Witek Morek, a postdoctoral researcher and tardigrade expert, carefully inspects an old brick-and-flint wall on the Cambridgeshire campus of the Wellcome Sanger Institute. Using what he calls a very advanced tool designed by bioengineers and evolved over millions of years – the human hand – he grabs some moss and places it in an envelope. This is tardigrade hunting, the first small step in a gargantuan, wildly ambitious scientific undertaking: to sequence the genomes of all life on Earth.
Collecting Samples
Accompanied by Prof Mark Blaxter, who leads the institute's Tree of Life programme, Morek collects lichen from a walnut tree on the lush campus before returning to the lab with his samples. The Tree of Life programme aims to sequence the genomes of all eukaryotic species on Earth, focusing initially on British and Irish species.
The Tree of Life Programme
In 1998, a millimetre-long nematode worm became the first animal to have its whole genome sequenced. The human genome was first sequenced just five years later, although it was not absolutely completed until 2021. A genome is the instructions for making an animal, written in a chemical code known as DNA. Genomics looks beyond genes to all the DNA found between the genes. Establishing reference genomes for species can help scientists better study organisms' biology and evolution, as well as identify new medicines and compounds.
Sequencing genomes used to take years. Blaxter sequenced 18 genomes over 25 years of study in his early career. Now, the Tree of Life programme is sequencing 48 each week, thanks to advances in sequencing technology. It has sequenced 2,600 genomes so far, from whales to fungi, mostly focusing on British and Irish species. Now it is the turn of microscopic tardigrades – the popular winner of last year's Guardian invertebrate of the year contest.
Tardigrade Biology
About 1,500 species of tardigrade – the name means slow stepper – have been identified around the world so far. They are famously indestructible, able to survive searing heat, extreme cold and even a spell in outer space. This is because of their ability to desiccate and enter a suspended animation until they are reawakened by water.
Morek begins the sequencing process by putting the moss and lichen samples he has collected in a beaker of water. Thirty minutes later, the tardigrades are wiggling away. He places tiny pieces of moss beneath a microscope and soon identifies a tardigrade. It is waggling its chubby-baby legs. This moss piglet is a translucent, middle-sized tardigrade, about 350 micrometres in length (a human hair is 50 micrometres in diameter). It has recently eaten: Morek can see the contents of its gut.
Species Identification
Morek, who has so far collected about 20 of the 50 tardigrades on the British list (a huge underestimate of the total species number, he says), will need to see its eggs to identify this exact species. Some tardigrades have smooth eggs; others have mushroom, conical or needle-like shapes on the surface. Tardigrades can be voracious carnivores, chasing down nematodes and eating them like spaghetti, says Morek. But he also reveals how they can demonstrate parental care. A mother sometimes sheds its cuticle (its skin) with eggs safely inside the shed skin, but she keeps the cuticle attached to her legs until the eggs are hatched.
Sequencing Process
Morek makes a temporary slide – putting the tardigrade between glass – to confirm its taxonomy as closely as possible. It has to be temporary because the water will evaporate and the tardigrade could be crushed by the glass. The tardigrade is kept alive and transferred to a barcoded plastic tube. This is frozen for later sequencing – kept in the lab's special double-doored freezers set at -71C.
There are four high-quality tardigrade genomes deposited in public databases; Morek is closely working on another 14, and there are approximately 50 species in the freezer awaiting sequencing. Before extracting the DNA for sequencing, Morek must manually disrupt his specimen. He can cut a 200-micrometre tardigrade by hand or use a form of mashing within a block of ice when frozen.
A tardigrade contains a tiny amount of DNA, just 200 to 500 picograms (one picogram is one trillionth of a gram). In the old days, researchers would need to pool 1,000 tardigrades to obtain enough DNA, an arduous process which was impossible with rare or hard-to-find species. Another strategy is to use a single female to produce large numbers of genetic clones. But the Wellcome Sanger Institute deploys a different approach: the picogram input multimodal sequencing protocol.
With this technique, genomic DNA and RNA are extracted from the tardigrade and separated into two tubes. Researchers then use a polymerase chain reaction (PCR) to amplify these fragments to create enough material. The quality of the DNA produced is checked and samples are handed to the institute's scientific operations team. After it is sequenced, the data is available on the institute's computer cluster. The sequence itself is millions-long strings of the four types of bases found in a DNA molecule: adenine, cytosine, guanine and thymine (ACTG).
Fortunately for tardigrade researchers, tardigrade genomes are small – 30 times smaller than the human genome. Although the PCR process is complex, scientists require less data to assemble the genome of a tardigrade.
Research Implications
For Morek, the sequencing of tardigrades will help reveal how species are related to each other. Incredibly, some tardigrades are separated by 550 million years of evolution. But genome sequencing could also reveal how the tardigrades' superpowers – such as resistance to freezing (cryobiosis), resistance to a lack of oxygen (anoxybiosis) and the ability to repeatedly survive desiccation (anhydrobiosis) – may help us.
And, because most of life on this planet is small, like the tardigrades, this new approach to genome sequencing promises to open the gates to sequencing all of life, says Blaxter. These genomes will in turn open up new ideas and opportunities in biomedicine and biotechnology. Through sequencing, scientists can pinpoint the genes and proteins required for these processes. If a certain protein is crucial in anhydrobiosis, can we use it to produce vaccines which are dry, or add it to crops to make them more drought-resistant?
There are a lot of research questions, says Morek. The more we know, the more questions we are asking. It's a never-ending story.
