Nuts about DNA barcoding

When University of Guelph informatics researcher Megan Milton found a tiny, roasted, salted -- and very dead – cocooned caterpillar in her bag of California pistachios, she was as intrigued as she was disgusted.

 

The insect, which had burrowed inside one of the nuts, was unfamiliar to her. 

 

And to someone working in biology, that’s intriguing.

 

But it was more than that for Milton. The discovery gave her a timely opportunity to field test a new species identification solution called LifeScanner, that she is helping to commercialize. It was developed by Prof. Sujeevan Ratnasingham at the university’s Centre for Biodiversity Genomics and a company called Biolytica.

 

LifeScanner puts species identification in producers’ hands. It’s useful in orchards, fields, gardens and parks across Canada – and as Milton found, even in desk drawers -- anywhere potentially harmful pests need to be quickly and accurately identified. 

 

And at approximately $15 per test, it’s incredibly accessible. 

 

These traits were among the features that made LifeScanner the winner of the inaugural innovation showcase and pitch competition run by the university’s Gryphon’s LAAIR (Leading to the Accelerated Adoption of Innovative Research) initiative.

 

Developer Ratnasingham says that besides being the only off-the-shelf solution that can identify more than 200,000 species, LifeScanner builds on the ongoing data collection from international research efforts to expand the global DNA library. 

 

“If a novel species to the database is encountered, it’s not long before we’re able to give it a name,” he says.

 

LifeScanner comes in a kit about the size of a wallet, with four vials of buffering solution  -- each with its own barcode -- tweezers and a pre-paid mailer. That’s it.

 

Users are instructed to download an app from the LifeScanner website or register on the web portal. When you find a mystery creature like Milton did, you scan one of the vials with the app, take a photo of the subject in question, pick it up with the tweezers, drop it in the vial, seal it in the mailer and drop it off in a Canada Post mailbox.

 

Normally, within two days, it’s delivered to the Centre for Biodiversity Genomics (CBG) on the second floor of the Biodiversity Institute of Ontario building on the University of Guelph’s west side.

 

There, a technician gives the specimen a unique identification number connected to the sender, extracts DNA from the specimen in the vial. Only a tiny portion is needed. The specimen is then analyzed with a DNA sequencer which compares its DNA to millions of other specimens that have been catalogued at CBG and at other institutions around the world.  

 

The numbers are eye-opening. Between 2010 and 2015, researchers involved in the International Barcode of Life (IBOL) consortium based at the University of Guelph developed DNA barcodes for 500,000 species. These barcodes are created by sequencing short fragments of DNA for standardized identification.

 

Last month, in Norway, Guelph researchers were part of an announcement for a new seven-year initiative called BIOSCAN. It involves more than 1,000 researchers from some 39 countries, aiming to raise the barcoded total to two million species. It’s an awesome, massive-scale undertaking.

 

LifeScanner uses these barcodes to make matches. When one is found, the specimen joins the rest of the catalogue, and the sender is informed. Appropriate action can then be taken.

 

For some fruit and vegetable producers, for example, who are vulnerable to the arrival of new pests -- let alone the reappearance of traditional ones – a LifeScanner identification could trigger an alarm bell. If the mystery pest is a true threat, immediate control measures may be taken to save the field. 

 

For Milton, the action was pretty simple – take a break from pistachios for a while, even though the nut company quickly acknowledged her finding. It explained the pest was a common Navel Orangeworm, and sent her coupons for free packages as an apology. In fact, she had an apology even before the completion of the DNA sequencing, which takes two to eight days.

 

But the story didn’t end there.

 

When Milton looked up Navel Orangeworm, she found its species name was Amyelois transitella. That, though, didn’t jibe with her specimen's DNA barcode, which was a match to specimens labelled as Pyralidae-BioLep47. That’s what’s called an “interim species name,” assigned in this case by researchers in Costa Rica. That means the species had been collected and barcoded before, but no one who was working with the barcoding data knew what species it was, or even if it was a known species.

 

And a few months later, by happenstance, she was contacted in her role as data manager at Barcode of Life Data Systems by a pest expert working in California on crop pests. He had also done independent DNA barcoding on an almond pest larvae, that he suspected was the Navel Orangeworm, but his DNA sequence also matched Pyralidae-BioLep47. Without DNA, it could easily have been misidentified by farmers and others for decades. Ultimately, all records of Pyralidae-BioLep47 on BOLD Systems were updated to reflect its true species name, Barberia addinitella.

 

Recently, a colleague of Milton’s eating the same brand of pistachios likewise found a dead, roasted larvae inside. She sent it in for sequencing via LifeScanner as well, and similarly got a match to Barberia addinitella.  

 

Like Milton, she too has yet to crack open another pistachio.

Publish date: 
Friday, August 2, 2019

Click to leave a comment

CAPTCHA
For security purposes, please confirm you are not a robot!