Barcodes for pest

Identifying potential pests based on morphology – their physical characteristics – has the advantage of being quick. However, besides demanding good samples, morphological identification is often only possible on adult specimens. Some groups require an expert to distinguish between them.

To expand our toolkit for identifying potential pests, Addison has been leading a barcoding project, co-funded by SATI, Winetech, and Hortgro. What is DNA barcoding? A DNA barcode works exactly like the barcode on a bottle of milk or a box of grapes. It’s a unique identifier that links the item to other information. But whereas groceries have barcodes on their packaging, living organisms have barcodes inside their cells.

When faced with an unknown organism, researchers can extract DNA from its cells, sequence it, and compare it to a database of known sequences to obtain an identification. In theory, this should work even if the sample is a squashed or slashed insect.

DNA barcoding targets particular genes. Addison’s team focused on the most barcoded animal gene, COI.

COI and other DNA barcodes are available on the open-access platform BOLD Systems, which is linked to GenBank, a public collection of genetic sequences and proteins contributed by researchers worldwide.

BOLD Systems currently boasts 265 000 animal species in their databank. This might sound like a lot, but it’s far from complete, considering that, for insects alone, more than a million species have been described, and scientists estimate that millions more remain undiscovered.

“A lot of the local pests that farmers bring to us don’t have barcodes,” says Addison. “It’s especially a problem with sporadic pests.” Hence, the barcoding project aimed to expand the collection of South African COI sequences.

Gathering genetic data

To generate a barcode, DNA must first be extracted from a potential pest. For this project, Addison’s team used samples that were either already stored at, or newly submitted to, the SU insect identification service. Samples were also requested from crop-protection advisers. “For certain pests, we identified a location to collect samples,” says Addison. “Often, when we went there, the farmer had sprayed, so we couldn’t find any of the pests. Black vine thrips was one such case.”

Nonetheless, they procured samples of 20 species from grapevines, representing beetles, bugs, flies, leafhoppers, mealy bugs, mites, moths, and thrips. Several specialists, including international experts, helped provide morphological identifications.

The old-fashioned morphological identifications were necessary to put names to the DNA sequences. Once this has been done, future identifications can be based solely on sequences rather than involving a scientist peering down a microscope.

Addison notes that the increasing scarcity of taxonomists who can identify particular species is one reason to prioritise barcoding. Although pest identification using barcoding still requires an entomologist, it doesn’t call for multiple experts, each of whom has spent their career learning the fine anatomical details of a single pest family.

The increasing scarcity of taxonomists who can identify particular species is one reason to prioritise barcoding.

As the project focused on the COI barcoding gene, the researchers sequenced this gene from their samples and then compared their sequences to those already contained in online databases such as GenBank.

Barcoding pros and cons

Like any tool, barcoding has benefits and drawbacks. The main benefits include not requiring well-preserved adult specimens or well-schooled specialist taxonomists. Drawbacks relate to time and cost.

“Barcoding is a bit more expensive than if someone were to bring me a worm, and all I have to do is say that it’s false codling moth,” says Addison. “Growers also have to wait about two weeks for a barcoding result.”

Nonetheless, barcoding promises the possibility of extracting DNA from samples of any suspected pest, sequencing the COI gene, matching it to an existing sequence, and obtaining an identification. Currently, the biggest shortcoming of DNA barcoding is a lack of named sequences. Although the number of sequences in GenBank has grown exponentially in recent years, doubling roughly every 18 months, it still represents only about a third of known species and a much smaller percentage of all species. Furthermore, South African species are underrepresented.

To unlock the value of barcoding, South African fruit industries would have to invest in continuously gathering and uploading sequences of potential pests.

“Ideally, this would run in the background, as long as you had a little money to do DNA sequences,” says Addison. “But you need long-term funding. It’s not a two- or three-year project.”