---
title: "Algae DNA barcoding"
chunk: 1/3
source: "https://en.wikipedia.org/wiki/Algae_DNA_barcoding"
category: "reference"
tags: "science, encyclopedia"
date_saved: "2026-05-05T14:00:50.628340+00:00"
instance: "kb-cron"
---

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.

== Diatoms ==
Diatom DNA barcoding is a method for taxonomical identification of diatoms even to species level. It is conducted using DNA or RNA followed by amplification and sequencing of specific, conserved regions in the diatom genome followed by taxonomic assignment.
One of the main challenges of identifying diatoms is that it is often collected as a mixture of diatoms from several species. DNA metabarcoding is the process of identifying the individual species from a mixed sample of environmental DNA (also called eDNA) which is DNA extracted straight from the environment such as in soil or water samples.

A newly applied method is diatom DNA metabarcoding 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 morphology is relatively difficult and requires a lot of time and expertise, high-throughput sequencing (HTS) DNA metabarcoding enables taxonomic assignment and therefore identification for the complete sample regarding the group specific primers chosen for the previous DNA amplification.
Until now, several DNA markers have already been developed, mainly targeting the 18S rRNA. Using the V4 hypervariable region of the ribosomal small subunit DNA (SSU rDNA), DNA-based identification was found to be more efficient than the classical morphology-based approach. Other conserved regions in the genomes which are frequently used as marker genes are ribulose-1-5-bisphosphate carboxylase (rbcL), cytochrome oxidase I (cox1, COI), ITS and 28S. 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 invertebrates 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 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.

=== Advantages ===
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.
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 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.
DNA metabarcoding can also increase the taxonomic resolution 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 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.

=== Challenges ===