. For example,
630:
gene is a common used barcode for phylogenetic studies on macroalgae. However, the SSU rDNA is a highly conserved region and typically lack resolution for species identification.
368:
which is used for ecological quality assessment of rivers and streams because of the specific response of diatoms to particular ecologic conditions. As species identification via
2061:
Utz, Laura R. P.; Eizirik, Eduardo (2007). "Molecular Phylogenetics of Subclass Peritrichia (Ciliophora: Oligohymenophorea) Based on Expanded Analyses of 18S rRNA Sequences".
530:
accessible through a website. Kermmarec et al. also successfully used the rbcL gene for ecological assessment of diatoms. The rbcL marker is also easily aligned and compared.
1010:
Stevenson, R. Jan; Pan, Yangdong; van Dam, Herman (2010), Smol, John P.; Stoermer, Eugene F. (eds.), "Assessing environmental conditions in rivers and streams with diatoms",
1221:
Zimmermann, Jonas; Jahn, Regine; Gemeinholzer, Birgit (2011). "Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols".
1892:
Vasselon, Valentin; Bouchez, Agnès; Rimet, Frédéric; Jacquet, Stéphan; Trobajo, Rosa; Corniquel, Méline; Tapolczai, Kálmán; Domaizon, Isabelle (2018). Mahon, Andrew (ed.).
1625:
Pawlowski, Jan; Kelly-Quinn, Mary; Altermatt, Florian; Apothéloz-Perret-Gentil, Laure; Beja, Pedro; Boggero, Angela; Borja, Angel; Bouchez, Agnès; Cordier, Tristan (2018).
462:). It has also been shown that taxonomic identification with DNA barcoding is not accurate above species level, to discriminate varieties for example (reference missing).
2545:
Seo, Yasuhisa; Ichida, Daisuke; Sato, Shingo; Kuroki, Kohji; Kishida, Tetsuko (2014). "An Improved Method for the Diatom Test Utilizing DNA Binding Ability of Silica".
978:
Lobo, Eduardo A.; Heinrich, Carla Giselda; Schuch, Marilia; Wetzel, Carlos Eduardo; Ector, Luc (2016), Necchi JR, Orlando (ed.), "Diatoms as Bioindicators in Rivers",
633:
Over the past 2 decades certain standards for DNA barcoding with the aim of species identification have been developed for each of the main groups of macroalgae. The
2706:
Leliaert, Frederik; Verbruggen, Heroen; Vanormelingen, Pieter; Steen, Frederique; LĂłpez-Bautista, Juan M.; Zuccarello, Giuseppe C.; De Clerck, Olivier (2014-04-03).
1557:
Stoeck, Thorsten; Behnke, Anke; Christen, Richard; Amaral-Zettler, Linda; Rodriguez-Mora, Maria J; Chistoserdov, Andrei; Orsi, William; Edgcomb, Virginia P (2009).
644:
The barcodes typically differ between the 3 main groups of macroalgae (red, green and brown) because their evolutionary heritage is very diverse. Macroalgae is a
2242:
Directive 2000/60/EC of the European Parliament and of the Council of 23 October 2000 establishing a framework for Community action in the field of water policy
1177:
Hamsher, Sarah E.; Evans, Katharine M.; Mann, David G.; PoulĂÄŤková, Aloisie; Saunders, Gary W. (2011). "Barcoding Diatoms: Exploring Alternatives to COI-5P".
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parameters and show a better relationship with environmental variables than other taxa e.g. invertebrates, giving a better overall picture of water quality.
1792:
Shaw, Jennifer L. A.; Weyrich, Laura; Cooper, Alan (2017). "Using environmental (e)DNA sequencing for aquatic biodiversity surveys: a beginner's guide".
637:
I (COI) gene is commonly used as a barcode for red and brown algae, while tufA (plastid elongation factor), rbcL (rubisco large subunit) and ITS (
251:
87:
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Saunders, Gary W.; Kucera, Hana (2010). "An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae".
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Hering, Daniel; Borja, Angel; Jones, J.Iwan; Pont, Didier; Boets, Pieter; Bouchez, Agnes; Bruce, Kat; Drakare, Stina; Hänfling, Bernd (2018).
118:
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Zimmermann, Jonas; Abarca, Nelida; Enk, Neela; Skibbe, Oliver; Kusber, Wolf-Henning; Jahn, Regine (2014-09-29). Schierwater, Bernd (ed.).
2779:"On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocol"
376:(HTS) DNA metabarcoding enables taxonomic assignment and therefore identification for the complete sample regarding the group specific
205:
1627:"The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems"
2901:
2492:"Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive"
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2135:
1894:"Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring"
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One of the main challenges of identifying diatoms is that it is often collected as a mixture of diatoms from several species. DNA
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copy number for other markers, such as the 18S marker, does not seem to be species specific, but have not been tested yet.
2368:"Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?"
1509:"Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?"
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Rimet, Frédéric; Bouchez, Agnès (2012). "Biomonitoring river diatoms: Implications of taxonomic resolution".
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351:(also called eDNA) which is DNA extracted straight from the environment such as in soil or water samples.
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224:
2648:"Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications"
1727:"Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research"
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Lavoie, Isabelle; Campeau, Stéphane; Darchambeau, François; Cabana, Gilbert; Dillon, Peter J. (2008).
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1991:
Moniz, MĂłnica B.J.; Kaczmarska, Irena (2010). "Barcoding of Diatoms: Nuclear Encoded ITS Revisited".
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Scicluna, Stephanie M.; Tawari, Blessing; Clark, C. Graham (2006). "DNA Barcoding of Blastocystis".
1829:"Abundance and local-scale processes contribute to multi-phyla gradients in global marine diversity"
1559:"Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities"
2153:"An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA"
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Vasselon, Valentin; Domaizon, Isabelle; Rimet, Frédéric; Kahlert, Maria; Bouchez, Agnès (2017).
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Vasselon, Valentin; Domaizon, Isabelle; Rimet, Frédéric; Kahlert, Maria; Bouchez, Agnès (2017).
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Pawlowski, J.; Lejzerowicz, F.; Apotheloz-Perret-Gentil, L.; Visco, J.; Esling, P. (2016).
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512:...), have been designed and successfully used for diatoms identification with NGS.
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641:) are commonly used for green algae. These barcodes are typically 600-700 bp long.
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2004:
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Detailed information on DNA barcoding of different organisms can be found here:
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heterogeneous group, meaning that the application of a single universal barcode/
2888:, Methods in Molecular Biology, vol. 858, Humana Press, pp. 207–222,
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1391:"Are diatoms good integrators of temporal variability in stream water quality?"
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Rimet, Frédéric (2012-03-01). "Recent views on river pollution and diatoms".
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Taberlet, Pierre; Bonin, Aurélie; Zinger, Lucie; Coissac, Eric (2018-03-22).
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is the process of identifying the individual species from a mixed sample of
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1310:"Protist metabarcoding and environmental biomonitoring: Time for change"
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Philosophical Transactions of the Royal Society B: Biological Sciences
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2114:"Diatoms and DNA barcoding: a pilot study on an environmental sample"
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is relatively difficult and requires a lot of time and expertise,
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Technique used for species identification and phylogenetic studies
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Baldauf, S. L. (2003-06-13). "The Deep Roots of Eukaryotes".
2120:. Botanic Garden and Botanical Museum Berlin-Dahlem: 63–68.
2118:
Proceedings of the 1st Central European Diatom Meeting 2007
2208:
Wilde, Erik (1999), "Hypertext Transfer Protocol (HTTP)",
1014:(2 ed.), Cambridge University Press, pp. 57–85,
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1071:
2879:
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982:, Springer International Publishing, pp. 245–271,
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1448:
Ecological Water Quality - Water Treatment and Reuse
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are applied for this aim in different algal groups.
2442:
2440:
1986:
1984:
391:have already been developed, mainly targeting the
2151:Nickrent, Daniel L.; Sargent, Malcolm L. (1991).
543:Genetic tool for biomonitoring and bioassessment
274:is commonly used for species identification and
2212:, Springer Berlin Heidelberg, pp. 53–135,
2777:McDevit, Daniel C.; Saunders, Gary W. (2009).
308:is a method for taxonomical identification of
703:Phycoerythrin, elongation factor, LSU rDNA
290:for species delimitation is unfeasible, thus
245:
8:
252:
238:
18:
2794:
2731:
2708:"DNA-based species delimitation in algae"
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1422:
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1046:. Vol. 1. Oxford University Press.
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432:DNA metabarcoding can also increase the
970:
908:Nuclear rDNA ITS, nucleomorph rDNA ITS
103:
55:
26:
2063:The Journal of Eukaryotic Microbiology
1676:Environmental Science & Technology
2753:
2751:
2701:
2699:
1620:
1618:
1616:
1614:
1612:
860:SSU rDNA, LSU rDNA, rDNA, rDNA ITS
836:SSU rDNA, LSU rDNA, rDNA, rDNA ITS
397:ribulose-1-5-bisphosphate carboxylase
7:
2590:"A DNA mini-barcode for land plants"
1216:
1214:
1212:
1210:
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1172:
1170:
1125:
1123:
1121:
1119:
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2449:Organisms Diversity & Evolution
1223:Organisms Diversity & Evolution
291:
1052:10.1093/oso/9780198767220.001.0001
340:followed by taxonomic assignment.
206:Consortium for the Barcode of Life
14:
364:A newly applied method is diatom
2796:10.1111/j.1440-1835.2009.00530.x
2075:10.1111/j.1550-7408.2007.00260.x
1901:Methods in Ecology and Evolution
1634:Science of the Total Environment
1415:10.1111/j.1365-2427.2007.01935.x
1352:Science of the Total Environment
1314:European Journal of Protistology
959:DNA barcoding in diet assessment
752:Chrysophytes and Synurophytes
219:
218:
34:
2646:Saunders, Gary W (2005-10-29).
2588:Little, Damon P. (2013-11-29).
1651:10.1016/j.scitotenv.2018.05.002
1368:10.1016/j.scitotenv.2013.11.144
796:SSU rDNA, LSU rDNA, rDNA ITS
779:SSU rDNA, LSU rDNA, rDNA ITS
683:SSU rDNA, LSU rDNA, rDNA ITS
1794:Marine and Freshwater Research
588:Cryptic species and databasing
1:
2712:European Journal of Phycology
2431:10.1016/j.ecolind.2017.06.024
1494:10.1016/j.ecolind.2011.09.014
316:level. It is conducted using
2894:10.1007/978-1-61779-591-6_10
2852:10.7872/crya.v36.iss1.2015.3
2733:10.1080/09670262.2014.904524
2547:Journal of Forensic Sciences
2516:10.1016/j.watres.2018.03.003
2245:, vol. OJ L, 2000-12-22
2040:10.1016/j.protis.2005.12.001
2005:10.1016/j.protis.2009.07.001
1967:10.1016/j.protis.2007.04.001
1752:10.1371/journal.pone.0108793
1191:10.1016/j.protis.2010.09.005
1020:10.1017/cbo9780511763175.005
988:10.1007/978-3-319-31984-1_11
635:cytochrome c oxidase subunit
380:chosen for the previous DNA
2594:Molecular Ecology Resources
2308:Molecular Ecology Resources
2218:10.1007/978-3-642-95855-7_4
1267:Molecular Ecology Resources
1080:Molecular Ecology Resources
3021:
2760:Cahiers de Biologie Marine
1327:10.1016/j.ejop.2016.02.003
639:internal transcribe spacer
476:Achnanthidium minutissimum
374:high-throughput sequencing
292:different markers/barcodes
176:High throughput sequencing
2461:10.1007/s13127-018-0359-5
2276:10.1007/s10750-011-0949-0
1235:10.1007/s13127-011-0050-6
661:
559:in biological assessment
113:Environmental DNA (eDNA)
2946:10.1126/science.1085544
2606:10.1111/1755-0998.12194
2559:10.1111/1556-4029.12390
2320:10.1111/1755-0998.12105
2112:Jahn, R. (2007-12-11).
1921:10.1111/2041-210X.12960
1279:10.1111/1755-0998.12668
1092:10.1111/1755-0998.12336
944:Microbial DNA barcoding
387:Until now, several DNA
2990:Authentication methods
2840:Cryptogamie, Algologie
2664:10.1098/rstb.2005.1719
2157:Nucleic Acids Research
1853:10.1126/sciadv.1700419
1636:. 637–638: 1295–1310.
1576:10.1186/1741-7007-7-72
563:
454:
361:
2820:Cryptogamie Algologie
2783:Phycological Research
2419:Ecological Indicators
1482:Ecological Indicators
925:SSU rDNA, LSU rDNA
920:SSU rDNA, LSU rDNA
816:LSU rDNA, rDNA ITS
755:SSU rDNA, rDNA ITS
561:of aquatic ecosystems
554:
483:Diatom target regions
448:
357:
2169:10.1093/nar/19.2.227
2127:10.3372/cediatom.113
1354:. 476–477: 768–776.
905:Chlorarachniophytes
719:L, Rubisco spacer
434:taxonomic resolution
401:cytochrome oxidase I
359:Diatom DNA barcoding
2938:2003Sci...300.1703B
2932:(5626): 1703–1706.
2724:2014EJPhy..49..179L
2658:(1462): 1879–1888.
2508:2018WatRe.138..192H
1913:2018MEcEv...9.1060V
1845:2017SciA....3E0419E
1743:2014PLoSO...9j8793Z
1688:2015EnST...49.7597V
1642:2018ScTEn.637.1295P
1407:2008FrBio..53..827L
1360:2014ScTEn.476..768A
146:Metatranscriptomics
22:Part of a series on
3000:Taxonomy (biology)
2375:Freshwater Science
1516:Freshwater Science
1395:Freshwater Biology
1133:Freshwater Science
954:Fish DNA barcoding
747:L, Rubisco spacer
659:Taxonomic group
564:
557:eDNA metabarcoding
516:18S and V4 subunit
455:
362:
171:Shotgun sequencing
88:macroinvertebrates
1696:10.1021/es506158m
1682:(13): 7597–7605.
1044:Environmental DNA
929:
928:
828:PsbA, 23S rDNA
793:Bacillariophytes
788:Rubisco spacer
451:Diatom morphology
366:DNA metabarcoding
349:environmental DNA
334:conserved regions
262:
261:
185:Extracellular RNA
119:environmental RNA
3012:
2974:
2973:
2921:
2915:
2914:
2881:
2872:
2871:
2834:
2828:
2827:
2815:
2809:
2808:
2798:
2774:
2768:
2767:
2755:
2746:
2745:
2735:
2703:
2694:
2693:
2683:
2643:
2634:
2633:
2585:
2579:
2578:
2542:
2536:
2535:
2487:
2481:
2480:
2444:
2435:
2434:
2413:
2407:
2406:
2372:
2363:
2357:
2356:
2354:
2346:
2340:
2339:
2302:
2296:
2295:
2259:
2253:
2252:
2251:
2250:
2237:
2231:
2230:
2205:
2199:
2198:
2188:
2148:
2142:
2141:
2129:
2109:
2103:
2102:
2058:
2052:
2051:
2023:
2017:
2016:
1988:
1979:
1978:
1949:
1943:
1942:
1932:
1930:20.500.12327/161
1907:(4): 1060–1069.
1898:
1889:
1883:
1882:
1872:
1839:(10): e1700419.
1833:Science Advances
1824:
1818:
1817:
1789:
1783:
1782:
1772:
1754:
1722:
1716:
1715:
1670:
1664:
1663:
1653:
1631:
1622:
1607:
1606:
1596:
1578:
1554:
1548:
1547:
1513:
1504:
1498:
1497:
1477:
1471:
1470:
1459:
1443:
1437:
1436:
1426:
1386:
1380:
1379:
1346:
1340:
1339:
1329:
1305:
1299:
1298:
1273:(6): 1231–1242.
1261:
1255:
1254:
1218:
1203:
1202:
1174:
1165:
1164:
1127:
1112:
1111:
1075:
1066:
1065:
1039:
1033:
1032:
1007:
1001:
1000:
975:
656:
599:Other Microalgae
284:phylogenetically
254:
247:
240:
227:
222:
221:
38:
19:
3020:
3019:
3015:
3014:
3013:
3011:
3010:
3009:
2980:
2979:
2978:
2977:
2923:
2922:
2918:
2904:
2883:
2882:
2875:
2836:
2835:
2831:
2817:
2816:
2812:
2776:
2775:
2771:
2757:
2756:
2749:
2705:
2704:
2697:
2645:
2644:
2637:
2587:
2586:
2582:
2544:
2543:
2539:
2489:
2488:
2484:
2446:
2445:
2438:
2415:
2414:
2410:
2370:
2365:
2364:
2360:
2352:
2348:
2347:
2343:
2304:
2303:
2299:
2261:
2260:
2256:
2248:
2246:
2239:
2238:
2234:
2228:
2207:
2206:
2202:
2150:
2149:
2145:
2138:
2111:
2110:
2106:
2060:
2059:
2055:
2025:
2024:
2020:
1990:
1989:
1982:
1951:
1950:
1946:
1896:
1891:
1890:
1886:
1826:
1825:
1821:
1806:10.1071/MF15361
1791:
1790:
1786:
1724:
1723:
1719:
1672:
1671:
1667:
1629:
1624:
1623:
1610:
1556:
1555:
1551:
1511:
1506:
1505:
1501:
1479:
1478:
1474:
1468:
1445:
1444:
1440:
1388:
1387:
1383:
1348:
1347:
1343:
1320:(Pt A): 12–25.
1307:
1306:
1302:
1263:
1262:
1258:
1220:
1219:
1206:
1176:
1175:
1168:
1129:
1128:
1115:
1077:
1076:
1069:
1062:
1041:
1040:
1036:
1030:
1009:
1008:
1004:
998:
977:
976:
972:
967:
937:
654:
617:
601:
590:
581:
562:
560:
545:
540:
527:
518:
485:
453:
443:
422:
360:
300:
264:
258:
217:
210:
201:Diet assessment
192:
180:
166:
150:
141:
125:
115:
99:
51:
49:
41:
17:
12:
11:
5:
3018:
3016:
3008:
3007:
3002:
2997:
2995:Bioinformatics
2992:
2982:
2981:
2976:
2975:
2916:
2902:
2873:
2829:
2810:
2789:(2): 131–141.
2769:
2747:
2718:(2): 179–196.
2695:
2635:
2600:(3): 437–446.
2580:
2553:(3): 779–784.
2537:
2496:Water Research
2482:
2436:
2408:
2387:10.1086/690649
2381:(1): 162–177.
2358:
2341:
2314:(4): 607–619.
2297:
2254:
2232:
2226:
2200:
2163:(2): 227–235.
2143:
2136:
2104:
2069:(3): 303–305.
2053:
2018:
1980:
1961:(3): 349–364.
1944:
1884:
1819:
1784:
1737:(9): e108793.
1717:
1665:
1608:
1549:
1528:10.1086/690649
1522:(1): 162–177.
1499:
1472:
1466:
1438:
1401:(4): 827–841.
1381:
1341:
1300:
1256:
1229:(3): 173–192.
1204:
1185:(3): 405–422.
1166:
1145:10.1086/675079
1139:(1): 349–363.
1113:
1086:(3): 526–542.
1067:
1060:
1034:
1028:
1002:
996:
969:
968:
966:
963:
962:
961:
956:
951:
946:
936:
933:
931:Adapted from
927:
926:
923:
921:
918:
917:Euglenophytes
914:
913:
911:
909:
906:
902:
901:
887:
885:
882:
878:
877:
867:
861:
858:
857:Raphidophytes
854:
853:
847:
837:
834:
830:
829:
826:
817:
814:
810:
809:
803:
797:
794:
790:
789:
786:
780:
777:
773:
772:
762:
756:
753:
749:
748:
738:
728:
725:
721:
720:
714:
704:
701:
697:
696:
686:
684:
681:
677:
676:
675:chloroplastid
673:
672:mitochondrial
670:
667:
664:
663:
660:
653:
652:Target regions
650:
616:
613:
600:
597:
589:
586:
580:
577:
555:
544:
541:
539:
536:
526:
523:
517:
514:
484:
481:
460:Eunotia incisa
449:
442:
439:
421:
418:
358:
336:in the diatom
299:
296:
260:
259:
257:
256:
249:
242:
234:
231:
230:
229:
228:
212:
211:
209:
208:
203:
198:
193:
187:
181:
179:
178:
173:
167:
165:
164:
163:
162:
151:
149:
148:
142:
140:
139:
138:
137:
126:
124:
123:
122:
121:
109:
106:
105:
101:
100:
98:
97:
96:
95:
90:
82:
77:
72:
67:
61:
58:
57:
53:
52:
39:
31:
30:
24:
23:
15:
13:
10:
9:
6:
4:
3:
2:
3017:
3006:
3005:DNA barcoding
3003:
3001:
2998:
2996:
2993:
2991:
2988:
2987:
2985:
2971:
2967:
2963:
2959:
2955:
2951:
2947:
2943:
2939:
2935:
2931:
2927:
2920:
2917:
2913:
2909:
2905:
2903:9781617795909
2899:
2895:
2891:
2887:
2880:
2878:
2874:
2869:
2865:
2861:
2857:
2853:
2849:
2845:
2841:
2833:
2830:
2825:
2821:
2814:
2811:
2806:
2802:
2797:
2792:
2788:
2784:
2780:
2773:
2770:
2766:(1/2): 25–38.
2765:
2761:
2754:
2752:
2748:
2743:
2739:
2734:
2729:
2725:
2721:
2717:
2713:
2709:
2702:
2700:
2696:
2691:
2687:
2682:
2677:
2673:
2669:
2665:
2661:
2657:
2653:
2649:
2642:
2640:
2636:
2631:
2627:
2623:
2619:
2615:
2611:
2607:
2603:
2599:
2595:
2591:
2584:
2581:
2576:
2572:
2568:
2564:
2560:
2556:
2552:
2548:
2541:
2538:
2533:
2529:
2525:
2521:
2517:
2513:
2509:
2505:
2501:
2497:
2493:
2486:
2483:
2478:
2474:
2470:
2466:
2462:
2458:
2454:
2450:
2443:
2441:
2437:
2432:
2428:
2424:
2420:
2412:
2409:
2404:
2400:
2396:
2392:
2388:
2384:
2380:
2376:
2369:
2362:
2359:
2351:
2350:"Kelly et al"
2345:
2342:
2337:
2333:
2329:
2325:
2321:
2317:
2313:
2309:
2301:
2298:
2293:
2289:
2285:
2281:
2277:
2273:
2269:
2265:
2264:Hydrobiologia
2258:
2255:
2244:
2243:
2236:
2233:
2229:
2227:9783642958571
2223:
2219:
2215:
2211:
2204:
2201:
2196:
2192:
2187:
2182:
2178:
2174:
2170:
2166:
2162:
2158:
2154:
2147:
2144:
2139:
2137:9783921800638
2133:
2128:
2123:
2119:
2115:
2108:
2105:
2100:
2096:
2092:
2088:
2084:
2080:
2076:
2072:
2068:
2064:
2057:
2054:
2049:
2045:
2041:
2037:
2033:
2029:
2022:
2019:
2014:
2010:
2006:
2002:
1998:
1994:
1987:
1985:
1981:
1976:
1972:
1968:
1964:
1960:
1956:
1948:
1945:
1940:
1936:
1931:
1926:
1922:
1918:
1914:
1910:
1906:
1902:
1895:
1888:
1885:
1880:
1876:
1871:
1866:
1862:
1858:
1854:
1850:
1846:
1842:
1838:
1834:
1830:
1823:
1820:
1815:
1811:
1807:
1803:
1799:
1795:
1788:
1785:
1780:
1776:
1771:
1766:
1762:
1758:
1753:
1748:
1744:
1740:
1736:
1732:
1728:
1721:
1718:
1713:
1709:
1705:
1701:
1697:
1693:
1689:
1685:
1681:
1677:
1669:
1666:
1661:
1657:
1652:
1647:
1643:
1639:
1635:
1628:
1621:
1619:
1617:
1615:
1613:
1609:
1604:
1600:
1595:
1590:
1586:
1582:
1577:
1572:
1568:
1564:
1560:
1553:
1550:
1545:
1541:
1537:
1533:
1529:
1525:
1521:
1517:
1510:
1503:
1500:
1495:
1491:
1487:
1483:
1476:
1473:
1469:
1467:9789535105084
1463:
1458:
1457:10.5772/33831
1453:
1449:
1442:
1439:
1434:
1430:
1425:
1420:
1416:
1412:
1408:
1404:
1400:
1396:
1392:
1385:
1382:
1377:
1373:
1369:
1365:
1361:
1357:
1353:
1345:
1342:
1337:
1333:
1328:
1323:
1319:
1315:
1311:
1304:
1301:
1296:
1292:
1288:
1284:
1280:
1276:
1272:
1268:
1260:
1257:
1252:
1248:
1244:
1240:
1236:
1232:
1228:
1224:
1217:
1215:
1213:
1211:
1209:
1205:
1200:
1196:
1192:
1188:
1184:
1180:
1173:
1171:
1167:
1162:
1158:
1154:
1150:
1146:
1142:
1138:
1134:
1126:
1124:
1122:
1120:
1118:
1114:
1109:
1105:
1101:
1097:
1093:
1089:
1085:
1081:
1074:
1072:
1068:
1063:
1061:9780198767220
1057:
1053:
1049:
1045:
1038:
1035:
1031:
1029:9780511763175
1025:
1021:
1017:
1013:
1006:
1003:
999:
997:9783319319834
993:
989:
985:
981:
974:
971:
964:
960:
957:
955:
952:
950:
949:DNA barcoding
947:
945:
942:
941:
940:
934:
932:
924:
922:
919:
916:
915:
912:
910:
907:
904:
903:
899:
895:
891:
888:
886:
883:
881:Xanthophytes
880:
879:
875:
871:
868:
865:
862:
859:
856:
855:
851:
848:
845:
841:
838:
835:
832:
831:
827:
825:
821:
818:
815:
812:
811:
807:
804:
801:
798:
795:
792:
791:
787:
784:
781:
778:
776:Cryptophytes
775:
774:
770:
766:
763:
760:
757:
754:
751:
750:
746:
742:
739:
736:
732:
729:
726:
723:
722:
718:
715:
712:
708:
705:
702:
699:
698:
694:
690:
687:
685:
682:
680:Chlorophytes
679:
678:
674:
671:
668:
666:
665:
658:
657:
651:
649:
647:
642:
640:
636:
631:
629:
625:
624:DNA barcoding
621:
614:
612:
608:
605:
598:
596:
595:
587:
585:
578:
576:
572:
568:
558:
553:
549:
542:
537:
535:
531:
524:
522:
515:
513:
511:
507:
503:
499:
495:
491:
482:
480:
477:
471:
467:
463:
461:
452:
447:
440:
438:
435:
430:
426:
419:
417:
414:
413:invertebrates
410:
406:
403:(cox1, COI),
402:
398:
394:
390:
385:
383:
382:amplification
379:
375:
371:
367:
356:
352:
350:
346:
345:metabarcoding
341:
339:
335:
332:of specific,
331:
327:
326:amplification
323:
319:
315:
311:
307:
306:
305:DNA barcoding
297:
295:
293:
289:
285:
281:
277:
273:
272:
268:
267:DNA barcoding
255:
250:
248:
243:
241:
236:
235:
233:
232:
226:
216:
215:
214:
213:
207:
204:
202:
199:
197:
194:
191:
188:
186:
183:
182:
177:
174:
172:
169:
168:
161:
158:
157:
156:
155:Amplification
153:
152:
147:
144:
143:
136:
133:
132:
131:
128:
127:
120:
117:
116:
114:
111:
110:
108:
107:
102:
94:
91:
89:
86:
85:
83:
81:
78:
76:
73:
71:
68:
66:
63:
62:
60:
59:
54:
48:
47:Metabarcoding
44:
43:DNA barcoding
37:
33:
32:
29:
28:DNA barcoding
25:
21:
20:
2929:
2925:
2919:
2886:DNA Barcodes
2885:
2843:
2839:
2832:
2823:
2819:
2813:
2786:
2782:
2772:
2763:
2759:
2715:
2711:
2655:
2651:
2597:
2593:
2583:
2550:
2546:
2540:
2499:
2495:
2485:
2455:(1): 51–62.
2452:
2448:
2422:
2418:
2411:
2378:
2374:
2361:
2344:
2311:
2307:
2300:
2267:
2263:
2257:
2247:, retrieved
2241:
2235:
2209:
2203:
2160:
2156:
2146:
2117:
2107:
2066:
2062:
2056:
2034:(1): 77–85.
2031:
2027:
2021:
1996:
1992:
1958:
1954:
1947:
1904:
1900:
1887:
1836:
1832:
1822:
1797:
1793:
1787:
1734:
1730:
1720:
1679:
1675:
1668:
1633:
1566:
1562:
1552:
1519:
1515:
1502:
1488:(1): 92–99.
1485:
1481:
1475:
1447:
1441:
1398:
1394:
1384:
1351:
1344:
1317:
1313:
1303:
1270:
1266:
1259:
1226:
1222:
1182:
1178:
1136:
1132:
1083:
1079:
1043:
1037:
1011:
1005:
979:
973:
938:
930:
897:
893:
889:
873:
869:
863:
849:
843:
839:
833:Haptophytes
823:
819:
805:
799:
782:
768:
764:
758:
744:
740:
734:
730:
724:Phaeophytes
716:
710:
706:
700:Rhodophytes
692:
688:
662:Marker gene
646:polyphyletic
643:
632:
618:
609:
604:Chlorophytes
602:
593:
591:
582:
573:
569:
565:
546:
538:Applications
532:
528:
519:
486:
475:
472:
468:
464:
459:
456:
431:
427:
423:
386:
363:
342:
324:followed by
302:
301:
276:phylogenetic
265:
263:
130:Metagenomics
79:
2846:(1): 3–29.
2502:: 192–205.
2270:(1): 1–24.
2210:Wilde's WWW
1999:(1): 7–34.
1563:BMC Biology
1012:The Diatoms
980:River Algae
813:Dinophytes
713:2-3 spacer
2984:Categories
2249:2019-03-28
1450:, InTech,
1424:2268/62412
965:References
620:Macroalgae
615:Macroalgae
441:Challenges
420:Advantages
370:morphology
330:sequencing
196:Healthcare
2954:0036-8075
2860:0181-1568
2742:0967-0262
2672:0962-8436
2614:1755-098X
2469:1439-6092
2395:2161-9549
2284:1573-5117
2177:0305-1048
2083:1066-5234
1861:2375-2548
1814:1323-1650
1800:(1): 20.
1761:1932-6203
1704:0013-936X
1585:1741-7007
1569:(1): 72.
1536:2161-9549
1433:0046-5070
1295:206947826
1243:1439-6092
1153:2161-9549
900:L spacer
884:RDNA ITS
727:RDNA ITS
579:Forensics
278:studies.
65:Microbial
2970:32788100
2962:12805537
2912:22684958
2868:84276804
2805:84811166
2690:16214745
2630:32631697
2622:24286499
2567:24502836
2524:29602086
2425:: 1–12.
2403:59043627
2328:23590277
2292:18668007
2099:31422075
2091:17552986
2048:16431158
2013:19674931
1975:17581782
1939:54010645
1879:29057321
1779:25265556
1731:PLOS ONE
1712:26052741
1660:29801222
1603:19886985
1544:59043627
1376:24342490
1336:27004417
1287:28296259
1251:39047583
1199:21239228
1161:85771495
1108:27291997
1100:25270047
935:See also
669:nuclear
628:SSU rDNA
399:(rbcL),
393:18S rRNA
312:even to
225:Category
84:Aquatic
2934:Bibcode
2926:Science
2720:Bibcode
2681:1609223
2575:1057761
2532:5008250
2504:Bibcode
2477:3879922
2336:2706722
2195:2014163
2028:Protist
1993:Protist
1955:Protist
1909:Bibcode
1870:5647131
1841:Bibcode
1770:4180937
1739:Bibcode
1684:Bibcode
1638:Bibcode
1594:2777867
1403:Bibcode
1356:Bibcode
1179:Protist
874:, rbc
389:markers
378:primers
314:species
310:diatoms
303:Diatom
298:Diatoms
282:form a
190:Chimera
135:viruses
56:By taxa
40:
2968:
2960:
2952:
2910:
2900:
2866:
2858:
2803:
2740:
2688:
2678:
2670:
2628:
2620:
2612:
2573:
2565:
2530:
2522:
2475:
2467:
2401:
2393:
2334:
2326:
2290:
2282:
2224:
2193:
2186:333584
2183:
2175:
2134:
2097:
2089:
2081:
2046:
2011:
1973:
1937:
1877:
1867:
1859:
1812:
1777:
1767:
1759:
1710:
1702:
1658:
1601:
1591:
1583:
1542:
1534:
1464:
1431:
1374:
1334:
1293:
1285:
1249:
1241:
1197:
1159:
1151:
1106:
1098:
1058:
1026:
994:
626:. The
594:
338:genome
288:marker
223:
75:Pollen
70:Fungal
50:
2966:S2CID
2864:S2CID
2801:S2CID
2626:S2CID
2571:S2CID
2528:S2CID
2473:S2CID
2399:S2CID
2371:(PDF)
2353:(PDF)
2332:S2CID
2288:S2CID
2095:S2CID
1935:S2CID
1897:(PDF)
1630:(PDF)
1540:S2CID
1512:(PDF)
1291:S2CID
1247:S2CID
1157:S2CID
1104:S2CID
892:L,
822:1,
767:A,
743:A,
733:1,
709:1,
691:A,
280:Algae
271:algae
104:Other
80:Algae
2958:PMID
2950:ISSN
2908:PMID
2898:ISBN
2856:ISSN
2826:(4).
2738:ISSN
2686:PMID
2668:ISSN
2618:PMID
2610:ISSN
2563:PMID
2520:PMID
2465:ISSN
2391:ISSN
2324:PMID
2280:ISSN
2222:ISBN
2191:PMID
2173:ISSN
2132:ISBN
2087:PMID
2079:ISSN
2044:PMID
2009:PMID
1971:PMID
1875:PMID
1857:ISSN
1810:ISSN
1775:PMID
1757:ISSN
1708:PMID
1700:ISSN
1656:PMID
1599:PMID
1581:ISSN
1532:ISSN
1462:ISBN
1429:ISSN
1372:PMID
1332:PMID
1283:PMID
1239:ISSN
1195:PMID
1149:ISSN
1096:PMID
1056:ISBN
1024:ISBN
992:ISBN
525:rbcL
502:5.8S
490:rbcL
407:and
328:and
93:fish
2942:doi
2930:300
2890:doi
2848:doi
2791:doi
2728:doi
2676:PMC
2660:doi
2656:360
2602:doi
2555:doi
2512:doi
2500:138
2457:doi
2427:doi
2383:doi
2316:doi
2272:doi
2268:683
2214:doi
2181:PMC
2165:doi
2122:doi
2071:doi
2036:doi
2032:157
2001:doi
1997:161
1963:doi
1959:158
1925:hdl
1917:doi
1865:PMC
1849:doi
1802:doi
1765:PMC
1747:doi
1692:doi
1646:doi
1589:PMC
1571:doi
1524:doi
1490:doi
1452:doi
1419:hdl
1411:doi
1364:doi
1322:doi
1275:doi
1231:doi
1187:doi
1183:162
1141:doi
1088:doi
1048:doi
1016:doi
984:doi
898:rbc
894:psb
890:Rbc
870:psa
864:cox
850:tuf
844:atp
842:1b-
840:cox
824:cob
820:cox
806:rbc
800:cox
783:cox
769:rbc
765:psa
759:cox
745:rbc
741:psb
735:cox
731:cox
717:rbc
711:cox
707:cox
693:rbc
689:tuf
510:18S
506:SSU
498:ITS
494:COI
409:28S
405:ITS
322:RNA
320:or
318:DNA
269:of
160:PCR
2986::
2964:.
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2940:.
2928:.
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2822:.
2799:.
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