Literature DB >> 29686065

Earth BioGenome Project: Sequencing life for the future of life.

Harris A Lewin1,2,3,4, Gene E Robinson5, W John Kress6, William J Baker7, Jonathan Coddington6, Keith A Crandall8, Richard Durbin9,10, Scott V Edwards11,12, Félix Forest7, M Thomas P Gilbert13,14, Melissa M Goldstein15, Igor V Grigoriev16,17, Kevin J Hackett18, David Haussler19,20, Erich D Jarvis21, Warren E Johnson22, Aristides Patrinos23, Stephen Richards24, Juan Carlos Castilla-Rubio25,26, Marie-Anne van Sluys27,28, Pamela S Soltis29, Xun Xu30, Huanming Yang31, Guojie Zhang30,32,33.   

Abstract

Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

Entities:  

Keywords:  access and benefit sharing; biodiversity; data science; genome sequencing; genomics

Mesh:

Year:  2018        PMID: 29686065      PMCID: PMC5924910          DOI: 10.1073/pnas.1720115115

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  37 in total

1.  The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

Authors:  Heather Bracken-Grissom; Allen G Collins; Timothy Collins; Keith Crandall; Daniel Distel; Casey Dunn; Gonzalo Giribet; Steven Haddock; Nancy Knowlton; Mark Martindale; Mónica Medina; Charles Messing; Stephen J O'Brien; Gustav Paulay; Nicolas Putnam; Timothy Ravasi; Greg W Rouse; Joseph F Ryan; Anja Schulze; Gert Wörheide; Maja Adamska; Xavier Bailly; Jesse Breinholt; William E Browne; M Christina Diaz; Nathaniel Evans; Jean-François Flot; Nicole Fogarty; Matthew Johnston; Bishoy Kamel; Akito Y Kawahara; Tammy Laberge; Dennis Lavrov; François Michonneau; Leonid L Moroz; Todd Oakley; Karen Osborne; Shirley A Pomponi; Adelaide Rhodes; Scott R Santos; Nori Satoh; Robert W Thacker; Yves Van de Peer; Christian R Voolstra; David Mark Welch; Judith Winston; Xin Zhou
Journal:  J Hered       Date:  2014 Jan-Feb       Impact factor: 2.645

Review 2.  Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being.

Authors:  Gretta T Pecl; Miguel B Araújo; Johann D Bell; Julia Blanchard; Timothy C Bonebrake; I-Ching Chen; Timothy D Clark; Robert K Colwell; Finn Danielsen; Birgitta Evengård; Lorena Falconi; Simon Ferrier; Stewart Frusher; Raquel A Garcia; Roger B Griffis; Alistair J Hobday; Charlene Janion-Scheepers; Marta A Jarzyna; Sarah Jennings; Jonathan Lenoir; Hlif I Linnetved; Victoria Y Martin; Phillipa C McCormack; Jan McDonald; Nicola J Mitchell; Tero Mustonen; John M Pandolfi; Nathalie Pettorelli; Ekaterina Popova; Sharon A Robinson; Brett R Scheffers; Justine D Shaw; Cascade J B Sorte; Jan M Strugnell; Jennifer M Sunday; Mao-Ning Tuanmu; Adriana Vergés; Cecilia Villanueva; Thomas Wernberg; Erik Wapstra; Stephen E Williams
Journal:  Science       Date:  2017-03-31       Impact factor: 47.728

3.  Sequencing all life captivates biologists.

Authors:  Elizabeth Pennisi
Journal:  Science       Date:  2017-03-03       Impact factor: 47.728

4.  White House unveils National Microbiome Initiative.

Authors:  Aaron Bouchie
Journal:  Nat Biotechnol       Date:  2016-06-09       Impact factor: 54.908

5.  Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.

Authors:  Christian Rinke; Janey Lee; Nandita Nath; Danielle Goudeau; Brian Thompson; Nicole Poulton; Elizabeth Dmitrieff; Rex Malmstrom; Ramunas Stepanauskas; Tanja Woyke
Journal:  Nat Protoc       Date:  2014-04-10       Impact factor: 13.491

6.  Contentious relationships in phylogenomic studies can be driven by a handful of genes.

Authors:  Xing-Xing Shen; Chris Todd Hittinger; Antonis Rokas
Journal:  Nat Ecol Evol       Date:  2017-04-10       Impact factor: 15.460

Review 7.  The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing.

Authors:  Kevin McCluskey; Katharine B Barker; Hazel A Barton; Kyria Boundy-Mills; Daniel R Brown; Jonathan A Coddington; Kevin Cook; Philippe Desmeth; David Geiser; Jessie A Glaeser; Stephanie Greene; Seogchan Kang; Michael W Lomas; Ulrich Melcher; Scott E Miller; David R Nobles; Kristina J Owens; Jerome H Reichman; Manuela da Silva; John Wertz; Cale Whitworth; David Smith
Journal:  mBio       Date:  2017-08-15       Impact factor: 7.867

8.  The Global Genome Biodiversity Network (GGBN) Data Portal.

Authors:  Gabriele Droege; Katharine Barker; Jonas J Astrin; Paul Bartels; Carol Butler; David Cantrill; Jonathan Coddington; Félix Forest; Birgit Gemeinholzer; Donald Hobern; Jacqueline Mackenzie-Dodds; Éamonn Ó Tuama; Gitte Petersen; Oris Sanjur; David Schindel; Ole Seberg
Journal:  Nucleic Acids Res       Date:  2013-10-16       Impact factor: 16.971

9.  A unifying model of genome evolution under parsimony.

Authors:  Benedict Paten; Daniel R Zerbino; Glenn Hickey; David Haussler
Journal:  BMC Bioinformatics       Date:  2014-06-19       Impact factor: 3.169

10.  The Global Genome Biodiversity Network (GGBN) Data Standard specification.

Authors:  G Droege; K Barker; O Seberg; J Coddington; E Benson; W G Berendsohn; B Bunk; C Butler; E M Cawsey; J Deck; M Döring; P Flemons; B Gemeinholzer; A Güntsch; T Hollowell; P Kelbert; I Kostadinov; R Kottmann; R T Lawlor; C Lyal; J Mackenzie-Dodds; C Meyer; D Mulcahy; S Y Nussbeck; É O'Tuama; T Orrell; G Petersen; T Robertson; C Söhngen; J Whitacre; J Wieczorek; P Yilmaz; H Zetzsche; Y Zhang; X Zhou
Journal:  Database (Oxford)       Date:  2016-10-02       Impact factor: 3.451

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  156 in total

1.  The 160K Natural Organism Library, a unique resource for natural products research.

Authors:  Siew Bee Ng; Yoganathan Kanagasundaram; Hao Fan; Prakash Arumugam; Birgit Eisenhaber; Frank Eisenhaber
Journal:  Nat Biotechnol       Date:  2018-07-06       Impact factor: 54.908

2.  Faraway, so close. The comparative method and the potential of non-model animals in mitochondrial research.

Authors:  Liliana Milani; Fabrizio Ghiselli
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-12-02       Impact factor: 6.237

3.  CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes.

Authors:  Heiner Kuhl; Ling Li; Sven Wuertz; Matthias Stöck; Xu-Fang Liang; Christophe Klopp
Journal:  Gigascience       Date:  2020-05-01       Impact factor: 6.524

4.  Opinion: Intercepting pandemics through genomics.

Authors:  W John Kress; Jonna A K Mazet; Paul D N Hebert
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-03       Impact factor: 11.205

5.  Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Authors:  Matthew T Parker; Katarzyna Knop; Anna V Sherwood; Nicholas J Schurch; Katarzyna Mackinnon; Peter D Gould; Anthony Jw Hall; Geoffrey J Barton; Gordon G Simpson
Journal:  Elife       Date:  2020-01-14       Impact factor: 8.140

6.  Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life.

Authors:  Jason A Somarelli; Amy M Boddy; Heather L Gardner; Suzanne Bartholf DeWitt; Joanne Tuohy; Kate Megquier; Maya U Sheth; Shiaowen David Hsu; Jeffrey L Thorne; Cheryl A London; William C Eward
Journal:  Mol Biol Evol       Date:  2020-01-01       Impact factor: 16.240

7.  Mercury exposure assessment in indigenous communities from Tarapaca village, Cotuhe and Putumayo Rivers, Colombian Amazon.

Authors:  Maria Alcala-Orozco; Karina Caballero-Gallardo; Jesus Olivero-Verbel
Journal:  Environ Sci Pollut Res Int       Date:  2019-11-14       Impact factor: 4.223

8.  A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals.

Authors:  Yatish Turakhia; Heidi I Chen; Amir Marcovitz; Gill Bejerano
Journal:  Nucleic Acids Res       Date:  2020-09-18       Impact factor: 16.971

9.  Efficient DNA sequence compression with neural networks.

Authors:  Milton Silva; Diogo Pratas; Armando J Pinho
Journal:  Gigascience       Date:  2020-11-11       Impact factor: 6.524

Review 10.  Strategic vision for improving human health at The Forefront of Genomics.

Authors:  Eric D Green; Chris Gunter; Leslie G Biesecker; Valentina Di Francesco; Carla L Easter; Elise A Feingold; Adam L Felsenfeld; David J Kaufman; Elaine A Ostrander; William J Pavan; Adam M Phillippy; Anastasia L Wise; Jyoti Gupta Dayal; Britny J Kish; Allison Mandich; Christopher R Wellington; Kris A Wetterstrand; Sarah A Bates; Darryl Leja; Susan Vasquez; William A Gahl; Bettie J Graham; Daniel L Kastner; Paul Liu; Laura Lyman Rodriguez; Benjamin D Solomon; Vence L Bonham; Lawrence C Brody; Carolyn M Hutter; Teri A Manolio
Journal:  Nature       Date:  2020-10-28       Impact factor: 49.962

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