Tag: 25 years

25 Genomes: The Common Starfish. Image credit: Ray Crundwell
25 GenomesSanger LifeSanger Science

25 Genomes: The Common Starfish

By: Alison Cranage
Date: 04.10.18


starfish_alex_cagan

The other-worldly, bright orange, 5 limbed creature is instantly recognisable. Paddling on a Cornish beach, or rockpooling on the Isle of Mull at low tide – it’s pretty likely you’ll come across one.

Lurking in the shallow waters of the UK and across the North Atlantic, the common starfish (Asterias rubens) is one of 1,500 starfish species in the world.

Asterias rubens was nominated by the scientific community and won a public vote to sequence the genome as part of our 25 genomes project. The common starfish falls into our ‘cryptic’ category of creatures. Cryptic, because their behaviour and many hidden talents are not well understood.

Hidden talents

Starfish sperm
The DNA we collected for Asterias rubens was from its sperm. Professor Elphick’s lab in central London is home to some 200 starfish where he collected the sample for us to sequence.

Possibly the most remarkable feature of starfish is their ability to re-generate limbs. If a starfish is attacked or is in danger, it can lose an arm in order to escape. It then grows a new one in its place. Nobody’s exactly sure how this works, but the key to finding out will be in its genome. Understanding the process would have huge implications for regenerative medicine.

The starfish genome could also help research into glue, including surgical adhesives that are used to heal wounds. Asterias rubens feasts on mussels and other molluscs. To get to the meat inside a mussel, it attaches its tube feet to the shell, by secreting a glue, and pulls it apart. Researchers are interested in that glue, and the genome sequence might reveal more about its production and structure.

Neuropeptides

Professor Maurice Elphick is working with us on the starfish genome. His research interests lie in neuropeptides. These tiny molecules act in the brain to control a whole range of processes including pain, reward, food intake, metabolism, reproduction, social behaviours, learning and memory.

Starfish don’t have a brain, but they are more closely related to humans than they are to most invertebrates. They do have neuropeptides – and his team have discovered many already. Several are involved in the unusual feeding behaviour of starfish.

To eat a mussel, once it’s forced open the shell, a starfish pushes its stomach out of its mouth. It partially digests its prey, takes up the resulting mussel ‘chowder’ and then retracts its stomach.

“I’m interested in understanding the evolution of neuropeptide systems, and also want to compare their functions and to find out what homologous molecules are doing in very different biological contexts.”
Maurice Elphick, Professor of Animal Physiology & Neuroscience, Queen Mary University of London.
One of the molecules they discovered triggers the stomach retraction. The equivalent molecule in humans clearly has a very different role. Professor Elphick explained: “Interestingly, we have also found that the neuropeptide behind the stomach retraction is evolutionarily related to a neuropeptide that regulates anxiety and arousal in humans.”

Professor Elphick explained how the genome sequence will enhance their ability to discover and study more neuropeptides. Because neuropeptides are tiny, the genes encoding them are not always easy to find. The team will study the genome in places where other species are known to have neuropeptide genes, to see if they can pinpoint an equivalent in the starfish (an approach known as synteny). This is only possible because we are using ‘long-read’ technology in the 25 genomes project – so the genomes will be the best possible quality, with few gaps.

The future

The starfish genome is now sequenced and the raw data available for any researcher to use. Over the coming months, our partners at EMBL-EBI will be assembling and annotating it, marking the position of genes and other features.

The finished genome will enable researchers to answer their own questions. About evolution, glue, neuropeptides or growing new arms.


About the author:

Alison Cranage is a science writer for the Wellcome Sanger Institute.

Links:

10 surprises from sequencing 25 new species
25 GenomesSanger LifeSanger Science

10 surprises from sequencing 25 new species

By: Alison Cranage
Date: 04.10.18


Sequencing human genomes is now routine at the Sanger Institute. Bacteria, yeast, worms, malaria, and other pathogens are also all regularly sequenced in their thousands. Our people are pretty well known for sequencing the human genome, but we’ve also contributed to the first sequencing of many others including the mouse, rat, zebrafish, pig and gorilla too.

The 25 genomes project is an entirely different beast. It’s posing some new, and frankly very odd, challenges. The diversity of the new species means we’ve had a steep learning curve. Here’s a peek at some of the weird and wonderful things we’ve discovered so far:


New Zealand flatworms will explode if you freeze them - not terribly helpful when trying to extract DNA from samples... Image Credit: S. Rae, Wikimedia Commons

New Zealand flatworms will explode if you freeze them – not terribly helpful when trying to extract DNA from samples… Image Credit: S. Rae, Wikimedia Commons

1. Don’t freeze flatworms

They explode.

You may well ask why we’d freeze them in the first place. But freezing samples, or in this case, whole worms, is standard practice to store them ready for DNA extraction.

Freezing New Zealand flatworms didn’t go so well though. The resulting sticky goop proved difficult to handle… and to get DNA from.


Is this the Oxford Ragwort you are looking for? The best way to know is take a picture and send it to an Oxford expert... Image credit: Rosser1954, Wikimedia Commons

Is this the Oxford Ragwort you are looking for? The best way to know is take a picture and send it to an Oxford expert… Image credit: Rosser1954, Wikimedia Commons

2. It’s good to get a second opinion when you’re identifying something

The Oxford ragwort was chosen to sequence in our flourishing category. We have ragwort growing here on campus, so we took a plant for sequencing.

But once we started, we soon realised it was not the ragwort we were looking for. The plant we had was hexaploid (it has 6 copies of its genome in every cell). The Oxford ragwort, which we were hoping to sequence, is diploid (it has 2 copies).

We sent a photo of the plant to an expert at Oxford University, who informed us we had the common ragwort.


There 300+ species of blackberry - and telling them apart can literally take years of observation. Image credit: Fir0002, Wikimedia Commons

There 300+ species of blackberry – and telling them apart can literally take years of observation. Image credit: Fir0002, Wikimedia Commons

3. There are over 300 species of blackberry in the UK

Yes, 300+.

They differ in a whole host of characteristics; sweetness, number of drooplets (the little blobs that make up the fruit), colour, size, thorns, flowers, lifecycle and more.

Finding the right one wasn’t easy, but we did sequence the correct one first time this time. Read more about the blackberry saga.


Fen Raft Spider - more popular than beavers, apparently. Image credit: Helen Smith, www.dolomedes.org.uk

Fen Raft Spider – more popular than beavers, apparently. Image credit: Helen Smith, www.dolomedes.org.uk

4. Fen raft spiders are more popular than beavers

In a public vote, the fen raft spider won out over the beaver to have its genome sequenced.

Both were contenders in the flourishing category of the project. Over 5,000 votes were cast in total, as part of “I’m A Scientist Get Me Out Of Here”.


Scottish Featherworts are a lonely bunch, they're all male and their female partners are almost half a world away. Image credit: David Freeman, RSPB

Scottish featherworts are a lonely bunch, they’re all male and their female partners are almost half a world away. Image credit: David Freeman, RSPB

5. All the featherworts in Scotland are male

Their potential partners are over 4,500 miles away in the Himalayas.

Botanists don’t know when the populations split, or how they got there. They only reproduce clonally in Scotland, and so it is uncertain how long they can last in this way.


Bush crickets have issues #1 - their genomes are 2.5 times bigger than we expected. Image credit: Richard Bartz

Bush crickets have issues #1 – their genomes are 2.5 times bigger than we expected. Image credit: Richard Bartz

6. Genomes are not always what you expect

We estimated that the genome of the bush cricket would be 2Gb, about 2/3rds the size of the human genome. We were wrong.

The estimate was based on the average cricket genome from the animal size genome database. But in fact it is 2.5 times larger than the human genome, coming in at 8.5Gb.

Read more about how this affected the sequencing.


7. It’s good to share

We knew this already, but this project has been a huge collaborative effort. It wouldn’t have been possible without scientists giving their time and sharing their expertise.

The Natural History Museum are a key partner for the 25 genomes project. They are helping with species identification and collection, as well as providing a link to natural historians and species experts across the UK.

The sequencing itself wouldn’t have been possible without PacBio. They have provided a machine for the project and provided expert technical support to enable the sequencing of the new species.

Our other collaborators include EMBL-EBI, The National Trust, The Wildlife Trust, Royal Society for the Protection of Birds (RSPB), Nottingham Trent University, Edinburgh University, 10x Genomics, Illumina and many more. See the full list here.


Bush crickets have issues #2 - they have cannibal tendencies. Image credit: Richard Bartz

Bush crickets have issues #2 – they have cannibal tendencies. Image credit: Richard Bartz

8. Don’t put bush crickets in a box together

They eat each other (or parts of each other).


Scallops are 20 times more genetically diverse than humans. Image credit: Asbjorn Hansen

Scallops are 20 times more genetically diverse than humans. Image credit: Asbjorn Hansen

9. Scallops are more diverse than people

We’ve found that scallops have 20 times the diversity of humans.

The king scallop was sequenced in the dangerous category of creatures. Human genomes are just 0.1 per cent different to each other – that is, only 0.1 per cent of your DNA code is different to any other person on the planet.

We have a pretty good idea why human genomes are so similar. It’s likely that events in our evolutionary past, like ice ages or infectious diseases caused a genomic bottleneck, which meant only a small group survived.

In scallops, 1.7 per cent of the DNA differs between any given individuals.


Using Pacbio machines, we read 25 new genome sequences in less than 10 months. Image credit: Wellcome Sanger Institute, Genome Research Limited

Using Pacbio machines, we read 25 new genome sequences in less than 10 months. Image credit: Wellcome Sanger Institute, Genome Research Limited

10. We can go faster than we thought

This project started in January 2018. We’re barely into October.

We’ve sequenced 25 new genomes in less than 10 months.

The PacBio machines we are using have doubled the amount of data they produce, per run, in the last 12 months. Next year, they will quadruple capacity.


About the author:

Alison Cranage is a science writer for the Wellcome Sanger Institute.

Links:

25 GenomesHuman Cell AtlasInfluencing PolicySanger LifeSanger Science

25 years of pushing the scientific boundaries

By: Alison Cranage
Date: 01.10.18


Wellcome_Sanger_Logo_Portrait_Digital_RGBThe Sanger Institute was set up to uncover the code of life – the human genome. We opened our doors 25 years ago and became the largest single contributor to the human genome project. The principles that sat behind those endeavours are still fundamental – tackling the biggest challenges, openness and collaboration. Those principles have also helped to make Sanger one of the world’s leaders in genomics and biodata.

The Human Genome Project transformed science. The seemingly simple order of four letters of DNA changes how we understand life. Vast new areas of research have opened up, impacting biology, medicine, agriculture, the environment, businesses and governments.

Alongside our sequencing facilities, our activities and research have grown to utilise genomic knowledge. Now we are using genomics to give us an unprecedented understanding of human health, disease and life on earth.


hgp_300

Read our original press release from 2003 announcing the completion of the Human Genome by clicking on the image above

Sequencing at scale

From the completion of the first human genome in 2003, we moved to the 1,000 and 10,000 genomes projects. Being able to compare sequences between individuals enables the understanding of diversity, evolution and the genetic basis of disease.

One of our latest projects is to work with UK Biobank to sequence the genomes of 50,000 individuals. Participants have already provided a wealth of data about their health and their lives – from blood samples to details of their diet. Linking this information to sequence data means we can understand more than ever before about the connections between our genomes and our health.

Kamilah the gorilla. Image courtesy of San Diego Zoo. To read about our work with the gorilla genome, please click the image

Kamilah the gorilla. Image courtesy of San Diego Zoo. To read about our work with the gorilla genome, please click on the image above

Across a wide range of species

Sanger researchers also sequence the genomes of pathogens and other organisms, as well as people. We have published the genomes of thousands of species – from deadly bacteria to worms to the gorilla. This enables research into evolution, infections, drug resistance, outbreaks, symbiosis, biology and host parasite interactions.

sequencing_output

The cumulative amount of DNA the Sanger Institute has read over time

At increasing speed and accuracy

Our sequencing teams, led by Dr Cordelia Langford, are constantly developing the technology to improve both accuracy and speed. In early 2018, we celebrated sequencing over five petabases of DNA (if you typed it all out, it would take 23 million years). The first petabyte took just over five years to produce. The fifth, just 169 days. The amount of genomic data now rivals that of the biggest data sources in the world – YouTube, Twitter and astrophysics.

sanger_data_centre

We run the largest life sciences data centre in europe

Supported by Europe’s largest life sciences data centre

The Sanger Institute is not only developing sequencing technology but also leading research in computational science, IT and bioinformatics, developing new ways to store and analyse petabytes of genomic and bio-data.


From sequence to clinic

How genome sequencing, or the sequence of any given individual, can be used hasn’t always been clear. But in the case of rare genetic diseases, it can change lives.

ddd_logo

To read more about the Deciphering Developmental Disorders project, please click on the image above

Giving families an answer

The Deciphering Developmental Disorders (DDD) study started 8 years ago, led by Dr Matt Hurles at the Sanger Institute. Over 13,600 children with rare developmental conditions, but without a diagnosis, joined the study. Sanger researchers, working together with clinical geneticists, have used genome sequencing to diagnose their conditions. 40 per cent of the children now have a diagnosis – giving the families some of the answers they were searching for. Knowing the genetic cause of a condition can help doctors manage it, help families connect with others as well as plan for the future.

Watch our video about tracking MRSA in real time

Watch our video about tracking MRSA in real time by clicking on the image above

Stopping outbreaks in hospitals

The ability of researchers to rapidly sequence and analyse bacterial genomes is also leading to advances for patients.

Dr Julian Parkhill and colleagues showed it was possible to track an MRSA outbreak in a neonatal ward in real-time. By sequencing MRSA isolates from patients and staff, they could track the outbreak, following its path from person to person. This enables clinicians to prevent further transmission and bring the outbreak under control.

Now, it is UK policy to sequence the genomes of pathogens in an outbreak.

Watch our video showing global tracking of infectious disease

Watch our video showing global tracking of infectious disease by clicking on the image above

Fighting epidemics at a global scale

But disease knows no borders. Pathogens can easily spread around the globe. Professor David Aanensen, group leader at the Sanger Institute, is also Director of the recently established Centre for Genomic Pathogen Surveillance. The centre co-ordinates global surveillance of pathogens (such as MRSA and the flu virus) using whole genome sequencing. The data is openly available. Countries around the world can monitor the rise and spread of pathogens as well as their growing resistance to antibiotics. This enables swift action – with the aim of stopping transmission and saving lives.


The forefront of human genomics

The rapid development of technology has led to the ability of researchers to sequence the DNA, or RNA, from a single cell. Previously, much larger quantities of material were needed. Single cell RNA sequencing is a powerful tool. It allows the study of an individual cell’s activity, functions and composition. And high throughput machines means hundreds of thousands of cells can be analysed at once.

human-cell-atlas-infographic-6_Aug UPDATED

To view the full infographic for the Human Cell Atlas project, please click on the image above

Capturing every type of cell in the human body, one at a time

The Human Cell Atlas is capitalising on these advances. The international collaboration is co-led by Dr Sarah Teichmann at the Sanger Institute. Launched in 2016, scientists are using Next-Generation Sequencing to sequence 30-100 million single cells from the human body – out of a total of roughly 37 trillion. The aim is to create a comprehensive, 3D reference map of all human cells. This will lead to a deeper understanding of cells as the building blocks of life. It will form a new basis for understanding human health and diagnosing, monitoring, and treating disease.

Like the human genome project before it, this huge project will disrupt science and human biology. And like the human genome project it will drive technology to make it possible.


The diversity of life

Beyond human health, genome sequence data allows the study of evolution, biology and biodiversity.

25logopng

To read more about our 25 Genomes Project, please click on the image above

25 Genomes for 25 years

For our 25th anniversary we have sequenced a more diverse range of species than ever before. 25 different species that represent biodiversity in the UK – from the golden eagle to the humble blackberry. Sequencing new species will push development of our technologies as each presents unique challenges. The sequences themselves will aid research into population genetics, evolution, biodiversity management, conservation and climate change.

But 25 species is just the beginning. Every single living thing has a genome, made up of exactly the same molecules of DNA or RNA. We want to uncover how the order of those molecules lead to the diversity of life on earth.

A_Novel_Representation_Of_The_Tree_Of_Life

To see the full sized tree of life diagram, please click on the image above

It took 13 years to sequence the first human genome. When the project began, no-one knew where it would lead. Now we sequence the equivalent of one gold-standard (30x) human genome in 24 minutes – faster and deeper genomic insights are enabling discoveries that improve health and our understanding of biology. These insights are happening right now, and they will lead to unimagined benefits for future generations – all possible from a sequence of four letters of DNA code.


About the author:

Alison Cranage is a science writer for the Wellcome Sanger Institute.

Links: