The secret lives of nematodes

Just visible to the naked eye, Caenorhabditis elegans is, on first sight, an unassuming worm. But to many, it is famous. Over the last 60 years, it has become a distinguished ‘model’ organism, studied by hundreds of laboratories worldwide. It was the first multi-cellular organism to have its entire DNA code determined, by John Sulston and colleagues, here at the Wellcome Sanger Institute¹. With no gaps, the genome sequence itself remains one of the highest quality available, for any species.

C. elegans, affectionately known as “the worm”, is now a workhorse of modern biology. The genome sequence has been the foundation of 25 years of research into how cells and bodies grow and function. The simple body plan of C. elegans – an adult female has only 959 cells but these form a full suite of functioning tissue and organs systems – has enabled discoveries into how memory works², how bodies develop and age and how genomes function, to name just a few areas of its influence.

But C. elegans is only one of many Caenorhabditis. 76 species have been discovered so far, including four this year. Researchers just need to look in their favoured habitats of rotting fruit, vegetation, or anywhere filled with bacteria, and they find new ones. And Caenorhabditis is just one genus of nematodes. It is estimated that there may be a up to 10 million nematode species, despite only around 27,000 being known to science³.

Compared to their abundance and importance, nematodes have been neglected so far in genome sequencing efforts. This is changing with a revived genome sequencing project that aims to determine the DNA sequence of [at least] 959 nematode species⁴. 959 may seem an odd number, but rather than aiming for a round 1000, the project celebrates the 959 cells in an adult C. elegans - the fundamental, simple cell biology that has made it such a powerful model system. The targets of this project include species across the diverse family tree of nematodes.

The researchers undertaking the project, a collaboration between the Sanger Institute and several universities in the UK, France, Germany, and the US, hope that the new genomes will be the foundations for the next 25 years of biology, building the nematode tree of life to put C. elegans in its evolutionary context.

C. elegans. Image credit: Bob Goldstein, WikiCommons

C. elegans is a nematode, or roundworm, and while it is a model organism for research, particularly for genetics and genomics, it is just one example of how to be a nematode. In isolation, it is difficult to know if “the worm” is typical of how a genome encodes an animal. Nematodes live in some of the most extreme environments on our planet – they have been isolated from alkaline soda lakes, vats of vinegar, deserts, the depths of the oceans and in deep within the earth’s crust. Other nematodes are important parasites of humans, farm animals and crop plants.

With the development of new, long-read DNA sequencing technologies over the past 10 years by companies such as PacBio, it is now possible to determine the DNA code of many more organisms for the first time. In the Tree of Life Programme at the Sanger Institute, researchers are part of global collaborations that are aiming to do just that.

Long-read DNA sequencing by the Sanger Institute using PacBio Revio machine. Image credit: Mark Thomson, Wellcome Sanger Institute.

Thousands of species are being collected, sent to the Sanger Institute, and the DNA sequence determined for the first time. The work is part of larger efforts to sequence the DNA of all complex life in the UK and Ireland (the Darwin Tree of Life Project) and on Earth (the Earth BioGenome Project).

Sequences so far

To date, over 100 species of nematode have been sequenced as part of the project. This includes C. sulstoni⁵, named in honour of John Sulston, who together with Sydney Brenner and Robert Horvitz won a Nobel Prize for their research into ‘the worm’⁶.

Many Caenorhabditis species are indistinguishable by sight – they are the same size and have the same body plan – but there is a huge diversity in their genomes. A paper published in 2004 states, ‘despite the lack of marked morphological diversity, more genetic disparity is present within this one genus than has occurred within all vertebrates.’⁷

Dr Lewis Stevens is a postdoctoral researcher in Professor Mark Blaxter’s team at the Sanger Institute. During his PhD he sequenced the genomes for 38 Caenorhabditis species, including one he isolated from a cow’s ear in Kenya, Caenorhabditis bovis⁸. Now he is working on assembling a much larger set of very high-quality Caenorhabditis genomes, using the data to explore the dynamics of evolution. Already he has discovered a new form of genome editing in some species, and identified gene duplications that have important implications for the nematodes’ biology.

“C. elegans is used for practically every type of research you can imagine, because it's such a valuable model – Alzheimer’s research, for example. We can learn things from C. elegans that we cannot learn from other, larger organisms. And that's how we want to use these new genomes – to understand animal genomes generally and how they evolve. Nematodes are a really useful model for that.”

Dr Lewis Stevens,
Postdoctoral Researcher, Wellcome Sanger Institute

Lewis is also enthusiastic about how comparative genomics can help place C. elegans research in an evolutionary context. “These new genomes will allow us to ask if what's been worked out in C. elegans over the last 60 years is true for all nematodes. We're finding that this depends on the piece of biology we look at: sometimes we think C. elegans will be the odd one out, but then we find it's the same in all species. Then other things you expect to be the same end up looking completely different in closely related species.”

One example is how sex is determined across the genus C. elegans and its close relative C. briggsae have both recently evolved to be hermaphrodites, but the genetic underpinnings of this change are completely different in the two species.

Collecting new species

Dr Erna King, also a postdoctoral researcher in Mark Blaxter’s team, studies nematodes found in the sea. Her interest in marine nematodes started during her PhD – she used them to understand the impacts of pollution on estuaries and realised that very little was actually known about the weird and wonderful species she was counting in her sediment samples. During her PhD she looked at sequence data from a single gene: now at the Sanger Institute, she is generating an unprecedented dataset of complete genomes for marine nematodes.

Unlike C. elegans, the species Erna is interested in cannot survive for long or be bred in a laboratory, and so they are less well understood. She samples from tidal mud flats and sandy beaches around the UK and filters the silt and mud to find the nematodes. “It’s like blind fishing,” she explains, as most species are not visible to the naked eye. “You just hope that you get something!” She is able to identify the different species under the microscope, based on their size and anatomical features.

Erna searching for nematodes at Blackwater Northey. Image credits: Erna King, Wellcome Sanger Institute.

Recently, a new way of extracting and processing the DNA has been developed by Dr Chris Laumer at the Sanger Institute. The method, called PiMmS, enables an entire genome to be sequenced from scratch, from a single nematode. It results in high-quality data from just picograms of DNA (a picogram is one trillionth of a gram). The method will have impacts beyond nematodes, as researchers at the Sanger Institute are adapting it for use in sequencing DNA for thousands of other tiny animals – the “meiobiota”.

“What’s exciting to me is that the incredible diversity in biology of these free-living nematodes is matched by the diversity of their genomes. We can explore this diversity to understand how they’re related to one another and how their chromosomes have evolved over time, which has never been studied before. As an ecologist, I’m also interested to learn how they’ve adapted to their different environments and evolved into so many different species.”

Dr Erna King,
Postdoctoral Researcher, Wellcome Sanger Institute

The future of nematode research

The 959 Nematode Genomes Project building high quality reference genomes for species not previously available for study. Because Lewis and Erna can now work from single specimens, they are illuminating parts of the tree of nematodes that have never been explored before. The completion of the C. elegans genome was a huge milestone for genome science, but that sequence in isolation cannot tell us everything. But it did provide a foundation for the 25 years’ worth of science that has followed, where scientists can understand their gene of interest within the context of the entire genome⁹. Lewis reflects on the future of the new data now becoming available:

“We hope the same will be true of the 959 Nematode Genomes project – yes, we have our own specific questions and we will discover new things along the way – but the lasting legacy will be the science we enable by generating this dataset.”