Intro to BGE for the Norwegian Biodiversity & Genomics Conference

9 February 2023

Gamle Festsal, Domus Academica, Oslo

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Overarching mission

Accelerate the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline

Overarching Objectives

BIODIVERSITY GENOMICS EUROPE

BIODIVERSITY GENOMICS EUROPE

BIODIVERSITY GENOMICS EUROPE

Camila Mazzoni

BGE Genome stream leader, IZW

BGE ERGA (Genome) Stream

Genome stream

BGE Genome stream general goals

BGE Genome Stream Project general goals:

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1. Support ERGA to become established and recognized as the European node of the Earth BioGenome Project
2. Support ERGA’s setting up of a multi-institutional European framework for the coordinated production of reference genomes following ERGA principles
3. Support ERGA’s actions that begin to address the imbalances of resources, expertise, and maturity in biodiversity genomics research across Europe
4. Demonstrate the use and potential of reference genomes in applications connected to society, policy makers, and other stakeholders
5. Support the ERGA consortium to become an umbrella network for promoting the generation and analysis of reference-quality genomes at scale across Europe

BIODIVERSITY GENOMICS EUROPE

Genome stream

WP structure and connections to ERGA

BIODIVERSITY GENOMICS EUROPE

Genome stream

WP connections to Genome Workflow

BIODIVERSITY GENOMICS EUROPE

Astrid Böhne

WP5 lead and LIB-ZFMK

WP5 ERGA Field to Lab

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BIODIVERSITY GENOMICS EUROPE · Kick-off meeting. 14-16 November 2022 - Naturalis Biodiversity Center, Leiden (Netherlands)

WP5 ERGA Field to Lab

Objectives / Deliverables

BIODIVERSITY GENOMICS EUROPE · Kick-off meeting. 14-16 November 2022 - Naturalis Biodiversity Center, Leiden (Netherlands)

WP5 ERGA Field to Lab

Objectives / Deliverables

Objectives / Deliverables

Development of Prioritization

Criteria

Species Catalog

https://goat.genomehubs.org

Species Sampling

Specimen voucher

Tissue/DNA voucher

Mark Blaxter | Olga Vinnere Pettersson

Sanger | SciLifeLabs

UK | Sweden

Genome Sequencing

WP 7

WP7: Genome Sequencing

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 Who are we? 

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a collaboration between established and emerging genome centres

• SciLifelab, SWEDEN
• Sanger Institute, UK
• CNAG, SPAIN
• Genoscope, FRANCE
• Italian Joint Research Unit, ITALY

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and (for T7.2)

• University of Oslo, NORWAY

 What do we plan to do? 

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for T7.1: provide expert, high-throughput genomic and transcriptomic sequencing for ERGA, including DNA and RNA extractions, sequencing and raw data QC

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for T7.2: build a community of researchers and genomics centres in Europe that develops and shares best practice in the laboratory protocols necessary for whole-biota reference-quality genomics

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Coordinating with WP6 throughout….

T7.1 Reference Genome Sequencing

T7.2 Sequencing knowledge network

Beyond BGE and ERGA

 Pan-European coordination and collaboration 

Synergy and synthesis across genome centres in Europe, sharing best practice, enthusiasm and vision, building systems fit for the future of biodiversity genomics

 Robust, dependable data generation protocols 

Processes to deliver data from a wide phylogenetic range of taxa from protists to plants to fungi to animals, including dedicated R&D

 Sequencing at scale 

A collective capacity that is sufficient for the needs of the ERGA community to 2025 and beyond, exploiting the economies of scale to reduce costs

 Innovation and understanding 

Developing new approaches to extraction and sequencing, including collaborations with technology developers and testing of new systems

 Development of an open knowledgebase 

Sharing technical discoveries and best practice to bring new sequencing partners on board and increase understanding of the actuality of biodiversity genomics

 Ready to build and grow from 2025 

A continent-wide collaboration ready to scale to the next level

WP7: Genome Sequencing

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José Melo-Ferreira

WP Leader BIOPOLIS - CIBIO

WP11 - Genome Applications

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WP 11 - Genome Applications

BIODIVERSITY GENOMICS EUROPE · Kick-off meeting. 14-16 November 2022 - Naturalis Biodiversity Center, Leiden (Netherlands)

Objectives / Deliverables

Objectives:

• Demonstrate the application of reference genomes in matters of biodiversity utility and concern.
• Applied Case Studies: Showcase how reference genomes are key components of biodiversity research, conservation and bioeconomy.
• Application support: Networking and other activities that will maximize applicability and the link with stakeholders and public engagement.

Robert Waterhouse

WP12 Coordinator, UNIL

WP12 JOINT NETWORK ACTIVITIES

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BIODIVERSITY GENOMICS EUROPE · Kick-off meeting. 14-16 November 2022 - Naturalis Biodiversity Center, Leiden (Netherlands)

WP12 Joint Network Activities

Overall Structure

T12.7 Intraspecific

Genetic Diversity

T12.3 Multi-Locus

Sequence Assays

T12.8 Developing

Genomic Barcodes

T12.4 Dark Biodiversity

Genomics

T12.2 Pollinator

Population Sampling

T12.6 Metadata

Change Management

T12.5 FAIR Data

Infrastructures

T12.1 Joint Network Training

Substream: intraspecific genetic diversity monitoring

R&D: non-described insects, & hard-2-discriminate plants

Metadata management for both genomes & barcodes

Genome+Barcode Workflow training: samples-focused

BIODIVERSITY GENOMICS EUROPE · Kick-off meeting. 14-16 November 2022 - Naturalis Biodiversity Center, Leiden (Netherlands)

WP12 Joint Network Activities

DIVERSITY

T12.7 Intraspecific

Genetic Diversity

T12.3 Multi-Locus

Sequence Assays

T12.2 Pollinator

Population Sampling

Substream: intraspecific genetic diversity monitoring

T12.7 M14-39 –CIBIO (24), CSIC/UiO (2):

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• Develop protocols to design monitoring tools for capturing intraspecific genetic compositions ⇒ Essential Biological Variable for biomonitoring
• Focused on pollinators (c.f. T12.2; T12.3) ⇒ will combine analyses of full reference genomes and population-level whole genome resequencing data
• Develop and validate multi-locus assays capable of capturing genetic diversity across species

Pollinator Diversity Tools

WP4 - Barcoding Sampling

Objectives & Deliverables

BIODIVERSITY GENOMICS EUROPE

T4.3 Museum Collection Sampling – NHM

• Tissue sample 33,000 expertly identified museum specimens from 11,000 species

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• Provide tissues to sequencing centres to fill gaps in DNA barcode reference libraries and aid in the development of intraspecific genetic diversity monitoring tools for priority taxa

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• Operate in close coordination with the field sampling Tasks T4.4 and T4.5

BIODIVERSITY GENOMICS EUROPE

WP4 - Barcoding Sampling

Objectives & Deliverables

T4.5 Aquatic Field Sampling – NTNU

• Sample 3,900 individual specimens of 1,300 species

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• Coordinate and perform sampling of eDNA from 55 sites for assessment of marine invasive species
• 5 ports extensively (5 sites, 3 reps, 5 times through season, 3 markers, 3 pcr replicates)
• 50 harbours, citizen science 3 times through season (collaboration with T2.4)
• => 525 sampling events across Europe

Rebekah Oomen

Torsten Struck

Ole K. Tørresen

Kjetill Jakobsen

Ave Tooming-Klunderud

Thomas Marcussen

Torbjørn Ekrem

Questions? Ask us!

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