Are you interested in teaching PCR and DNA barcoding in a classroom environment?
DNA barcoding is a method of specimen characterisation and identification using short, standardized segments of DNA.
As an educational activity, DNA barcoding offers an opportunity to bring together many different skills required in many undergraduate science courses, from core molecular biology skills (such as PCR) to bioinformatics. It is also particularly relevant in light of the ongoing global biodiversity crisis and climate change.
Importantly, DNA barcoding can allow students to become investigators using their own samples, taking much more ownership of the scientific process and becoming much more invested in the outcomes.
Here we’ve chosen some of our favourite articles on DNA barcoding in classrooms to help illustrate some of the different approaches, learning frameworks, learning objectives, and methodologies that have been used.
We hope that you’ll find these articles interesting and useful, and that between them you’ll be able to find something that suits your teaching needs!
1. DNA barcoding stoneflies (Plecoptera) by Erasmus (2021)
You should read this article if:
- You want a concise article that does a great job of introducing DNA barcoding in an undergraduate context.
- You’re interested in DNA barcoding invertebrates or other animal groups, using transferable methods for diverse taxa.
“This laboratory exercise is easy to do and students enjoyed analyzing DNA sequences they generated themselves. They also enjoyed working with different materials such as insects. [which is not typical of most biochemistry and molecular biology laboratories.]”
This article describes a laboratory exercise for undergraduate students to explore DNA sequencing and analysis through the activity of DNA barcoding stoneflies (Plecoptera). It consists of a one-hour lecture and three three-hour practicals run as part of a lab-based course for a Biochemistry and Molecular Biology Major. It’s written by Erasmus (2021) from the University of Northern British Columbia (Canada).
Erasmus developed the practical to facilitate the development of DNA sequence generation and analysis skills — an essential set of skills for majors in biochemistry and molecular biology. They chose DNA barcoding as the focal activity to provide students with a different experience of molecular techniques to that taught in the rest of the course, focusing on biodiversity, taxonomy, and ecology, rather than on understanding human disease, biochemistry, and biotechnology.
This is a particularly nice and relatively short example of a DNA barcoding teaching lesson, and the methods (including proteinase K-based DNA extraction) should be transferable to the study of most other organismal groups.
The course covered the following topics:
- Molecular Techniques
- DNA extraction using Proteinase K incubation with Chelex resin
- PCR using a standard master mix and universal animal barcoding primers
- Gel electrophoresis and amplicon visualisation
- Sequencing and Data Analysis
- Understanding the principles and workflow of Sanger sequencing
- Bioinformatics and interpretation
The article also includes a questionnaire and example sequences in the supplementary data to help guide student learning.
Reference
2. DNA barcoding caddis flies (Trichoptera) by Shevcenko et al. (2019)
You should read this article if:
- You want a detailed breakdown of each step in DNA barcoding, from collection to analysis, with suggested undergraduate-level learning outcomes
- You are interested in DNA barcoding insects
“Teaching in “silos” inhibits the formation of connections among subjects. […] Future scientists need to think for themselves, to look at a problem and work towards a solution. DNA barcoding exposes students to advanced scientific equipment and gives them a chance to experience something from the beginning to the end.”
This article describes a series of one-hour lessons spread over 10 days, initially developed as a course run as a side activity during a symposium on caddis flies (Trichoptera) in 2015. It was written by Shevcenko et al. (2019), a team from Rutgers University-New Brunswick, Brigham Young University, and the Smithsonian Institution.
The authors aimed to use DNA barcoding to help students make connections between different technical skills in field collection, molecular biology, and bioinformatics. By bringing together learning objectives from different scientific fields and applying them practically, the students could gain a diverse range of problem-solving skills, and an appreciation that all science is connected.
“Often there is a divide between organismal and molecular biologists, or those who work in the field and those who operate in the lab. […] Lessons learned from DNA sequencing take a student from field collection to generating and analyzing DNA sequences.”
The team chose caddis flies (Trichoptera) as the target group because the species are very diverse in North America, they are well-represented in reference databases, and the flies are relatively easily collected as larvae (from streams) or adults (by light trapping).
This article is particularly notable for its comprehensive breakdown of each process in a typical DNA barcoding workflow, and each step is accompanied by suggested learning outcomes. It’s a very detailed article and is a great resource for anyone starting to learn about DNA barcoding for any taxonomic group.
However, the authors did report that their original time allocation for sessions during the symposium course (one hour per session) wasn’t enough for participants to properly learn all of the content. The authors suggested allocating more time to each section, for example by spreading the curriculum for fieldwork, labwork, and lectures across an entire semester.
The course covered the following topics:
- Field and collection skills
- Collecting in the field
- Insect diversity
- Vouchering and photographing specimens
- Molecular biology skills
- Extracting DNA using the HotSHOT method
- PCR amplification of the COI barcode region using freeze-dried PCR beads and universal animal barcoding primers
- Agarose gel electrophoresis and amplicon visualisation
- Sanger sequencing
- Bioinformatics and interpretation
- Editing DNA sequences using the free APE software package
- Submitting data to the BOLD reference databases for identification
- Phylogenetic analysis using BOLD, with suggested use of SeaView and Paup*
Reference
3. DNA barcoding of fungi by Casanova & Shumskaya (2021)
You should read this article if:
- You want to teach or learn the use of phylogenetics software, and want a guide to using the free MEGA phylogenetics package for DNA barcoding.
- You’d like to DNA barcode fungi, or analyse fungal DNA barcode sequences as a separate exercise.
“[After the course, most] of the students felt that the DNA barcoding activity reinforced their theoretical knowledge on PCR technique and gel electrophoresis. For many, construction of a phylogeny was a completely new activity that made them think again of DNA mutations as a driving force to speciation.”
This article describes a three-class practical (two lab, one remote, each 2.5 hours), designed to teach a wide range of transferable molecular biology and bioinformatics skills to biochemistry, genetics, and molecular biology students. The practical involves DNA barcoding fungi, but it could be equally applicable to most other organismal groups. It was developed for an upper-level class of Biochemistry Laboratory course for the Biology program of Kean University (USA) by Casanova & Shumskaya (2021).
This article could be particularly useful for any teachers or students who would like to use phylogenetics. It has a great introduction to using the free MEGA phylogenetics software, and the supplementary data contains an ITS reference sequence alignment and several “unidentified” sequences to assist the phylogenetic analysis section.
Additionally, for those wanting resources on how to grade DNA barcoding work, it has a useful short section on report assessment marking, and refers to a previous publication by one of the authors on how to teach the writing of scientific reports (see Shumskaya et al., 2020).
The course covered the following topics:
- Molecular biology skills:
- DNA isolation of shop-bought mushrooms using a spin column DNA extraction kit
- Amplification of the ITS barcode region using PCR
- Agarose gel electrophoresis
- DNA sequencing preparation
- Bioinformatics and interpretation
- Sequence analysis via BLAST searching for sequence matches in Genbank
- Phylogenetic analysis of an unknown fungal species from Agaricales by constructing phylogenies in the phylogenetics software MEGA
- Assessment
- Student learning was assessed in three sections: DNA isolation, gel electrophoresis and DNA sequence analysis, and a final lab report of all results. Assessment was done following Shumskaya et al. (2020).
Reference
4. DNA barcoding macroalgae by Tateno-Bisel & Perez (2022)
You should read this article if:
- You want an introductory course on DNA barcoding for high school students
- You want a good example of using a formal Claim, Evidence, and Reasoning (CER) framework, with marking criteria, for teaching DNA barcoding
“We wanted students to be able to answer the question: “How do you know that this sample of algae is (species X)?” [and] we wanted our students to get hands-on experience in doing real-world research”
This article covers a series of activities on DNA barcoding developed as part of a larger two-week summer course on the biodiversity of Hawai’i’s wetlands. It was written by Tateno-Bisel & Kauahi Perez (2022) from the University of Hawai’i at Mānoa (USA).
The authors wanted to run an inquiry activity using a Claim, Evidence, and Reasoning (CER) framework to guide students to reach answers and achieve learning for themselves. They also wanted to give students hands-on experience of real-life work, bioinformatics processes and software, and group collaboration to answer research questions. They chose DNA barcoding as it covers all these requirements in one activity.
Earlier in the summer course the students had already collected a small number of algal specimens during a fieldwork exercise, and they had learnt how to extract, amplify, and visualise DNA. Six student specimens were sequenced using Sanger sequencing and these samples were used for the inquiry activity to give students a greater sense of ownership.
The students participated in a series of presentations, group work, and guided tutorials based around DNA barcoding. These activities culminated in an investigation into the identity of an unidentified alga using morphological and DNA sequence-based identification methods. The various activities took between 10 minutes and 1.5 hours and ran over three days, although the authors suggest giving these activities more time if run again in the future.
One of the interesting aspects of the approach described in this article is that students were given the tools to generate taxonomic hypotheses and were guided in groups to provide evidence to support or disprove their claims. This procedure provided a much more true-to-life experience of taxonomic hypothesis testing than just following a protocol and getting a result. It also allowed them to use a system of reasoning that can be used in many other types of scientific inquiry.
The activities covered the following topics:
- Taxonomy and classification
- A recap of morphological classification
- Molecular biology skills
- A lecture, with videos, on DNA barcoding
- Bioinformatics and interpretation
- Instructor-guided tutorials on how to use software to check and edit DNA sequences
- Searching and retrieving sequences from databases
- Creating DNA sequence alignments
- Generating and interpreting phylogenetic trees using a “scaffolding tool” that had instructions on how to use MEGA and questions to help students organise their thoughts
- Generating taxonomic hypotheses based on morphology and molecular information
Reference
