What makes a gene a good choice for barcoding?

What makes a gene a good choice for barcoding?

To be practical as a DNA barcode a gene region must satisfy three criteria: (i) contain significant species-level genetic variability and divergence, (ii) possess conserved flanking sites for developing universal PCR primers for wide taxonomic application, and (iii) have a short sequence length so as to facilitate …

What genes are used for DNA barcoding?

The most commonly used barcode region for animals and some protists is a portion of the cytochrome c oxidase I (COI or COX1) gene, found in mitochondrial DNA. Other genes suitable for DNA barcoding are the internal transcribed spacer (ITS) rRNA often used for fungi and RuBisCO used for plants.

How do you generate a barcode for a fish?

The process of generating DNA barcodes suitable for species identification from an unknown fish tissue sample can be broken down into the following steps:

1. Tissue Sampling.
2. Tissue Lysis and DNA Extraction.
3. Polymerase Chain Reaction – COI Amplification.
4. PCR Cleanup.
5. Cycle Sequencing Reaction.
6. Sequencing Reaction Cleanup.

Why is the CO1 gene used for DNA barcoding?

The CO1 gene is present in most eukaryotes. This gene is highly conserved across species where energy is generated from mitochondria. Because the gene is highly conserved, it can be copied from unknown organisms.

What does the cox1 gene do?

Use in DNA barcoding MT-CO1 is a gene that is often used as a DNA barcode to identify animal species. The MT-CO1 gene sequence is suitable for this role because its mutation rate is often fast enough to distinguish closely related species and also because its sequence is conserved among conspecifics.

What is the role of the cox1 protein in an organism?

Molecular function for MT-CO1 Gene UniProtKB/Swiss-Prot Function: Component of the cytochrome c oxidase, the last enzyme in the mitochondrial electron transport chain which drives oxidative phosphorylation. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water.

How is DNA barcoding used in a particular field?

Over the last decade the field of DNA barcoding has emerged as a molecular method for species identification. DNA barcoding relies on a uniform region of the mitochondrial gene being amplified, sequenced, and analyzed by comparison to an open access database.

Why is COI used for barcoding animal?

A region of the mitochondrial gene COI (cytochrome c oxidase subunit I) is used for barcoding animals. COI is involved in the electron transport phase of respiration. Thus, many genes used for barcoding are involved in the key reactions of life: storing energy in carbohydrates and releasing it to form ATP.

How do you make a DNA barcode?

The Process

1. Step 1: Isolate DNA from the sample.
2. Step 2: Amplify the target DNA barcode region using PCR.
3. Step 3: Sequence the PCR products.
4. Step 4: Compare the resulting sequences against reference databases to find the matching species.

Does fish contain DNA?

DNA barcoding methods for fish are used to identify groups of fish based on DNA sequences within selected regions of a genome. These methods can be used to study fish, as genetic material, in the form of environmental DNA (eDNA) or cells, is freely diffused in the water.

What is use of cytochrome oxidase 1 in species identification?

In 2003, a standardized 658 bp fragment of the mitochondrial cytochrome C oxidase subunit I gene (cox1 or COI) was proposed as a universal marker for species identification – to be used as a “DNA barcode” tagging any taxon in the animal kingdom1.

What does the COX-1 protein do in animals?

COX-1 is constitutively expressed and is responsible for the biosynthesis of PGs involved in various housekeeping functions, such as the regulation of renal, gastrointestinal, and platelet function [1].