What is GGBN? Titelmasterformat durch Klicken bearbeiten. Textmasterformat bearbeiten. Zweite Ebene

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1 Titelmasterformat durch Klicken bearbeiten Dritte Ebene What is GGBN? (Global» Fünfte Genome Ebene Biodiversity Network) Jonathan Coddington GGBN Executive Committee Smithsonian Institution FAPESP August 14-18, 2017

2 Titelmasterformat durch Klicken bearbeiten The Goal of GGBN Genome-quality samples across the Tree of Life Research, Training, Development Dritte Ebene Conservation of Global Genetic Diversity» Fünfte Ebene

3 Titelmasterformat The durch Mission Klicken of GGBN bearbeiten molecular biodiversity repositories collaborate ensure quality standards, best practices, interoperability Dritte Ebene» Fünfte Ebene exchange of material follow national and international legislation and conventions

4 Titelmasterformat Target Audiences durch Klicken bearbeiten Biorepositories Textmasterformat bearbeiten Gardens, Zoos, Museums Researchers Dritte Ebene» Fünfte Ebene Any organization or biobank interested in: Non-human samples Interactions and partnerships GGBN goals

5 Tissues Titelmasterformat durch Klicken bearbeiten Lack of information on vouchers and samples Dritte Ebene The Problem Taxa» Fünfte Ebene Vouchers Sequences

6 Titelmasterformat Opening the Bottleneck durch via Klicken GGBNbearbeiten Easy to find via GGBN Data Portal Dritte Ebene Information available on: Genetic» Sample Fünfte Ebene quality Associated vouchers and specimens Associated legal information

7 Titelmasterformat GGBN Contributorsdurch Klicken bearbeiten Dritte Ebene» Fünfte Ebene

8 Titelmasterformat 66 members, 22 countries: durch Klicken 650,000 bearbeiten samples, ~3000 families, ~18,000 genera, ~55,000 species (sandbox) Dritte Ebene» Fünfte Ebene

9 Biodiversity Genomics: Costs and Progress ,817 Eukaryotic Genomes, Animals Fungi 100 Other Plants Protists 10 1

10 ,533 Eukaryotic Genomes Animals Fungi Other Plants Protists x.y scores: x=10 X N50 contig (kb). y=10 Y N50 scaffold (kb) 10

11 Dark Taxa Dark taxa outpacing names (58% spiders) Taxonomists dwindle Practical, mesoscale ID s urgently needed 11 R. Page 2016 PeerJ PrePrints 1649v1

12 Before GGI Goals After Sources: Hard-to-find, ambiguous quality tissues ambiguously owned by individual PI s Publically accessible, genomequality tissues in enterprise biorepositories following best practices and Int. treaties Data: Expensive boutique sequencing of a few model genomes Knowledge: Phenotype, expertbased taxonomy, underpinning environmental biology, evolution, conservation, ecology, biotech Affordable, coordinated, sequencing of a thoughtful synopsis of all of Life Approximate taxonomic IDs of most organisms anywhere Cheap, precise, scalable tools

13 Phyla: 74% Class: 61% Order: 42% Family: 23% Feasibility: Moorea Biocode Ex worldatlas.com

14 Titelmasterformat Brazilian Families (of durch 3,154, Klicken 1,611 bearbeiten not in GGBN) Count of families in Brazil (by state) that would be new to GGBN. State inventories downloaded from GBIF. Online visualization (with interactivity and more statistics) can be found here: Dritte Ebene s/brazilggbnfamilies/choropl eth?:embed=y&:display_count =yes» Fünfte Ebene Last updated 11 Aug 2017

15 Titelmasterformat Brazilian Genera (of durch 15265,11,701 Klicken bearbeiten new to GGBN) Count of genera in Brazil (by state) that would be new to GGBN. State inventories downloaded from GBIF. Online visualization (with interactivity and more statistics) can be found here: s/brazilggbngenerarelabele d_0/choropleth?:embed=y&:di splay_count=yes&publish=yes Dritte Ebene» Fünfte Ebene Last updated 11 Aug 2017

16 Percent 2010 Total Discovery of Species Earliest Description Bees Mammals Birds Spiders 16

17 Percent 2010 Total Discovery of Families 1,00 0,90 0,80 0,70 0,60 0,50 0,40 0,30 0,20 0,10 0,00 Bees Mammals Birds Spiders Angiosperms Bacteria-Archaea Earliest Description 17

18 GGBN Distribution of Families (2815) N Families BioBanks Percent 1918 One BioBank Two BioBanks Three BioBanks 5 38 Four BioBanks 1 48 Five BioBanks 2 23 Six BioBanks 1 7 Seven BioBanks 0

19 Cancer Scary? Death Inevitable? Payoffs Shorefishes of the Tropical Eastern Pacific Online Information System Old age a drag? Peter Schuchert Superbugs? animalsadda.com

20 Bolt Threads 20

21 DNA Quality

22 University of Alaska Museum Cryomech LNP120 LN2 Plant (120K) or LNP40 (40K) Ex Kyndall Hildebrandt 22

23 Feasibility: Phylogeny Domains 3 Phyla/ Divisions 89 Classes 258 Orders 1,148 Families 1 ~8,850 Genera 2 ~149,000 Species >15,000,000 Sampling coarse medium fine 1 8,613, 2 83,066 in Genbank (08/2017)

24 Phyla Catalogue of Life (99) NCBI GenBank DNA Barcodes (18) 13 6 Global Genome Biodiversity Network Tissues/DNA (63) Smithsonian Institution In-Progress Pipeline (29)

25 Families Catalogue of Life (8538) NCBI GenBank DNA Barcodes (2146) Global Genome Biodiversity Network Tissues/DNA (2482) Smithsonian Institution In-Progress Pipeline (1342)

26 Titelmasterformat History and Framework durch Klicken bearbeiten Founded in 2011 Botanic Garden and Botanical Museum Dritte Berlin Ebene(Technical) Smithsonian (Programmatic)» Fünfte Ebene MOU, By-Laws Membership: Core (pushes data), Associate (wants to push data), Observer

27 Titelmasterformat GGBN current structure durch Klicken bearbeiten Executive Committee Operations oversight Dritte Ebene Proposes strategy Operational management» Fünfte Ebene General Assembly Secretariat and Technical Management Decision making body Approves strategy Implement work plans Report outcomes Data Standards and Access Policies Biobank Procedures Document Library Communication and Outreach

28 Titelmasterformat GGBN Leadership Committee durch Klicken bearbeiten Dritte Ebene» Fünfte Ebene

29 GGBN Data Portal: Request samples Titelmasterformat durch Klicken bearbeiten Request DNA or tissue samples through GGBN portal Download of sample information Dritte Ebene Request forwarded to GGBN member holding the sample(s) o Institution» Fünfte responsible Ebene for all further steps Checking availability, compliance with ABS, and loaning conditions Provide price offer to scientist Request signing of Material Transfer Agreement (MTA) Shipping samples Citation guidelines for samples coming soon

30 Why Titelmasterformat GGBN world s durch genomic Klicken assets? bearbeiten GGBN data standard Complements other community standards Two technical implementations Dritte Ebene BioCASe and IPT Open source» software Fünfte Ebene Manage DNA and tissue collections GGBN Data Portal Standardized access to genomic sample and accompanying data Network of biodiversity biobanks Bring biobanking communities together

31 Titelmasterformat GGBN Online Sample durch Klicken Growth bearbeiten , , , , , , ,00 0,00 ~100% annual increase Dritte Ebene» Fünfte Ebene Samples Online Samples Online

32 Titelmasterformat 2017 GGBN-GGI durch Awards Klicken Program bearbeiten Dritte Ebene» Fünfte Ebene Six awardees, five countries 2,397 million samples 2,478 families 12,586 genera Collections discoverability by summer 2018

33 Titelmasterformat Looking Forwarddurch Klicken bearbeiten Increase discoverability Biorepositories (new/existing) Vouchers, genetic samples, new taxa Aggregators Dritte Ebene GGBN data Vierte standard Ebene Sequencing portals Implement ABS» Fünfte Ebene Increase vouchered sequences Grow collaborations, exchange knowledge across the globe Support biodiversity biobanks in biodiverse-rich countries Provide network of trusted collections

34 Titelmasterformat durch Klicken bearbeiten 2018 Conference Vienna calling Dritte Ebene» Fünfte Ebene Save the date: 22 nd 25 th May nd May = International Day for Biological Diversity

35 Titelmasterformat Thank you durch Klicken bearbeiten Dritte Ebene» Fünfte Ebene Deutsche Forschungsgemeinschaft Ministry of Higher Education and Science, Denmark ESBB ISBER SPNHC SYNTHESYS 3 GGBN Collaborators GGBN Interim Executive Committee GGBN Members GGBN Task Forces NMNH, Smithsonian Institution Botanischer Garten und Botanisches Museum, Berlin-Dahlem Natural History Museum of Denmark