Alina Avanesyan

DNA Barcoding for Everyone

DNA barcoding is a method of species identification using a short fragment of DNA (i.e., a DNA barcode) from a specific gene or multiple genes. You can think of the DNA barcodes as the unique species identifiers which you need to “scan” in order to identify the species. This works similar to scanning the Universal Product Codes (UPC) in a grocery store. Each product has the UPC which is shown as scannable lines (bars) of various width; these bars represent a 12-digit unique code for the product you buy. At checkout, barcode scanners will read the bars and “identify” the code for your product.

The DNA barcoding process is, of course, a bit more complicated: here, you first need to obtain the DNA barcode which you want to “scan”. So, it is more like a journey, at the end of which you can obtain a sequence for the DNA barcode you are interested in and then identify the species you are working with. As you will see in this course, however, DNA barcoding has way more applications beyond species identification.

DNA barcoding is sometimes referred to as a single-specimen DNA barcoding as it deals with identification of one species per one sample. In contrast, meta-barcoding is a method of simultaneous identification of species from multiple taxa within one sample, using a specific fragment of DNA (or RNA). Environmental DNA (eDNA) barcoding is an especially exciting process during which we can simultaneously identification of species from multiple taxa within one environmental sample, such as soil samples, water samples, species gut contents, feces, etc.

DNA barcoding is a very exciting process, and every day we do small (and sometimes big) discoveries. It is amazing how we can go from a small piece of tissue to a DNA sequence, right here, in the lab, in as little as a few hours. This DNA barcoding course includes all the training materials which will help you isolate DNA from virtually any organism you are working with, obtain the DNA barcode you are interested in, and identify the taxa the organism belongs to.

Learning objectives

LO#1: Become familiar with the main steps of the DNA barcoding process, such as DNA extraction, PCR, DNA purification, gel electrophoresis, obtaining sequences and species identification. (Bloom’s taxonomy levels: “remember”, “understand”)

LO#2: Develop an understanding of the basic molecular biology mechanisms behind each step of the DNA barcoding process. (Bloom’s taxonomy levels: “understand”, “apply”)

LO#3: Analyze species identification in the evolutionary context and recognize the complexity of DNA barcodes. (Bloom’s taxonomy levels: “analyze”, “evaluate”, “create”)

Learning outcomes

  1. After completion of the course students will know:
    • the main steps of the DNA barcoding process, as well as the place and purpose of each step (LO#1 and #2)
    • how to choose an organism, state the purpose of the DNA barcoding study, and choose the most effective DNA barcoding approach (LO#3)
    • The main ecological mechanisms underlying interactions between native and invasive species (LO#3)
  2. After completion of the course the students will be able to:
    • independently conduct all the steps of the DNA barcoding process: from tissue preparation to obtaining sequences and species identification; and troubleshoot any step if needed (LO#1 and #2)
    • annotate and deposit the obtained sequences to the NCBI GenBank database; the students will be the first authors on their GenBank submissions (LO#3)

Course modules

Module 1: Let's get started

  • DNA barcoding: overview

Module 2: DNA extraction

  • DNA extraction: video tutorial

Module 3: Polymerase chain reaction (PCR)

  • PCR: video tutorial

  • PCR: slides
  • PCR protocols:
    (a) Amplification of COI gene for species identification (Isopoda, Odonata feces): protocol
    (b) Amplification of trnL, rbcl genes for insect gut content analysis (potato leafhopper, spotted lanternfly): protocol

Module 4: DNA purification

  • DNA purification: video tutorial

Module 5 (optional): Gel electrophoresis

  • Gel preparation and gel electrophoresis: tutorial
  • Gel electrophoresis: protocol

Module 6: DNA sequences and species identification

  • Sequence analysis and conclusions: video

  • Sequencing analysis: resources

(a) Sequence editing using 4Peaks - guidelines (Prepared by Cameron McPherson)

(b) Sequence aligning using Unipro UGENE - guidelines (Prepared by Cameron McPherson)

(c) Sequence editing and aligning using BioEdit - guidelines (Prepared by Alina Avanesyan)

(d) Working with GenBank: BLAST and retrieving the sequences - guidelines (Prepared by Cameron McPherson)

Module 7 (extra): DNA Barcoding Experience - fun, challenges, and more