Quest begins to sequence genomes of all UK life
An ambitious plan to sequence the genomes of all living organisms in the UK is underway.
Researchers from the Museum and Natural England undertook a three-day bioblitz in the north west of England. They were able to collect and identify hundreds of species of invertebrates, and even began sequencing DNA in a pop-up field lab.
Scientists, naturalists and volunteers were out in force collecting invertebrates in the sand dunes of Ainsdale National Nature Reserve in Merseyside.
Located in the north west of England, the reserve and the surrounding environment provided a diversity of habitats - from dunes and beach to freshwater and salt marsh - in which the teams could search for a huge variety of species.
After collecting the invertebrates, which included insects, crustaceans, polychaetes, molluscs and arachnids, the researchers brought them back to a pop-up laboratory built on site. There, Museum researchers had set up all the necessary equipment to isolate, amplify and even sequence parts of the animals' DNA.
The Museum's Principal Curator in Charge of Insects, Dr Gavin Broad, says, 'We have been collaborating with Natural England to get many of their experts and surveyors along with our scientists out in the field. Together, we want to do a lot of invertebrate recording and specifically to start building a DNA barcode library.'
This will become a reference library, linked to images of the invertebrates that were sampled and the specimens themselves, which can then be used for the Darwin Tree of Life project.
When a species' genome is sampled for this project, it will then be compared to the DNA barcode library to corroborate an identification of what species it belongs to.
Earth BioGenome Project
The Darwin Tree of Life project was announced late last year. It is being led by the Sanger Institute, but involves a whole host of other institutions in addition to the Museum, from the Royal Botanic Gardens (Kew) to the University of Edinburgh.
The initial goal is to sample and sequence the genomes of all 66,000 species of plants, fungi, protozoa and animals that are found in the UK. This will then feed into the Earth BioGenome Project, which has an ambitious aim to sequence the genomes of all life on Earth.
It is hoped that this information could help researchers investigate a range of questions, from how and when certain groups or species colonised the British Isles to the evolution of wasp venom or how salamanders are able to regenerate their limbs.
This could be of significance to both the biomedical world and the bioengineering sector, as it could allow scientists to better understand how to build entire genomes from the bottom up.
But the project is also part of a longer term initiative.
'Various people have described this as "moonshot" science,' explains Gavin. 'We're not necessarily doing it for a particular purpose.
'But if you look at how sequencing the human genome unleashed a huge amount of progress in medicine and genetics research, just imagine what sequencing the genomes of a huge slice of life is going to open up in different research fields.'
Tracking species you can't see
Sequencing these DNA 'barcodes' - the short regions of the genome that vary enough between species to be diagnostic - of all the species that live in the UK will also be important in setting a new baseline for biodiversity assessments.
For Andy Nisbet, the Evidence Programme Manager at Natural England, this could be a powerful tool in keeping track of how well they are conserving nature in England.
'We do a lot of biological surveying and monitoring of species and special sites, but that is quite difficult,' explains Andy. 'We tend to monitor groups that are easy to find and species that are easy identify - so typically taxa such as birds, butterflies, dragonflies and flowering plants.
'Other groups, such as many other invertebrates and fungi, are really difficult to find and there are very few people who can comprehensively identify them. So we're interested in using DNA and eDNA to get around that, to find and identify more species that are difficult to find.'
As species move about their environment, they typically shed bits of their DNA. Known as environmental DNA, or eDNA for short, there has been an increased interest in using these traces to see whether or not a species - particularly rare or elusive ones - has been in an area recently.
'We are responsible for protected sites such as Sites of Special Scientific Interest and National Nature Reserves,' says Andy. 'So we need to know if their special features are still there and still doing well, while more generally we want to know what the state of the environment is, and how it is changing.'
The use of eDNA could radically change how scientists can keep track of how these special sites are faring. That's because researchers can simply take a sample of water and test it for different kinds of life.
By conducting this trial in Ainsdale, the team were testing the process of collecting specimens in the field, taking them back to be identified and then sequencing their DNA all in one day, with the aim of replicating it at other sites around the country.
The Museum is building up collections of this DNA, the specimens and their associated data and so will need to target a large variety of habitats, something that will only be possible through collaborations with other groups, institutions and experts.