Tested and Approved: Affordable Application of New DNA Sequencing Technologies

A wild bee of the Halictidae family (©Alain Pauly, RBINS) in front of a tiny part of its DNA sequence
21/12/2018
Tested and Approved: Affordable Application of New DNA Sequencing Technologies
post by
Siska Van Parys

Scientists of our institute and the RMCA (Royal Museum for Central Africa) have successfully applied a technique enabling the collection of DNA of many specimens at a relatively cheap cost. Good news for researchers of institutes with large collections, that want to compare as many specimens as possible.

Analysing the DNA of different animal species can tell us more than what we would learn simply by looking at their morphology. This is of great value for taxonomists, scientists that describe and classify species, for example in the case of species that can hardly be distinguished from each other based on their looks. With the improvements of DNA sequencing technologies, sequencing the entire genome of an organism is no longer science fiction - if you can spend several thousands of euros. Taxonomists usually study many organisms and sequencing the whole genome of all of them quickly becomes unaffordable. In addition, they often only need a few specific parts of the genome, and sequencing all of it would be a useless cost. So, despite the availability of those advanced techniques, they are often still doing it the old-fashioned way, using "Sanger sequencing". With this traditional technique, relatively short DNA fragments – sometimes called “DNA barcodes” – are sequenced one by one for each specimen, with a low entry price. However, scientists have recently found ways to adapt the advanced sequencing technologies so that they can also be used to target only the genes of interest and consequently become more affordable to analyse many specimens.

Like reading a book

The JEMU team of the KBIN and the RMCA tested this out on a group of wild bees. ‘What we did here is evaluating in which situation which method is the most advantageous option.’ Says Gontran Sonet, one of the researchers of the team. ‘We compared the traditional Sanger sequencing with a customised protocol of a more advanced method, called NGS or "Next-Generation Sequencing".’ He compares it with reading the sentences of a book, where the book is the whole genome of an individual and a sentence is one DNA fragment: ‘With the Sanger method, you can read only one sentence at a time. Each sentence costs about 10 euros. NGS, however, can read a whole book at once. Logically, this is also more expensive: several thousands of euros per book. The principle of the customized protocol that we used, is that instead of the whole book, you choose specific sentences to read, so just like in the Sanger method. The big difference is that with Sanger you read the sentences one by one, while with NGS you read all of them at once, in parallel.’ You can read one million times more DNA with one round of NGS than with one round of Sanger sequencing. Consequently, if you need to read the DNA of a lot of organisms, the customised NGS method becomes the cheapest option. They found the adapted NGS to be more cost efficient than Sanger when more than five sequences must be read of more than 100 organisms. ‘This approach adds the flexibility to target the genes we really want to study,’ concludes Sonet.

Evolutionary history

The customised protocol is an additional tool to support the taxonomists of the institute in their research. In their paper, Sonet and his colleagues also provide guidelines for scientists to choose the most appropriate and cost-effective technique in their case. The JEMU team proved that this customised protocol can be used to investigate some interesting scientific questions at a relatively low cost. ‘With the obtained results we could improve our knowledge about the evolutionary history of the group of bees under study, and at the same time, survey the presence of an intracellular bacterium,’ comments Massimiliano Virgilio, another member of the team. This study could confirm that this bacterium, called Wolbachia, is often found in this family of wild bees.

The study is published in the journal of Apidology.

 

This study was initiated by the Joint Experimental Molecular Unit (JEMU), which is an integrated research infrastructure financed by the Belgian Science Policy and supported by the Royal Belgian Institute of Natural Sciences, the Royal Museum for Central Africa and the FWO Research Community W0.009.11N ‘Belgian Network for DNA Barcoding’ (BeBoL). JEMU conducts research on natural history collections in the fields of molecular systematics, DNA barcoding, biological classification and archiving biological specimens and samples.

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