International Consortium Officially Launches Earth BioGenome Project in London

The Genome Center is the administrative home for the Earth BioGenome Project, a global effort to sequence the genetic code of all the planet’s eukaryotes — some 1.5 million known species including all known plants, animals, protozoa and fungi. (Credit: Thinkstock)

Key scientific partners and funders from around the globe gathered in London today to officially launch the Earth BioGenome Project (EBP), a global effort to sequence the genetic code of all the planet’s eukaryotes — some 1.5 million known species, including all plants, animals, protozoa and fungi.

Today also marks the announcement by the Wellcome Sanger Institute that it will lead the UK contribution to the EBP by sequencing all 66,000 eukaryotic species across the British Isles, a new project known as the Darwin Tree of Life ProjectThe Wellcome Sanger Institute, a nonprofit based in the UK, is one of the world’s leading genome centers.

Harris Lewin

The UC Davis Genome Center is currently the administrative home for the EBP, led by Harris Lewin, a distinguished professor of evolution and ecology at UC Davis and chair of the EBP Working Group.

“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,” said Lewin. “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.”

Currently, fewer than 3,500, or about 0.2 per cent of all known eukaryotic species on Earth have had their genome sequenced. Sequencing all known eukaryotic genomes will revolutionize the 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.

“The Earth BioGenome Project can be viewed as infrastructure for the new biology,” said Lewin. “Having the roadmap, the blueprints for all living species of eukaryotes, will be a tremendous resource for new discoveries, understanding the rules of life, how evolution works, new approaches for the conservation of rare and endangered species and provide new resources for researchers in the fields of agriculture and medicine.”

Committing to a common goal

The EBP has made extraordinary progress in the last year leading up to today’s official launch. Seventeen institutions from across the globe, including the USA, United Kingdom, China, Germany, Denmark and Brazil, have signed a Memorandum of Understanding that commits each institution to work together towards the common goals of the project. In addition, 15 scientific communities and national and regional projects are also affiliated with the EBP.

The project builds on recent achievements of sequencing sets of species’ genomes for the first time. For example, the Vertebrate Genomes Project, chaired by Erich Jarvis of Rockefeller University, released the genomes of 14 species, including bat and fish species, the Canadian lynx and kakapo, with the ultimate aim of sequencing the genetic code of all 66,000 extant vertebrates.

The Beijing Genomics Institute (BGI) in Shenzhen, China, is also playing a major role in the project by leading the effort to sequence 10,000 plant genomes. The Global Ant Genomes Alliance aims to sequence approximately 200 ant genomes. Similarly, the USDA is launching an effort to sequence 100 genomes of agriculturally important insects and mites.

Recent and future advances in genomic sequencing and information technology make the project possible. It is expected to take ten years at an estimated cost of about $4.7 billion. By comparison, the Human Genome Project today would cost $5 billion, accounting for inflation. The EBP activities are currently funded by the participating organizations as well as private foundations, governmental organizations and crowd-funding sources.

“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,” said Sir Jim Smith, director of science at the Wellcome Sanger Institute. “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 aging, generate new approaches to feeding the world or create new bio materials,” said Smith.

Custodians of life on Earth

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. Overcoming these challenges requires new scientific knowledge of evolution and interactions among millions of the planet’s organisms.

“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,” said Professor Sir Mike Stratton, director of the Wellcome Sanger Institute. “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,” said Stratton.

The amount of biological data that will be collected and produced from this project is expected to be massive — more than the data accumulated by Twitter or YouTube. As part of the EBP Memorandum of Understanding, the project’s participants have agreed that data will be stored in public domain databases and access will be open to all for research purposes.

Current Partners and Participating Communities

• Australian Museum
• Baylor College of Medicine
• BioPlatforms Australia
• Beijing Genomics Institute at Shenzhen
• George Washington University
• Natural History Museum of Denmark
• Max-Planck Society
• Novim Group
• Royal Botanic Gardens at Kew
• SpaceTime Ventures
• University of California, Davis
• University of California, Santa Cruz
• University of Santiago
• University of Florida
• University of Illinois at Urbana-Champaign
• University of Sydney
• Wellcome Sanger Institute

Affiliated communities, regional and national projects

• 1000 Fungal Genomes Project (1KFG)
• Global Invertebrate Genomics Alliance (GIGA)
• Global Ant Genomics Alliance (GAGA)
• 5,000 Insect Genome Project (i5K)
• Ag100 Pests (USDA)
• 10,000 Plant Genomes Project (10KP)
• Bird 10,000 Genomes (B10K)
• Genome 10K Project
• Oz Mammals Genomics Framework Data Initiative (OMG)
• Darwin Tree of Life
• LOEWE-Centre for Translational Biodiversity Genomics
• University of California Consortium for the Earth BioGenome Project (CalEBP)
• Chilean 1000 Genomes Project
• Taiwan Biogenome Project
• Global Genome Initiative (GGI)

Contacts

Selected Websites

Media Resources

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Lisa Howard is with the UC Davis Office of Research

Posted in Highlights, News

Upcoming Talks and Events

Events on January 14, 2019
WCMC: Hands-on LC-MS Data processing and Statistics
Starts: 12:00 am
Ends: January 19, 2019 - 12:00 am
Location: UC Davis Conference Center, 550 Alumni Ln, Davis, CA 95616, USA
Description: Registration: http://ucanr.edu/survey/survey.cfm?surveynumber=15575

This course will feature hands-on training with real-world metabolomics data covering LC/MS compound identification, data processing, statistical analysis, network mapping and data interpretation.

We will instruct using a variety of software, workflows, and algorithms but also give theoretical background information and overviews. We will focus on utilizing open source software and only refer to commercial or vendor software when necessary.

All participants will be trained on laptops that were specifically purchased for course training, with all software already installed and data available to use.

The course will include:

untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
The course fees are $ 2,500 per participant to cover expenses for instructors, organization, materials and meals.

more Info:

Jeannette Martins

email: jmartins@ucdavis.edu

phone: +1-530-754-5357

Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.
Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:


1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.

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