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DNA barcoding of algae

DNA barcoding of algae is commonly used for species identification and phylogenetic studies. Algae form a phylogenetically heterogeneous group, meaning that the application of a single universal barcode/marker for species delimitation is unfeasible, thus different markers/barcodes are applied for this aim in different algal groups.

Cyanobacteria
Cyanobacteria is a group of photosynthetic prokaryotes. Similar as in other prokaryotes (see Microbial DNA metabarcoding), taxonomy of cyanobacteria using DNA sequences is mostly based on similarity in 16S sequences. Thus, the most common barcode used for identification of cyanobacteria is 16S rDNA marker. While it is difficult to define species within prokaryotic organisms, 16S marker can be used for determining individual operation taxonomic units (OTUs). In some cases, these OTUs can also be linked to traditionally defined species and can therefore be considered a reliable representation of the evolutionary relationships.

However, when analysing a taxonomic structure or biodiversity of a whole cyanobacterial community (see Metabarcoding), it is more convenient to use markers more specific for cyanobacteria. Universal 16S bacterial primers have been used successfully to isolate cyanobacterial rDNA from environmental samples, but they also recover many bacterial sequences. For focusing only on cyanobacteria, we can use cyano-specific or phyto-specific 16S markers. A few sets of such primers have been tested for barcoding or metabarcoding of environmental samples and gave good results, screening out majority of non-photosynthetic or non-cyanobacterial organisms.

DNA barcoding of cyanobacteria can be applied in various ecological, evolutionary and taxonomical studies. Some of the examples include assessment of cyanobacterial diversity and community structure, identification of harmful cyanobacteria in ecologically and economically important water bodies and assessment of cyanobacterial symbionts in marine invertebrates.

Microalgae
Chlorophytes 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.

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 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).

Macroalgae
Macroalgae 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 DNA barcoding. The SSU rDNA 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.

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 cytochrome c oxidase subuinit 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 (internal transcribe spacer) are commonly used for green algae (3,8). These barcodes are typically 600-700 bp long.

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 polyphyletic, 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.