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How to ID plants through DNA barcoding

It’s not just humans and animals that have DNA in their cells, plants and fungi do too.

In fact, DNA barcoding can be used to identify plants, detect invasive species and help conservation work, as our Senior Ecological Advisor Sarah Shuttleworth explains.

DNA barcoding course

Like all living organisms, plants and fungi have DNA (deoxyribonucleic acid) in their cells. DNA is the genetic code, which is the blueprint for genes, which gives an organism its specific characteristics. Different species will have a different DNA blueprint (with small variations within that as well) and these can help us tell species apart and see which ones are closely related.

I was recently offered a place on an exciting course to learn all about DNA barcoding and how it can help my work as a botanist.

Sarah Shuttleworth at DNA barcoding course

So, what is a DNA barcode?

Put simply, we can compare different DNA blueprints by comparing just a small section of the DNA sequence. This small section is referred to as the DNA barcode. There is a reference library which contains information about many species with their corresponding barcode.

In order to compare DNA barcodes of different species, the shortened sequence (region) needs to be the same region of the comparison species. However, which region you select to shorten and use for comparison is different depending on which type of organism you have. For example, all organisms within the animal kingdom are identified using the same specific DNA region, whilst all plants are identified using a different region.


The DNA region used for barcoding differs between kingdoms:

  • In fungi, the most commonly used DNA barcode is the internal transcribed spacer (ITS) region. This is the specific part of the DNA sequence used for fungi.
  • There are several candidates for DNA barcoding in plants. The two gene targets recommended are maturase K (matK) and ribulose bisphosphate carboxylase (rbcL).

DNA barcoding relies on a region of DNA that varies significantly between different species to allow the different species to be identified.

Attendees at DNA barcoding course

How do you extract the DNA and barcode it?

First, we need to collect a tiny bit of plant and/or fungi samples for our study. We don’t need much, just a small amount to get the DNA. To get the DNA out, we cut really tiny pieces from the samples. Then, we put these pieces in a tube with a special liquid solution and smush them with a small tool to break the cells apart and release the DNA.

Next, we need to make lots of copies of the DNA which we do by using a special mix of certain chemicals (there are different special mixes for plants and fungi).

To check if we’ve done it right, we use a method called gel electrophoresis. This method is used to separate mixtures of DNA, RNA, or proteins to molecular size (you will see a nice clear line in the gel if it has been successful.) This helps us see if the DNA we extracted is good and whether we can send it to the lab. The lab will then send us the DNA sequence so it can be compared it to other sequences in a big database.

How can DNA barcoding help with plant conservation?

Using these DNA barcoding skills can help us in many ways, including identifying single species or a community of species.

  • Single species barcoding – is when you collect a sample from a plant, fungus or animal, extract DNA from the sample, amplify the DNA barcode and send the DNA barcode for sequencing. This can help us record species accurately and identify species we have on our reserves that are difficult to identify. (The International Barcode of Life (iBOL) project seeks to make DNA barcoding globally accessible for the discovery and identification of all multicellular life on Earth.)
  • Community barcoding or metabarcoding – is when a sample contains a mixture of species, so DNA is extracted, amplified and sequenced from all the species in the mix that are targeted by the DNA barcode used. An example of metabarcoding is identifying the fungal diversity in a soil sample.
  • Detection of invasive species – DNA sampled from the environment (eDNA) can be barcoded to monitor the presence of invasive species of concern.

It is quite a technical process but as local groups (mainly fungi recording organisations) are starting to invest in the kit, more people should be able to get involved in DNA barcoding.

Sarah Shuttleworth on a DNA barcoding course

I hadn’t had a chance to do anything like this since my first year at university and I was surprised about how much came flooding back to me. The course was a great opportunity to learn and refresh my skills, as well as meet other people with an interest in species identification and conservation.

After more practicing, we hope to use these skills to add to the genomic database and assist our own species recording accuracy.

In the future, perhaps Plantlife can utilise these skill sets for looking at species assemblages on our reserves or places we are hoping to maximise conservation efforts.

Volunteer biological recording group RoAM (Recorders of the Avalon Marshes) at Somerset Wetlands NNR (National Nature Reserve) organised the DNA barcoding course with funding from Natural England through the Natural Capital and Ecosystem Assessment Programme. I was offered a spot on this exciting course due to my work and contacts in a voluntary capacity with the North Somerset and Bristol Fungi Group.

Natural England: EDNA (Environmental DNA) approaches to environmental monitoring are incredibly valuable to Natural England’s work, but recognise their limitations, not least that some groups of fungi, lichen and invertebrates are poorly represented in genomic databases. By helping to train our highly skilled taxonomic recorders with DNA barcoding means better records and more effective eDNA outputs.