DNA barcoding

Audience

Secondary school, Tertiary
Learning stage

Stage 6
Learning area

Science
Type

Learning resources

DNA barcoding is a genetic technique that scientists at the Australian Museum use to identify species and measure biodiversity. Use this series of video modules to learn more about laboratory 'tools of the trade', good scientific practice, and technologies such as the polymerase chain reaction (PCR), gel electrophoresis and DNA sequencing.

Then put your skills and knowledge to the test with our DNA barcoding activity! You can use real DNA sequences from scientists in the Australian Museum Research Institute (AMRI) and bioinformatic tools in 'DNA Subway' to solve a scientific puzzle.

The modules and activity can be completed over a series of lessons or set as part of a longer unit.

The Australian Museum would like to thank Sydney Grammar School for funding this project and acknowledge their commitment to supporting the development of science education resources for NSW schools.

3D animations by Dr Andrew Lilja and A/Prof John McGhee, 3D Visualisation Aesthetics Lab, UNSW Sydney.

NSW Syllabus (for the Australian curriculum)
Biology Stage 6 Syllabus

Knowledge and Understanding
Module 5: Heredity
Inheritance Patterns in a Population
Students: investigate the use of technologies to determine inheritance patterns in a population using, for example: (ACSBL064, ACSBL085) DNA sequencing and profiling (ACSBL086)

Module 6: Genetic change
Genetic Technologies
Students: describe techniques and applications used in recombinant DNA technology

Working Scientifically Skills
Questioning and Predicting
Students:
● develop and evaluate inquiry questions and hypotheses to identify a concept that can be investigated scientifically, involving primary and secondary data (ACSBL001, ACSBL061, ACSBL096)

Analysing Data and Information
Students:
● assess error, uncertainty and limitations in data (ACSBL004, ACSBL005, ACSBL033, ACSBL099)
● assess the relevance, accuracy, validity and reliability of primary and secondary data and suggest improvements to investigations (ACSBL005)

Problem Solving
Students:
● use scientific evidence and critical thinking skills to solve problems

Communicating
Students:
● select and use suitable forms of digital, visual, written and/or oral communication
● select and apply appropriate scientific notations, nomenclature and scientific language to communicate in a variety of contexts (ACSBL008, ACSBL036, ACSBL067, ACSBL102)

Watch all eight DNA barcoding modules below and answer the guiding questions.
Read through and complete the DNA barcoding activity at the bottom of this page.

DNA barcoding modules

Module 1
What is DNA barcoding?

Guiding questions
What are the eight levels of taxonomy?
Think of your favourite animal. Write down the name of its taxonomic group at each level of classification (for example, domain = eukarya, kingdom = animalia etc.). What features does it have with other organisms in each of these groups?
What gene do scientists look at when they do DNA barcoding in animals? Can you think of two ways DNA barcoding can be used to answer a biological question?
Module 2
Sample collection and labelling.

Guiding questions
Can you think of three ways to record your methods and results in an experiment? Why do you think it is important to keep accurate records in a scientific study?
Give one example of a standard method to collect samples on a field trip. Why do you think it is important to collect data in a standardised way?
Module 3
How to pipette

Guiding questions
You are to measure 0.4 mL of a solution with a pipette. How many microlitres is this?
What are three ways you might contaminate a DNA sample in the laboratory? Describe how good laboratory practice could reduce the chance of this happening to you.
Module 4
DNA extraction

Guiding questions
What is the name of the DNA structures inside the nucleus of a cell? Which organelle in animal cells also contains DNA? What is the main function of this organelle?
What forms the outer border of an animal cell? Research a little further to describe how this is different to a plant cell.
Name three of the unlabelled structures in the cell diagram in the video. What is the function of each of them?
List the three main stages in a DNA extraction.
Module 5
Ploymerase chain reaction (PCR)

Guiding questions
A PCR make many copies of a specific piece of DNA. Is this an exponential, bimodal or linear process?
Name the three main stages in a PCR and describe in one sentence what happens in each stage.
List the different reagents in a PCR. Explain how they ‘work together’ to produce a PCR product.
Module 6
Agarose gel electrophoresis

Guiding questions
Are the following statements about agarose gel electrophoresis true or false?
– It separates pieces of DNA based on their shape.
– Long pieces of DNA migrate through an agarose gel faster than short pieces.
– DNA has a negative charge and moves towards the positively charged terminal.
– A dye in the agarose gel binds to DNA as it moves through the gel. This is illuminated by blue or ultraviolet light.
Module 7
DNA sequencing

Guiding questions
What are the important differences between a PCR and a DNA sequencing reaction?
What are the sequence of events that occur in this reaction?
How does a sequencing machine produce a DNA sequence trace?
Module 8
Databases and analysis

DNA barcoding activity

Read the information about the case you need to solve under the Background drop-down heading.
Click on the DNA sequence traces drop-down heading.
Download the DNA sequence file for each of the five specimens and save them in a new folder on you computer. Each specimen has two sequences - a forward and reverse. Forward is the sequence of one strand of the CO1 PCR product, while reverse is the sequence of the complementary strand.
Re-watch the video in module 8 'Databases and analysis' to learn how to use DNA Subway to identify each species.
After you've identified the names of each species, read Barcoding bollworms at the Australian Museum to help you determine which of the five specimens are destructive crop pest species.

You are a DNA barcoding expert at Australia Biosecurity in the Department of Agriculture. Some moth specimens arrived in the weekly postal delivery. One of your colleagues, an experienced entomologist, was unable to identify them based on their physical features. She suspects they belong to the Noctuidae family of moths. Some species in this family are native to Australia, while others are introduced species and are some of the world’s most destructive crop pests. You have been asked to identify the five species using DNA barcoding.

Specimen 1 – found in a cargo ship at a shipping terminal at Botany Bay.

Specimen 2 – found by a moth and butterfly enthusiast in western NSW.

Specimen 3 – found on the leaf of a cotton plant in the Daring Downs in Queensland.

Specimen 4 – found by a farmer in the Northern Territory.

Specimen 5 – a caterpillar found on a sorghum leaf in southern Queensland.

Use the website DNA Subway to view the DNA sequence files.

This PDF contains additional information explaining how a DNA sequencing reaction is converted into a trace, or chromatogram, that can be read and analysed by scientists.