DNA Barcoding and Sequencing

These flashcards cover essential vocabulary and concepts related to DNA barcoding and sequencing techniques.

DNA Barcoding

A method that uses short, standardized DNA sequences for species identification and biodiversity studies.

Species Identification

The process of distinguishing organisms based on their unique DNA sequences.

Mitochondrial Cytochrome c Oxidase I (COI) Gene

A commonly amplified gene region in animal DNA barcoding.

rbcL/matK Genes

Commonly used gene regions in plant DNA barcoding.

X-Amp Reagent

A specialized reagent that lyses cells to release DNA while protecting it from degradation.

PCR Master Mix

A mixture containing components like buffer, dNTPs, MgCl₂, DNA polymerase, and primers used in PCR.

Multiplexing

The process of pooling multiple samples in one sequencing run using tagged PCR primers.

Good 260/280 Absorbance Ratio

An ideal ratio of ~1.8, indicating pure DNA; lower suggests protein contamination, higher indicates RNA contamination.

Nanopore Sequencing

A sequencing method that detects base differences by measuring disruptions in ionic current as DNA passes through a nanopore.

BLAST Search

A tool used to compare a sequence against a database to identify species or genes based on similarity.

General Workflow of DNA Barcoding

1. Sample collection 2. DNA extraction 3. PCR amplification of target gene 4. DNA sequencing 5. Data analysis (e.g., BLAST search).

Role of Primers in PCR

Short, single-stranded DNA sequences that bind to the start and end of the target DNA region, providing a starting point for DNA polymerase to synthesize new strands.

Advantages of DNA Barcoding

Rapid and accurate species identification, effective for all life stages, aids in detecting cryptic species, useful for fragmented or processed samples.

Limitations of DNA Barcoding

May not distinguish very closely related species, requires a comprehensive reference database, potential for contamination, relatively high cost compared to morphological identification for some applications.