25 Genomes for 25 Years

The project's primary goal was to sequence 25 novel genomes representing UK biodiversity, as part of the Wellcome Sanger Institute's wider 25th Anniversary celebrations. This project was a pathfinder for long-read sequencing projects to demonstrate the Institute’s capabilities and provided reference genomes for the global scientific community.

About

The 25 Genomes for 25 Years project brought together a wide range of experts from a diverse range of research fields and organisations.

Outcomes

We hope that the provision by the Sanger Institute of reference genomes for 25 previously unsequenced UK species will lead to significant follow-on studies in population genetics, evolution studies, biodiversity management and conservation, and climate change effects.

Method

The Sanger Institute will perform DNA extraction, sequence using PacBio and Illumina X to 50x depth, perform 10x Chromium analysis, assemble the genomes and perform basic annotation.

Data use policy

The Wellcome Sanger Institute are committed to the principles of rapid data release. The 25 Genomes Project releases sequence data, assemblies, transcriptomes and other variant calls as a service to the research community. These data are released in accordance with the Fort Lauderdale and Toronto agreements, following Sanger Institute policies. The Sanger Institute and our collaborators intend to publish the results of our analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Wellcome Sanger Institute reserves the right to first publication. We strongly encourage researchers to contact us if there are any queries about referencing or publishing analyses based on pre-publication data from this project.

The 25 genomes

The 25 genomes represent five key areas of biodiversity in Britain.

Cryptic

Species that are out of sight, or have identical forms that are different in behaviour.

Brown Trout

Latin name: Salmo trutta

The brown trout has three isoforms that differ in their migratory patterns, for no apparent reason

Research partners: Mark Ives, Fisheries and Aquaculture Scientist at CEFAS (Centre for Environment, Fisheries and Aquaculture Science), Professor Sigbjørn Lien, Research Director, Norwegian University of Life Sciences (NMBU), and Professor Paulo Prodohl School of Biological Sciences – Professor of Ecology, Evolution, Behaviour and Environmental Economics, Institute for Global Food Security, Queen’s University Belfast

Common Pipistrelle Bat

Latin name: Pipistrellus pipistrellus

Two species of this the common pipistrelle bat co-exist, the genetics of which have not been determined

Research partners: Emma Teeling, Associate Professor at UCD Dublin and Manuel Ruedi, Curator (mammals and ornithology) at the Natural History Museum of Geneva

Carrington’s Featherwort

Latin name: Plagiochila carringtonii

Male Carringon featherworts are exclusively found in Scotland, while the females are in the Himalayas

Research partner: Neil Bell, Bryology Research Scientist at the Royal Botanical Garden Edinburgh

Video about the work

Summer truffle

Latin name: Tuber aestivum

Summer Truffles grow underground and are some of the most expensive of all edible fungi. Known as mycorrhizal, these fungi form a symbiotic association with a host plant on which they are dependent throughout their lifecycle.

Research partner: Dr Paul Thomas, MD and Scientific Manager, Mycorrhizal Systems Ltd

Dangerous

Giant Hogweed

Latin name: Heracleum mantegazzianum

Giant Hogweed has been called Britain’s most dangerous plant by UK newspapers. Its sap is highly toxic and can cause blistering of the skin following exposure to sunlight. The plant originates from Southern Russia and Georgia and was widely planted in ornamental gardens in the 1890s. It can grow more than 3 metres tall with flower heads up to 60cm wide.

Research partner: Sakshi Sharda, Ecole Polytechnique federale de Lausanne, Switzerland

Indian Balsam

Latin name: Impatiens glandulifera

A difficult to control invasive plant species spreading across the UK

Research partner: Lisa Outhwaite, Senior Gardener, Grounds team at the Wellcome Genome Campus

King Scallop, Great Scallop, Coquilles Saint-Jacques

Latin name: Pecten maximus

Some king scalllops harbour a dangerous toxin secreting bacteria

Research partner: Suzanne Williams, Head of Invertebrate Division at the Natural History Museum

New Zealand Flatworm

Latin name: Arthurdendyus triangulatus

This invasive species is a predator of UK earthworms

Research partners: Roy Neilson, Researcher at the James Hutton Institute and Rene Van der Wal, Professor of Ecology at the School of Biological Sciences at the University of Aberdeen and OPAL (Open Air Laboratories) at Imperial College London

Floundering

Endangered and declining species.

Red Squirrel

Latin name: Sciurus vulgaris

The 25 genomes for 25 years project may help reveal the genetic basis of the red squirrel’s vulnerability to the squirrelpox virus

Research partners: Rachel Cripps, Red Squirrel Officer, The Wildlife Trust for Lancashire, Manchester and North Merseyside, and Kat Fingland, Academic Associate, School of Animal Rural & Environmental Sciences (Nottingham Trent University)

Water Vole

Latin name: Arvicola amphibius

Understanding the genome of the water vole may help with population conservation management efforts

Research partner: Angus Carpenter, Head of education, training, research and conservation at the Wildwood Trust

Video about the work

Turtle Dove

Latin name: Streptopelia turtur

Studying the genome of the turtle dove may help with efforts to preserve the genetic diversity of the dwindling population

Research partners: Jenny Dunn, Lecturer in Animal Health and Disease at University of Lincoln and John Mallord, Senior Conservation Scientist at the RSPB (Royal Society for the Protection of Birds)

Northern February Red Stonefly

Latin name: Brachyptera putata

The genome of the Northern February red stonefly may help identify the genetic determinants of its need to live in its niche habitat

Research partner: Craig Macadam, Conservation Director at Buglife

Flourishing

Species on the up in the UK.

Grey Squirrel

Latin name: Sciurus carolinensis

This squirrel harbours the squirrelpox virus with apparently no ill effects

Research partner: Graham Smith, Head of Wildlife Epidemiology and Modelling at the Animal and Plant Health Agency

Ringlet Butterfly

Latin name: Aphantopus hyperantus

The ringlet butterly can fly in overcast skies and has a dwarf variety at higher altitutes

Research partner: To be announced

Roesel’s Bush-Cricket

Latin name: Metrioptera roeselii

This species is now spreading out of it’s usual salty habitats, is there a genetic change that has allowed this?

Research partners: Peter Sutton, Science Teacher at Redbourne Upper School and Björn Beckmann, Outreach and Recording Officer at the Centre for Ecology and Hydrology

Oxford Ragwort

Latin name: Senecio squalidus

This plant has some intersting reproduction habits and unknown species origin

Research partner: Lisa Outhwaite, Senior Gardener, Grounds team at the Wellcome Genome Campus

Iconic

Species that represent the British countryside.

Golden Eagle

Latin name: Aquila chrysaetos chrysaetos

There are only 440 breeding pairs of golden eagle left in the UK

Research partners: Rob Ogden, Head of Conservation Genetics, Royal (Dick) School of Veterinary Studies (Edinburgh) and Anna Meredith, Personal Chair of Zoological and Conservation Medicine, Royal (Dick) School of Veterinary Studies

Blackberry

Latin name: Rubus ulmifolius

The blackberry is ubiquitous in the UK, yet it is understudied

Research partners: Professor Mario Caccamo, Managing Director of NIAB EMR, Dr Felicidad Fernadez (NIAB EMR), Research Leader at NIAB EMR, Dr Hamid Ashrafi, Assistant Professor in Horticultural Science at NC State University, Dr Nahla Bassil, Plants Geneticist, National Clonal Germplasm Repository, Corvalllis, Oregon, USDA-ARS, Dr Michael Dosset, Research Scientist at BC Berry Cultivar Development Inc, Dr Margaret Worthington, Assistant Professor, Director Experiment Station, Horticulture, University of Arkansas, and Lisa Outhwaite, Senior Gardener, Grounds team at the Wellcome Genome Campus

European Robin

Latin name: Erithacus rubecula

European robins have magneto-receptors in their eyes that may allow them to ‘see’ magnetic fields

Research partners: Derek Gruar, Senior Research Assistant, Conservation Science at the RSPB (Royal Society for the Protection of Birds) and Jenny Dunn, Lecturer in Animal Health and Disease at the University of Lincoln

Video about the work

Red Mason Bee

Latin name: Osmia bicornis

The Red Mason Bee is about the size of a honeybee, but unlike honey bees they are solitary, with the females making nests in empty holes or stems of plants. These bees also prefer slightly colder temperatures which may result in them struggling in future due to climate change.

Research partner: David Notton, Senior curator (Insects division) at the Natural History Museum

Public vote

Five species were decided by a public vote through I’m a scientist get me out of here platform:

The five chosen by the public are:

Common Starfish

Latin name: Asterias rubens

Asterias rubens is the most common starfish species around the coast of the UK. An understanding of the adhesives starfish use to pull apart the mussels they feed on could lead to the development of novel bioadhesives for medical surgery. Whereas, the remarkable ability of starfish to regenerate their arms could provide important new insights in regenerative medicine.

Fen Raft Spider

Latin name: Dolomedes plantarius

The fen raft spider is one of the UK’s rarest animals, but they’re coming back. After 6,000 spiders were released, monitoring shows that populations are on the up. Genomics could shed light on how they are coping, and reveal secrets of the spider’s venom that could be useful in medicine, and how its silk could help improve mechanical engineering.

Video about the work

Lesser Spotted Catshark

Latin name: Scyliorhinus canicula

The lesser spotted catshark’s egg-cases or ‘mermaid’s purses’ are frequently found along the UK coastline. Understanding the shark’s ability to regenerate teeth and skin could help us heal human wounds.

Yellow-Legged Asian Hornet

Latin name: Vespa velutina

The Asian Hornet is an invasive species native to South East Asia, which is invading Europe at a rate of 100km every year. It is a voracious predator of insects, especially honeybees, and poses a negative impact on the beekeeping industry. Sequencing its genome could help in the design of specific pesticides to control its invasion, and give insights into social living in bees.

Video about the work

Eurasian Otter

Latin name: Lutra lutra

The Eurasian otter is a keystone species in the UK, but the population is listed as ‘Near Threatened’ on the IUCN Red List. Their position at the top of the freshwater food chain means otters serve as an environmental indicator species, and they can give clues about the pollution of their environment. Sequencing the otter genome will open the door for research into otters adaptations, parasites, scent communication and behaviour, and will ultimately help in protecting them.