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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| Algae DNA barcoding | 3/3 | https://en.wikipedia.org/wiki/Algae_DNA_barcoding | reference | science, encyclopedia | 2026-05-05T14:00:50.628340+00:00 | kb-cron |
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 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). 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. 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.
==== Forensics ==== 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 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.
==== Cryptic species and databasing ==== 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.
== Other 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—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 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 subunit 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. 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 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.
== Target regions ==
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== See also == Detailed information on DNA barcoding of different organisms can be found here:
Microbial DNA barcoding DNA barcoding Fish DNA barcoding DNA barcoding in diet assessment
== References ==