• Research

Earth Biogenome Project

A global partnership to sequence the genomes of all lifeforms so we can better understand and harness biodiversity

Project summary.

Led by: Seanna McTaggart - Programme Manager

Start date: 2019

End date: 2022

Funding: Wellcome Trust and BBSRC

Our planet is home to an astounding range of lifeforms, collectively described as biodiversity.

Those millions of species, and the ecosystems they inhabit, are crucial for cycling crucial nutrients, providing us with food, medicines, fuel and materials, and generating the oxygen in the air we breathe. However, climate change and human activity are negatively impacting biodiversity at an alarming rate.

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 a deep understanding of the genetic diversity and population dynamics of life on Earth. One way to investigate these topics is through genome analysis, which allows a wide range of scientific questions to be answered. 

The Earth Biogenome Project (EBP) is a global consortium whose ambitious long-term goal is to produce high quality (chromosome level) genome assemblies for all eukaryotic life on the planet.

Details.

Several Earlham Institute teams are contributing to different aspects of this endeavour. 

1. Data, Documentation and Process

Earlham Institute is an Institutional member of the EBP consortium, participating in the development of the documentation and processes that will ensure the best chances of a successful project.

2. Darwin Tree of Life

Earlham Institute is one of 9 partners in the Darwin Tree of Life (DToL) project, a Wellcome funded initiative that is part of the EBP, which has the goal of sequencing all eukaryotic life in the UK. That includes:

  • Developing a high-throughput pipeline to sequence, assemble and annotate genomes from single protist cells 
  • Developing and providing the computational infrastructure to share genome data according to FAIR principles (COPO)
  • Barcoding The Broads - a public engagement project that enables schools and nature groups to use DNA barcoding methods to identify and understand biodiversity on their doorstep

3. Pollinators and Mining Meadows

We are undertaking two BBSRC pump-priming projects that aim to demonstrate the power of a completed genome as a foundation for further scientific study.

  • The first of these is focussed on understanding the dynamics of several pollinator species within the UK. Specifically, whole genome sequencing will be used to allow a detailed population genomics analysis of bee species that show opposing trends of decline and growth.
  • The second pump-priming study is seeking to identify the genes involved in the synthesis of specific metabolites that may have medicinal properties in the common pot marigold plant. 

4. European Reference Genome Atlas (ERGA)

Earlham is playing a vital role in the European Reference Genome Atlas (ERGA), an initiative to produce reference genomes for all the flora and fauna of Europe, with Earlham providing:

  • COPO as a core partner on the project
  • Five reference genomes as part of the pilot project to sequence at least one reference genome for each country in Europe. In addition to a grass from the UK, the institute will work with Germany and Finland to sequence two bee genomes, the Czech Republic to sequence a fungus, and with a consortium from Sweden, Finland and Iceland to sequence a fish.

    

Tools.

Collaborative OPen Omics (COPO)

COPO is a portal for plant scientists to describe, store and retrieve data more easily. Data description is critical to increase the value of the data itself, allowing scientists (and online search tools) to better understand its relevance.

Wellcome Open Genome Portal

Collaborators.

Darwin Tree of Life

This is a collaboration between the listed partners below. Those with the designation of Genome Acquisition Lab (GAL) are primarily responsible for sample collection, vouchering and biobanking. Those with SEQ are primarily responsible for the sequencing and assembly of genomes. All genomes are annotated by EMBL-EBI, although they may be additionally annotated by other partners. Metadata brokering is provided by COPO, hosted and managed by the Earlham Institute. Wellcome Sanger Institute is the lead partner of the consortium.

  • Natural History Museum (GAL)
  • Royal Botanical Gardens Kew (GAL)
  • Royal Botanical Gardens Edinburgh (GAL)
  • Edinburgh University (SEQ)
  • Wellcome Sanger Institute (SEQ)
  • Marine Biological Association (GAL)
  • University of Oxford (GAL)
  • University of Cambridge (GAL)
  • EMBL-EBI, Earlham Institute (SEQ))

Protist Research

The Tom Richards lab at the University of Oxford is collaborating with Earlham researchers on the protist single cell sequencing project.

Impact statement.

This global project aims to sequence the genome of every living eukaryote species - animal, plant, fungus and protist - on Earth. Genomes provide a critical foundation in an increasingly data-rich world, allowing scientists to explore a wide range of interesting scientific topics, including addressing fundamental questions about the origin, evolution and maintenance of biodiversity, how to conserve, restore and protect the globe’s biota, and to harness biodiversity to benefit society and human welfare.