Why sequence all eukaryotes?

Mark Blaxter¹, John M Archibald², Anna K Childers³, Jonathan A Coddington⁴, Keith A Crandall^{5

6}, Federica Di Palma⁷, Richard Durbin^{8

9}, Scott V Edwards^{10

11}, Jennifer A M Graves^{12

13}, Kevin J Hackett¹⁴, Neil Hall¹⁵, Erich D Jarvis^{16

17}, Rebecca N Johnson¹⁸, Elinor K Karlsson^{19

20}, W John Kress²¹, Shigehiro Kuraku^{22

23}, Mara K N Lawniczak⁸, Kerstin Lindblad-Toh^{20

24}, Jose V Lopez^{25

26}, Nancy A Moran²⁷, Gene E Robinson^{28

29}, Oliver A Ryder^{30

31}, Beth Shapiro³², Pamela S Soltis^{33

34}, Tandy Warnow³⁵, Guojie Zhang^{36

37}, Harris A Lewin^{38

39}

Affiliations

¹ Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; mb35@sanger.ac.uk.
² Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada.
³ Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705.
⁴ Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560.
⁵ Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052.
⁶ Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013.
⁷ School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
⁸ Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.
⁹ Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom.
¹⁰ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
¹¹ Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138.
¹² School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia.
¹³ University of Canberra, Bruce, ACT 2617, Australia.
¹⁴ Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705.
¹⁵ Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom.
¹⁶ Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065.
¹⁷ Howard Hughes Medical Institute, Chevy Chase, MD 20815.
¹⁸ National Museum of Natural History, Smithsonian Institution, Washington, DC 20560.
¹⁹ Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605.
²⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142.
²¹ Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012.
²² Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
²³ Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan.
²⁴ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden.
²⁵ Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004.
²⁶ Guy Harvey Oceanographic Center, Dania Beach, FL 33004.
²⁷ Integrative Biology, University of Texas at Austin, Austin, TX 78712.
²⁸ Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
²⁹ Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
³⁰ Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027.
³¹ Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039.
³² Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064.
³³ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611.
³⁴ Biodiversity Institute, University of Florida, Gainesville, FL 32611.
³⁵ Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301.
³⁶ Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.
³⁷ China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China.
³⁸ Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616.
³⁹ Department of Population Health and Reproduction, University of California, Davis, CA 95616.

PMID: 35042801
PMCID: PMC8795522
DOI: 10.1073/pnas.2115636118

Why sequence all eukaryotes?

Mark Blaxter et al. Proc Natl Acad Sci U S A. 2022.

. 2022 Jan 25;119(4):e2115636118.

doi: 10.1073/pnas.2115636118.

Authors

Affiliations

¹ Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; mb35@sanger.ac.uk.
² Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada.
³ Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705.
⁴ Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560.
⁵ Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052.
⁶ Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013.
⁷ School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
⁸ Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.
⁹ Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom.
¹⁰ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
¹¹ Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138.
¹² School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia.
¹³ University of Canberra, Bruce, ACT 2617, Australia.
¹⁴ Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705.
¹⁵ Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom.
¹⁶ Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065.
¹⁷ Howard Hughes Medical Institute, Chevy Chase, MD 20815.
¹⁸ National Museum of Natural History, Smithsonian Institution, Washington, DC 20560.
¹⁹ Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605.
²⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142.
²¹ Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012.
²² Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
²³ Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan.
²⁴ Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden.
²⁵ Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004.
²⁶ Guy Harvey Oceanographic Center, Dania Beach, FL 33004.
²⁷ Integrative Biology, University of Texas at Austin, Austin, TX 78712.
²⁸ Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
²⁹ Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
³⁰ Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027.
³¹ Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039.
³² Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064.
³³ Florida Museum of Natural History, University of Florida, Gainesville, FL 32611.
³⁴ Biodiversity Institute, University of Florida, Gainesville, FL 32611.
³⁵ Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301.
³⁶ Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.
³⁷ China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China.
³⁸ Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616.
³⁹ Department of Population Health and Reproduction, University of California, Davis, CA 95616.

PMID: 35042801
PMCID: PMC8795522
DOI: 10.1073/pnas.2115636118

Abstract

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.

Keywords: conservation; diversity; ecology; evolution; genome.

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Conflict of interest statement

The authors declare no competing interest.

Figures

**Fig. 1.**
Outcomes of the Earth BioGenome Project. Sequencing all eukaryotic life on Earth will transform our understanding of how life evolved, help us build a sustainable future, provide biosecurity, and support an innovative bioeconomy. Here, we summarize the impact of these new genomes on basic research, which is described in detail in the text. Some practical benefits of this project are captured in the gray circles.

See this image and copyright information in PMC

References

1. Wilson E. O., Half-Earth: Our Planet’s Fight for Life (Liveright Publishing, 2016).
1. Aristotle, On the Parts of Animals, W. Ogle, Trans. (Kegan Paul, French, London, 1882).
1. Linnaeus C., Systema Naturae (Holmiae Salvius, ed. 10, 1758).
1. Mora C., Tittensor D. P., Adl S., Simpson A. G. B., Worm B., How many species are there on Earth and in the ocean? PLoS Biol. 9, e1001127 (2011). - PMC - PubMed
1. Darwin C., The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (Penguin Classics Reprint, 1985; John Murray, ed. 1, 1859).

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Why sequence all eukaryotes?

Affiliations

Why sequence all eukaryotes?

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources