How Nanopore Sequencing Is Revolutionising Biology
When the first human genome was sequenced completely, it cost an estimated $450 million[i]. Now, thanks to incredible technological advances, just 20 years later we can sequence the entire DNA of a human (foetus or octogenarian) for $600[ii], a cost that is constantly reducing. Various benefits of this technology have been widely publicised, such as in health and medicine, with preventative screenings saving lives earlier, identifying risk factors for cancers, and giving parents of babies born through In Vitro Fertilisation (IVF) more informed choices about healthy embryos.
One of the key players in this journey towards cheaper sequencing has been nanopore technology. This technology uses microscopic holes in delicate membranes that pull single strands of DNA or RNA through. An electrode and computer chip detect the electrochemical charge characteristic of different organic bases. Thus, as a current is passed through the pore, and detected on the other side, slight fluctuations can tell the chip the difference between an A, C, T, G, or U (in RNA). This process boasts a total read accuracy of over 99%[iii]. One of the pioneering biotechnology companies engineering this is Oxford Nanopore, which sells its smallest (single-use) sequencers for as little as £90, giving unparalleled access to powerful technology to scientists around the world. Nanopore technology has revolutionised genetics with portable and incredibly fast sequencing potential and has many incredible applications, none more evident than in ecology.In surveying the environment for biodiversity, scientists are rarely interested in the precise genome and variation within an individual species. It is unproductive to sequence every sampled organism’s entire genome to work out what it is, but there are more ways to gain rapid information about which species are present. Each organism’s mitochondria have their own smaller genome, and as all mitochondria are inherited from their mothers, there is far less variation in mitochondrial genetics than in the rest of our DNA that is jumbled around when we are conceived sexually. One element of mitochondrial DNA, the cytochrome c oxidase 1 (or CO1) gene, can be used effectively as a barcode for species-level identification[iv]. (For those with a penchant for the Krebs cycle and respiration, you may know the cytochrome oxidase from the electron transport chain in the mitochondria.)
These neat 648 base pairs in the CO1 gene vary very little between organisms in the same species, but sufficiently between different species that organisms can be identified just by their CO1 gene. Thus, instead of having to phone up an entomologist to identify the subtlest distinctions between similar genera and species every time you collect an insect, simply record the CO1 gene for that species once, and every time you pick up that same precise sequence again, you’ll know what it is. While this may signal a decline in the need for experts in taxonomic differences, the potential for this technology could fuel incredibly fast development in expertise and understanding of organisms at the species level, especially as the cost decreases.
This technology is already transforming ecological research today, especially coupled with Environmental DNA, or eDNA, a method of sampling genetic information from a sample location and quickly discerning the different species that reside there. Typically, this eDNA sampling would have been done in water, picking up samples of polynucleotides (DNA or RNA) that came off into the water as outer cells die, or additionally in faecal matter. Recently, advancements have been made in metagenomics (studying the genetics of a sampled location) of the air. So-called aerial metagenomic “sniffers” can now pick up DNA fragments that flake off dead cells and become airborne. Last year a team at Copenhagen Zoo used aerial methods to identify all the species present in nearby enclosures, as well as tens of other mammals and birds likely in or around the zoo[v]. While it should be noted that lots of eDNA sampling is currently being done with PCR sequencing and tests, the advancements in nanopore technology should be able to provide cheaper, more accurate, and more detailed information in years to come.
In the past, to sample identification sites, an ecologist would have had to spend hours detailing the many flora, fauna, and funga in a quadrat, and at best get most organisms to taxonomic species. Now, for under £1,000, around thirty of these locations could have their metagenomic DNA sequenced to identify exactly how many different species there are in a site. This cost is still prohibitive for some research, but for the high accuracy and rapid speeds it provides, in many scenarios it really is revolutionising ecology, and many scientific papers already feature the use of eDNA and metabarcoding.
It’s fascinating to watch such a powerful technology advance so swiftly, as well as seeing its applications emerge in real-time. Oxford Nanopore holds the ambitious aim to “enable the analysis of anything, by anyone, anywhere”, and though this may just be the beginning, nanopore sequencing technology is truly paving the way for a fascinating biological future, accessible to all!
[iii],[iv] Oxford Nanopore: https://nanoporetech.com/, GIF from them too and free to use
[v] eDNA sniffing/ Metagenomics: https://www.economist.com/science-and-technology/2022/01/08/wildlife-can-now-be-detected-by-sniffing-dna-in-the-air
Ecology Sampling- Dr Will Pearse of Imperial College London (with thanks for chatting to me at length over Feb LL 2022)
Media: https://www.usgs.gov/media/images/edna-environmental-dna and https://en.wikipedia.org/wiki/Nanopore_sequencing#/media/File:202001_nanopore_sequencing.svg