Genetic code of 60,000 UK species to be sequenced
The genetic codes of 60,000 species in the UK are planned to be sequenced by the Wellcome Sanger Institute and its collaborators as part of a global effort to sequence the genomes of all 1.5 million known species of animals, plants, protozoa and fungi on Earth.
The UK effort, known as the Darwin Tree of Life Project, officially launches today in London (1 November) alongside the global effort, the Earth BioGenome Project (EBP). The launch is marked by a gathering of key scientific partners and funders from around the globe to discuss progress in organising and funding the project.
The EBP will ultimately create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies.
A greater understanding of Earth’s biodiversity and the responsible stewarding of its resources are among the most crucial scientific and social challenges of the new millennium. The overcoming of these challenges requires new scientific knowledge of evolution and interactions among millions of the planet’s organisms.
The Sanger Institute will serve as the genomics hub in the UK and will collaborate with the Natural History Museum in London, Royal Botanic Gardens, Kew, Earlham Institute, Edinburgh Genomics, University of Edinburgh, EMBL-EBI and others in sample collection, DNA sequencing, assembling and annotating genomes and storing the data. Further, the Sanger Institute will coordinate with other groups contributing to the EBP, such as the G10K Vertebrate Genomes Project (VGP) and the 10,000 Genomes Plant Project, to ensure there is no redundancy of effort, and that each project contributes to the other.
The Darwin Tree of Life project is estimated to cost approximately £100 million over the first five years, and the sequencing of 60,000 species’ genomes will take around 10 years.
To mark the 25th anniversary of the Wellcome Sanger Institute, the institute and its collaborators used PacBio® long-read technology and protocols developed by the VGP to sequence the genomes of 25 UK species for the first time*, including red and grey squirrels, the European robin, Fen raft spider and blackberry. The insights gained from the 25 Genomes Project form a basis for scaling up to sequence the genomes of 60,000 species.
The Darwin Tree of Life project is now possible due to recent and expected advances in sequencing and information technology that will enable the reading and interpretation of thousands of species’ genomes each year by the Sanger Institute and its partner institutions across the UK and internationally. All of the data will be stored in public domain databases and made freely available for research use.
Sequencing the eukaryotic species in the UK and worldwide will revolutionise our understanding of biology and evolution, bolster efforts to conserve, help protect and restore biodiversity, and in return create new benefits for society and human welfare.
“Globally, more than half of the vertebrate population has been lost in the past 40 years, and 23,000 species face the threat of extinction in the near future. Using the biological insights we will get from the genomes of all eukaryotic species, we can look to our responsibilities as custodians of life on this planet, tending life on Earth in a more informed manner using those genomes, at a time when nature is under considerable pressure, not least from us.”
Professor Sir Mike Stratton Director of the Wellcome Sanger Institute
“The Darwin Tree of Life Project is a tremendously important advance for the Earth BioGenome Project and will serve as a model for other parallel national efforts. The Wellcome Sanger Institute brings decades of experience in genome sequencing and biology to help build the global capacity necessary to produce high quality genomes at scale. The Earth BioGenome Project and its partner organizations welcome the outstanding leadership that the Wellcome Sanger Institute brings to our efforts to sequence all known eukaryotic life on our planet.”
Professor Harris Lewin University of California, Davis, United States and Chair of the Earth BioGenome Project
“When the Human Genome Project began 25 years ago, we could not imagine how the DNA sequence produced back then would transform research into human health and disease today. Embarking on a mission to sequence all life on Earth is no different. From nature we shall gain insights into how to develop new treatments for infectious diseases, identify drugs to slow ageing, generate new approaches to feeding the world or create new bio materials.”
Sir Jim Smith Director of Science at Wellcome
More information
Eukaryotic species are defined as organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes, which are unicellular organisms that lack a membrane-bound nucleus, mitochondria or any other membrane-bound organelle (Bacteria and Archaea).
The Earth BioGenome Project (EBP) aims to sequence, catalogue and categorise the genomes of all of Earth’s eukaryotic biodiversity over a period of ten years. The estimated cost of the EBP is $4.7 billion. Accounting for inflation, the Human Genome Project today would cost $5 billion.
* For more information on the Sanger 25 Genomes Anniversary Project news story, visit: https://www.sanger.ac.uk/news_item/25-uk-species-genomes-sequenced-first-time
Funding:
The Wellcome Sanger Institute will use core funding from Wellcome to introduce a research programme in Tree of Life genomics. Further funding support for sample collection, sequencing machines, data infrastructure is required.
Activities of the EBP are currently being funded by the participating organisations as well as private foundations, governmental organisations and crowd-funding sources. Participating institutions are committed to raising funds to complete the project in 10 years. Significant funds have already been raised by taxon-based communities, national and regional projects to meet the $600 million goal necessary to complete Phase 1 of the project, which aims to produce approximately 9000 reference quality genomes across all taxonomic families.
Appendix of quotes from partners:
“The Natural History Museum is proud to be collaborating with the Wellcome Sanger Institute on the Darwin Tree of Life project. It is hoped that together we can uncover the blueprints of the diversity of UK life, which will effectively re-write what we know about these species. By comparing those blueprints within and between species we can understand the genetic diversity of fauna and flora from the UK and beyond. Sequencing the genomes of all life will reveal aspects of evolution we’ve not even dreamt of.”
Dr Tim Littlewood Head of Life Sciences at the Natural History Museum, London
“This project not only has the potential to tell us a lot about the evolution of the diversity of life on Earth, as well as preserving valuable genetic information for future generations, but also to harness this data for the public good. This information will enable us to better protect ecosystems and understand how they function. We will also be able to mine genomic data for valuable new materials and medicines as well as new genetic diversity that can be used to protect crops from disease or climate change.”
Professor Federica Di Palma Director of Science at the Earlham Institute
“The launch of the Darwin Tree of Life project is the realisation of a longstanding dream. Having the full genomes of all the organisms we share the planet with will change our ability to understand and care for them. The UK environmental and evolutionary research community has for many years been leading the way in sequencing the DNA of diverse species, and this revolutionary project will transform the science we can do.”
Professor Mark Blaxter Of Edinburgh Genomics and the University of Edinburgh
“Sequencing genomes will not only help us to understand better how species have evolved and diversified but will also provide vital insights into how they impact and influence ecosystem functioning and global change response. At Kew, we’re utilising our unique collections for large sequencing projects, where genome data can provide us with diagnostic tools to be able to effectively respond to disease outbreaks and minimise the impact on food security.”
Dr Ester Gaya A senior mycologist and Dr Felix Forest, a senior scientist at Royal Botanic Gardens, Kew
“The Darwin Tree of Life project is an exciting opportunity to understand life, evolution, ecosystems and biodiversity by leveraging genomics and our experience in creating biological data resources that are freely available to everyone in the world.”
Dr Paul Flicek A senior scientist and team leader at EMBL’s European Bioinformatic Institute
“PacBio recently provided the foundational technology to enable completion of the 25 Genomes Project at the Wellcome Sanger Institute, and we are honored to be an integral part of the Darwin Tree of Life project as it deploys the power of our sequencing technology on a much broader scale. With the recent and ongoing improvements in our technology, we are well positioned to support the needs for scaling the sequencing and assembling of the genomes for the large number of species targeted by this project as well as the Earth BioGenome Project.”
Dr Jonas Korlach Chief Scientific Officer at Pacific Biosciences
Selected websites
Earth BioGenome Project
Carl R. Woese Institute for Genomic Biology
University of California, Davis Genome Center
The UC Davis Genome Center serves the Omics needs of a large community of scientists, government and industry partners. State-of-the-art facilities for genome sequencing, gene expression analysis, an NIH-funded metabolomics core, proteomics and bioinformatics support research activities of 40 full-time faculty members involved in fundamental and translational research on agriculture, the environment and human health. The Genome Center is the current administrative home of the Earth BioGenome Project. http://genomecenter.ucdavis.edu/
Royal Botanic Gardens, Kew
The Royal Botanic Gardens, Kew is a world famous scientific organisation, internationally respected for its outstanding collections as well as its scientific expertise in plant diversity, conservation and sustainable development in the UK and around the world. Kew Gardens is a major international and a top London visitor attraction. Kew’s 132 hectares of landscaped gardens, and Wakehurst, Kew’s Wild Botanic Garden, attract over 2.1 million visits every year. Kew was made a UNESCO World Heritage Site in July 2003 and celebrated its 250th anniversary in 2009. Wakehurst is home to Kew’s Millennium Seed Bank, the largest wild plant seed bank in the world. Kew receives approximately one third of its funding from Government through the Department for the Environment, Food and Rural Affairs (Defra) and research councils. Further funding needed to support Kew’s vital work comes from donors, membership and commercial activity including ticket sales. www.kew.org
The Earlham Institute
The Earlham Institute (EI) is a world-leading research Institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) – £5.43m in 2017/18 – as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities. www.earlham.ac.uk
Natural History Museum
The Natural History Museum exists to inspire a love of the natural world and unlock answers to the big issues facing humanity and the planet. It is a world-leading science research centre, and through its unique collection and unrivalled expertise it is tackling issues such as food security, eradicating diseases and managing resource scarcity. The Natural History Museum is the most visited natural history museum in Europe and the top science attraction in the UK; we welcome more than 4.5 million visitors each year and our website receives over 500,000 unique visitors a month. People come from around the world to enjoy our galleries and events and engage both in-person and online with our science and educational activities through innovative programmes and citizen science projects. http://www.nhm.ac.uk/
Edinburgh Genomics
Edinburgh Genomics is world renowned for the provision of advanced genomics services. Rooted in the University of Edinburgh, it produces high-quality, high-volume data for global collaborators and customers across academia, government and industry. Investment in the latest genome sequencing technologies have enabled the organization to lead the way for genomics in Scotland, providing a richer picture of genetic diversity in evolution and ecology and improved patient diagnosis and disease management. With trusted experts and the confidence to deliver high quality results, Edinburgh Genomics is rapidly changing global research and future patient care. http://genomics.ed.ac.uk
European Bioinformatics Institute (EMBL-EBI)
The European Bioinformatics Institute (EMBL-EBI) is a global leader in the storage, analysis and dissemination of large biological datasets. We help scientists realise the potential of ‘big data’ by enhancing their ability to exploit complex information to make discoveries that benefit humankind.
We are at the forefront of computational biology research, with work spanning sequence analysis methods, multi-dimensional statistical analysis and data-driven biological discovery, from plant biology to mammalian development and disease.
We are part of EMBL and are located on the Wellcome Genome Campus, one of the world’s largest concentrations of scientific and technical expertise in genomics. Website: www.ebi.ac.uk
About Pacific Biosciences
Pacific Biosciences of California, Inc. (NASDAQ:PACB) offers sequencing systems to help scientists resolve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT®) technology, Pacific Biosciences’ products enable: de novo genome assembly to finish genomes in order to more fully identify, annotate and decipher genomic structures; full-length transcript analysis to improve annotations in reference genomes, characterize alternatively spliced isoforms in important gene families, and find novel genes; targeted sequencing to more comprehensively characterize genetic variations; and real-time kinetic information for epigenome characterization. Pacific Biosciences’ technology provides high accuracy, ultra-long reads, uniform coverage, and the ability to simultaneously detect epigenetic changes. PacBio® sequencing systems, including consumables and software, provide a simple, fast, end-to-end workflow for SMRT Sequencing. More information is available at www.pacb.com
Forward-Looking Statements
All statements in this press release that are not historical are forward-looking statements, including, among other things, statements relating to future availability, uses, accuracy, quality or performance of, or benefits of using, products or technologies, product improvements or enhancements, the suitability or utility of methods, products or technologies for particular applications, studies or projects, the expected costs or benefits of sequencing projects, and other future events. You should not place undue reliance on forward-looking statements because they involve known and unknown risks, uncertainties, changes in circumstances and other factors that are, in some cases, beyond Pacific Biosciences’ control and could cause actual results to differ materially from the information expressed or implied by forward-looking statements made in this press release. Factors that could materially affect actual results can be found in Pacific Biosciences’ most recent filings with the Securities and Exchange Commission, including Pacific Biosciences’ most recent reports on Forms 8-K, 10-K and 10-Q, and include those listed under the caption “Risk Factors.”
Pacific Biosciences undertakes no obligation to revise or update information in this press release to reflect events or circumstances in the future, even if new information becomes available.
The Wellcome Sanger Institute
The Wellcome Sanger Institute is one of the world’s leading genome centres. Through its ability to conduct research at scale, it is able to engage in bold and long-term exploratory projects that are designed to influence and empower medical science globally. Institute research findings, generated through its own research programmes and through its leading role in international consortia, are being used to develop new diagnostics and treatments for human disease. To celebrate its 25th year in 2018, the Institute is sequencing 25 new genomes of species in the UK. Find out more at www.sanger.ac.uk or follow @sangerinstitute
Wellcome
Wellcome exists to improve health for everyone by helping great ideas to thrive. We’re a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. wellcome.org
