%0 Journal Article %J Proc Natl Acad Sci U S A %D 2022 %T The Earth BioGenome Project 2020: Starting the clock. %A Lewin, Harris A %A Stephen Richards %A Lieberman Aiden, Erez %A Allende, Miguel L %A Archibald, John M %A Bálint, Miklós %A Barker, Katharine B %A Baumgartner, Bridget %A Belov, Katherine %A Bertorelle, Giorgio %A Blaxter, Mark L %A Cai, Jing %A Caperello, Nicolette D %A Carlson, Keith %A Castilla-Rubio, Juan Carlos %A Chaw, Shu-Miaw %A Chen, Lei %A Childers, Anna K %A Coddington, Jonathan A %A Conde, Dalia A %A Corominas, Montserrat %A Crandall, Keith A %A Crawford, Andrew J %A DiPalma, Federica %A Durbin, Richard %A Ebenezer, ThankGod E %A Edwards, Scott V %A Fedrigo, Olivier %A Flicek, Paul %A Formenti, Giulio %A Richard A Gibbs %A Gilbert, M Thomas P %A Goldstein, Melissa M %A Graves, Jennifer Marshall %A Greely, Henry T %A Grigoriev, Igor V %A Hackett, Kevin J %A Hall, Neil %A Haussler, David %A Helgen, Kristofer M %A Hogg, Carolyn J %A Isobe, Sachiko %A Jakobsen, Kjetill Sigurd %A Janke, Axel %A Jarvis, Erich D %A Johnson, Warren E %A Jones, Steven J M %A Karlsson, Elinor K %A Kersey, Paul J %A Kim, Jin-Hyoung %A Kress, W John %A Kuraku, Shigehiro %A Lawniczak, Mara K N %A Leebens-Mack, James H %A Li, Xueyan %A Lindblad-Toh, Kerstin %A Liu, Xin %A Lopez, Jose V %A Marques-Bonet, Tomas %A Mazard, Sophie %A Mazet, Jonna A K %A Mazzoni, Camila J %A Myers, Eugene W %A O'Neill, Rachel J %A Paez, Sadye %A Park, Hyun %A Robinson, Gene E %A Roquet, Cristina %A Ryder, Oliver A %A Sabir, Jamal S M %A Shaffer, H Bradley %A Shank, Timothy M %A Sherkow, Jacob S %A Soltis, Pamela S %A Tang, Boping %A Tedersoo, Leho %A Uliano-Silva, Marcela %A Wang, Kun %A Wei, Xiaofeng %A Wetzer, Regina %A Wilson, Julia L %A Xu, Xun %A Yang, Huanming %A Yoder, Anne D %A Zhang, Guojie %K Animals %K Base Sequence %K Biodiversity %K Eukaryota %K Genomics %K Humans %B Proc Natl Acad Sci U S A %V 119 %8 2022 Jan 25 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/35042800?dopt=Abstract %R 10.1073/pnas.2115635118 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2018 %T Earth BioGenome Project: Sequencing life for the future of life. %A Lewin, Harris A %A Robinson, Gene E %A Kress, W John %A Baker, William J %A Coddington, Jonathan %A Crandall, Keith A %A Durbin, Richard %A Edwards, Scott V %A Forest, Félix %A Gilbert, M Thomas P %A Goldstein, Melissa M %A Grigoriev, Igor V %A Hackett, Kevin J %A Haussler, David %A Jarvis, Erich D %A Johnson, Warren E %A Patrinos, Aristides %A Richards, Stephen %A Castilla-Rubio, Juan Carlos %A van Sluys, Marie-Anne %A Soltis, Pamela S %A Xu, Xun %A Yang, Huanming %A Zhang, Guojie %K Biodiversity %K Earth, Planet %K Endangered Species %K Genome %K High-Throughput Nucleotide Sequencing %X

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.

%B Proc Natl Acad Sci U S A %V 115 %P 4325-4333 %8 2018 Apr 24 %G eng %N 17 %1 https://www.ncbi.nlm.nih.gov/pubmed/29686065?dopt=Abstract %R 10.1073/pnas.1720115115 %0 Journal Article %J Science %D 2014 %T The sheep genome illuminates biology of the rumen and lipid metabolism. %A Jiang, Yu %A Xie, Min %A Chen, Wenbin %A Talbot, Richard %A Maddox, Jillian F %A Faraut, Thomas %A Wu, Chunhua %A Muzny, Donna M %A Li, Yuxiang %A Zhang, Wenguang %A Stanton, Jo-Ann %A Brauning, Rudiger %A Barris, Wesley C %A Hourlier, Thibaut %A Aken, Bronwen L %A Searle, Stephen M J %A Adelson, David L %A Bian, Chao %A Cam, Graham R %A Chen, Yulin %A Cheng, Shifeng %A DeSilva, Udaya %A Dixen, Karen %A Dong, Yang %A Fan, Guangyi %A Franklin, Ian R %A Fu, Shaoyin %A Guan, Rui %A Highland, Margaret A %A Holder, Michael E %A Huang, Guodong %A Ingham, Aaron B %A Jhangiani, Shalini N %A Kalra, Divya %A Kovar, Christie L %A Lee, Sandra L %A Liu, Weiqing %A Liu, Xin %A Lu, Changxin %A Lv, Tian %A Mathew, Tittu %A McWilliam, Sean %A Menzies, Moira %A Pan, Shengkai %A Robelin, David %A Servin, Bertrand %A Townley, David %A Wang, Wenliang %A Wei, Bin %A White, Stephen N %A Yang, Xinhua %A Ye, Chen %A Yue, Yaojing %A Zeng, Peng %A Zhou, Qing %A Hansen, Jacob B %A Kristensen, Karsten %A Gibbs, Richard A %A Flicek, Paul %A Warkup, Christopher C %A Jones, Huw E %A Oddy, V Hutton %A Nicholas, Frank W %A McEwan, John C %A Kijas, James %A Wang, Jun %A Worley, Kim C %A Archibald, Alan L %A Cockett, Noelle %A Xu, Xun %A Wang, Wen %A Dalrymple, Brian P %K Amino Acid Sequence %K Animals %K Fatty Acids, Volatile %K Gene Expression Regulation %K Genome %K Keratins, Hair-Specific %K Lipid Metabolism %K Molecular Sequence Data %K Phylogeny %K Rumen %K Sheep, Domestic %K Transcriptome %K Wool %X

Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.

%B Science %V 344 %P 1168-1173 %8 2014 Jun 06 %G eng %N 6188 %1 https://www.ncbi.nlm.nih.gov/pubmed/24904168?dopt=Abstract %R 10.1126/science.1252806