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1. The Earth BioGenome Project 2020: Starting the clock

Author

Harris A. Lewin, Stephen Richards, Erez Lieberman Aiden, Miguel L. Allende, John M. Archibald, Miklós Bálint, Katharine B. Barker, Bridget Baumgartner, Katherine Belov, Giorgio Bertorelle, Mark L. Blaxter, Jing Cai, Nicolette D. Caperello, Keith Carlson, Juan Carlos Castilla-Rubio, Shu-Miaw Chaw, Lei Chen, Anna K. Childers, Jonathan A. Coddington, Dalia A. Conde, Montserrat Corominas, Keith A. Crandall, Andrew J. Crawford, Federica DiPalma, Richard Durbin, ThankGod E. Ebenezer, Scott V. Edwards, Olivier Fedrigo, Paul Flicek, Giulio Formenti, Richard A. Gibbs, M. Thomas P. Gilbert, Melissa M. Goldstein, Jennifer Marshall Graves, Henry T. Greely, Igor V. Grigoriev, Kevin J. Hackett, Neil Hall, David Haussler, Kristofer M. Helgen, Carolyn J. Hogg, Sachiko Isobe, Kjetill Sigurd Jakobsen, Axel Janke, Erich D. Jarvis, Warren E. Johnson, Steven J. M. Jones, Elinor K. Karlsson, Paul J. Kersey, Jin-Hyoung Kim, W. John Kress, Shigehiro Kuraku, Mara K. N. Lawniczak, James H. Leebens-Mack, Xueyan Li, Kerstin Lindblad-Toh, Xin Liu, Jose V. Lopez, Tomas Marques-Bonet, Sophie Mazard, Jonna A. K. Mazet, Camila J. Mazzoni, Eugene W. Myers, Rachel J. O’Neill, Sadye Paez, Hyun Park, Gene E. Robinson, Cristina Roquet, Oliver A. Ryder, Jamal S. M. Sabir, H. Bradley Shaffer, Timothy M. Shank, Jacob S. Sherkow, Pamela S. Soltis, Boping Tang, Leho Tedersoo, Marcela Uliano-Silva, Kun Wang, Xiaofeng Wei, Regina Wetzer, Julia L. Wilson, Xun Xu, Huanming Yang, Anne D. Yoder, Guojie Zhang, Lewin, Harris A [0000-0002-1043-7287], Richards, Stephen [0000-0001-8959-5466], Allende, Miguel L [0000-0002-2783-2152], Blaxter, Mark L [0000-0003-2861-949X], Coddington, Jonathan A [0000-0001-6004-7730], Conde, Dalia A [0000-0002-7923-8163], Corominas, Montserrat [0000-0002-0724-8346], Crandall, Keith A [0000-0002-0836-3389], Durbin, Richard [0000-0002-9130-1006], Edwards, Scott V [0000-0003-2535-6217], Gilbert, M Thomas P [0000-0002-5805-7195], Graves, Jennifer Marshall [0000-0001-6480-7856], Greely, Henry T [0000-0002-1105-6734], Grigoriev, Igor V [0000-0002-3136-8903], Hogg, Carolyn J [0000-0002-6328-398X], Jakobsen, Kjetill Sigurd [0000-0002-8861-5397], Janke, Axel [0000-0002-9394-1904], Johnson, Warren E [0000-0002-5954-186X], Karlsson, Elinor K [0000-0002-4343-3776], Kress, W John [0000-0002-0140-5267], Leebens-Mack, James H [0000-0003-4811-2231], Lindblad-Toh, Kerstin [0000-0001-8338-0253], Marques-Bonet, Tomas [0000-0002-5597-3075], Mazet, Jonna AK [0000-0002-8712-5951], Myers, Eugene W [0000-0002-6580-7839], Robinson, Gene E [0000-0003-4828-4068], Roquet, Cristina [0000-0001-8748-3743], Ryder, Oliver A [0000-0003-2427-763X], Sabir, Jamal SM [0000-0003-4785-9894], Shaffer, H Bradley [0000-0002-5795-9242], Sherkow, Jacob S [0000-0002-9724-9261], Soltis, Pamela S [0000-0001-9310-8659], Tang, Boping [0000-0002-3241-7914], Yoder, Anne D [0000-0002-1781-9552], Zhang, Guojie [0000-0001-6860-1521], and Apollo - University of Cambridge Repository

Subjects
Introduction, Multidisciplinary, Base Sequence, Evolution, Botany, Ambientale, Eukaryota, Genomics, Botanik, Biodiversity, Biological Sciences, Biodiversitat, Biodiversity [MeSH], Genomics [MeSH], Eukaryota/genetics [MeSH], Humans [MeSH], Base Sequence/genetics [MeSH], Animals [MeSH], Animals, Humans, The Earth BioGenome Project: The Launch of a Moonshot for Biology, Genomes, Uncategorized
Abstract

November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project's goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP's major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.

Published
2022

2. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Shwetha C. Murali, Hsiao-ling Lu, Siegfried Roth, Huyen Dinh, Peter K. Dearden, Barbara M. I. Vreede, M. Emília Santos, Evgeny M. Zdobnov, Viera Kovacova, Christopher J. Holmes, Stefano Colella, Yuichiro Suzuki, Tamsin E. M. Jones, Chun-che Chang, Stefan Koelzer, Jeffery W. Jones, Essia Sghaier, Thorsten Horn, Richard A. Gibbs, Mackenzie Lovegrove, Panagiotis Ioannidis, Lucila Traverso, Subba Reddy Palli, Megan L. Porter, Olivia Tidswell, Peter Nagui Refki, Neta Ginzburg, Rolando Rivera-Pomar, Sandra L. Lee, Chris Jacobs, Cassandra G. Extavour, Jan Seibert, Amanda Dolan, David Armisén, Jayendra Nath Shukla, Kristen A. Panfilio, Christopher P. Childers, Matthew T. Weirauch, Daniel S.T. Hughes, Jiaxin Qu, Kim C. Worley, Hugh M. Robertson, Monica Munoz-Torres, Markus Friedrich, Emily C. Jennings, Elizabeth J. Duncan, Andrew G. Cridge, Hsu Chao, J. Spencer Johnston, Maurijn van der Zee, Mei-Ju May Chen, John H. Werren, Abderrahman Khila, Shannon Dugan, Stephen Richards, Lena Sachs, Joshua B. Benoit, Antonin J.J. Crumière, Nicolas Parisot, Megan Leask, Yen-Ta Chen, Harshavardhan Doddapaneni, Gérard Febvay, Donna M. Muzny, Ariel D. Chipman, Rose Richter, Robert M. Waterhouse, Leslie Pick, Monica F. Poelchau, Patricia J. Moore, Chloé Suzanne Berger, Richard J. Stancliffe, Yi Min Hsiao, Séverine Viala, Chien-Yueh Lee, Yi Han, Iris M. Vargas Jentzsch, Elise M. Didion, Deniz F. Erezyilmaz, Yong Lu, Andrew J. Rosendale, Peter Heger, Patrice Baa-Puyoulet, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), University of Illinois [Chicago] (UIC), University of Illinois System, Department of Biology, Georgetown University, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of Edinburgh, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology [Lexington], University of Kentucky, Cologne Biocenter, Institute of Developmental Biology, Institute of Developmental Biology, University of Basel (Unibas), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Human Genome Sequencing Center [Houston] (HGSC), Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), United States Department of Health & Human Services National Institutes of Health (NIH) - USA [U54 HG003273], German Research Foundation (DFG) [PA 2044/1 1 SFB 680], Swiss National Science Foundation (SNSF) [31003A_143936, PP00P3_170664], European Research Council grant ERC-CoG [616346], German Research Foundation (DFG) [SFB 680], National Science Foundation (NSF) [US NSF DEB1257053], United States Department of Health & Human Services National Institutes of Health (NIH) - USA [5R01GM080203, 5R01HG004483, R01GM113230], United States Department of Energy (DOE) [DE-AC02-05CH11231], École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Université de Lausanne = University of Lausanne (UNIL), University of Kentucky (UK), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Genève = University of Geneva (UNIGE), Panfilio, Kristen A [0000-0002-6417-251X], Vargas Jentzsch, Iris M [0000-0003-4527-1560], Benoit, Joshua B [0000-0002-4018-3513], Erezyilmaz, Deniz [0000-0001-8416-8561], Suzuki, Yuichiro [0000-0002-0957-3564], Colella, Stefano [0000-0003-3139-6055], Poelchau, Monica F [0000-0002-4584-6056], Waterhouse, Robert M [0000-0003-4199-9052], Ioannidis, Panagiotis [0000-0003-0939-6745], Weirauch, Matthew T [0000-0001-7977-9122], Werren, John H [0000-0001-9353-2070], Jacobs, Chris GC [0000-0002-3128-2288], Duncan, Elizabeth J [0000-0002-1841-504X], Vreede, Barbara MI [0000-0002-5023-4601], Chang, Chun-Che [0000-0002-3586-1607], Chen, Mei-Ju M [0000-0001-7768-8905], Chen, Yen-Ta [0000-0002-4570-6061], Childers, Christopher P [0000-0002-1253-5550], Chipman, Ariel D [0000-0001-6696-840X], Cridge, Andrew G [0000-0002-1399-5188], Crumière, Antonin JJ [0000-0003-2214-2993], Dearden, Peter K [0000-0001-7790-9675], Didion, Elise M [0000-0002-4987-8901], Dinh, Huyen [0000-0003-0336-0362], Doddapaneni, Harsha Vardhan [0000-0002-2433-633X], Dugan, Shannon [0000-0003-1482-816X], Extavour, Cassandra G [0000-0003-2922-5855], Febvay, Gérard [0000-0002-0654-2340], Friedrich, Markus [0000-0002-5622-7920], Han, Yi [0000-0001-7605-8979], Holmes, Christopher J [0000-0001-9612-366X], Horn, Thorsten [0000-0001-8181-939X], Hsiao, Yi-Min [0000-0002-1817-0302], Jennings, Emily C [0000-0002-7687-5319], Johnston, J Spencer [0000-0003-4792-2945], Jones, Tamsin E [0000-0002-0027-0858], Khila, Abderrahman [0000-0003-0908-483X], Kovacova, Viera [0000-0003-4581-4254], Lee, Chien-Yueh [0000-0002-4304-974X], Lu, Hsiao-Ling [0000-0002-4029-6470], Moore, Patricia J [0000-0001-9802-7217], Munoz-Torres, Monica C [0000-0001-8430-6039], Muzny, Donna M [0000-0002-3055-0359], Palli, Subba R [0000-0002-0873-3247], Parisot, Nicolas [0000-0001-5217-8415], Pick, Leslie [0000-0002-4505-5107], Porter, Megan L [0000-0001-7985-2887], Qu, Jiaxin [0000-0002-1122-9391], Rivera-Pomar, Rolando [0000-0002-7720-7064], Rosendale, Andrew J [0000-0002-2463-8856], Roth, Siegfried [0000-0001-5772-3558], Shukla, Jayendra N [0000-0003-1589-1929], Stancliffe, Richard J [0000-0002-6972-9655], van der Zee, Maurijn [0000-0002-8728-8646], Worley, Kim C [0000-0002-0282-1000], Richards, Stephen [0000-0001-8959-5466], and Apollo - University of Cambridge Repository

Subjects
gene family evolution, Lineage (evolution), [SDV]Life Sciences [q-bio], Genome, Insect, Gene Transfer, Gene Dosage, Insect, Genome, purl.org/becyt/ford/1 [https], 0302 clinical medicine, CYS2-HIS2 Zinc Fingers, phytophagy, ddc:576.5, lcsh:QH301-705.5, media_common, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, Large milkweed bug, Ecology, Pigmentation, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genes, Homeobox, Biological Sciences, Lygaeidae, Hemiptera, séquence du génome, Smell, evolution of development, TRANSCRIPTION FACTORS, puceron, Biotechnology, lcsh:QH426-470, Gene Transfer, Horizontal, ddc:025.063/570, Evolution, Bioinformatics, media_common.quotation_subject, 1.1 Normal biological development and functioning, Transcription Factors/genetics, Zoology, Amino Acid Sequence, Animals, Evolution, Molecular, Feeding Behavior, Gene Expression Profiling, Hemiptera/genetics, Hemiptera/growth & development, Hemiptera/metabolism, Pigmentation/genetics, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, GENE FAMILY EVOLUTION, Genomics, Biotechnologies, LATERAL GENE TRANSFER, Horizontal, 03 medical and health sciences, Molecular evolution, Underpinning research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Information and Computing Sciences, transcription factors, RNAI, Genetics, Homeobox, GENE STRUCTURE, purl.org/becyt/ford/1.6 [https], SB, Genome size, Ciencias Exactas, 030304 developmental biology, Whole genome sequencing, QL, QH, Research, gene structure, lateral gene transfer, Human Genome, fungi, Molecular, biology.organism_classification, Hemiptera/genetics/growth & development/metabolism, diversité des populations, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, PHYTOPHAGY, lcsh:Biology (General), Genes, Animal ecology, Evolutionary biology, EVOLUTION OF DEVELOPMENT, Evolutionary developmental biology, 030217 neurology & neurosurgery, Environmental Sciences
Abstract

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos

Published
2019

3. Hemichordate genomes and deuterostome origins

Author

Shannon Dugan, Oleg Simakov, Ryo Koyanagi, Andrew Cree, Fuki Gyoja, Nicholas H. Putnam, Asao Fujiyama, Miyuki Kanda, Michael Holder, Geoffrey Okwuonu, Lynne V. Nazareth, Atsuko Sato, Christopher B. Cameron, Christopher J. Lowe, Jens H. Fritzenwanker, Yi Chih Chen, Therese Mitros, Paul Gonzalez, Daniel S. Rokhsar, Jireh Santibanez, Donna M. Muzny, Rui Chen, Kenneth W. Baughman, Jessen V. Bredeson, Shinichi Yamasaki, Hiroki Goto, Noriyuki Satoh, Nana Arakaki, Shalini N. Jhangiani, Richard A. Gibbs, Kanako Hisata, Takeshi Kawashima, Jia-Xing Yue, Jiaxin Qu, Donna Morton, Huyen Dinh, Christie Kovar, Jeremy Schmutz, Lora Lewis, Sandra L. Lee, Leonid Peshkin, Jerry Jenkins, Judith Levine, Stephen Richards, Kunifumi Tagawa, Kim C. Worley, John C. Gerhart, Robert Freeman, Manabu Fujie, Michael Wu, Yan Ding, Jr-Kai Yu, Marc W. Kirschner, Tom Humphreys, Ferdinand Marlétaz, Akane Sasaki, Andrew Gillis, Ariel M. Pani, Tomoe Hikosaka-Katayama, Eiichi Shoguchi, Yi-Hsien Su, Simakov, Oleg [0000-0002-3585-4511], Marlétaz, Ferdinand [0000-0001-8124-4266], Koyanagi, Ryo [0000-0002-9694-0288], Bredeson, Jessen [0000-0001-5489-8512], Yue, Jia-Xing [0000-0002-2122-9221], Fritzenwanker, Jens H [0000-0002-5201-4100], Richards, Stephen [0000-0001-8959-5466], Gillis, Andrew [0000-0003-2062-3777], Putnam, Nicholas H [0000-0002-1315-782X], Tagawa, Kunifumi [0000-0001-5634-9373], Worley, Kim C [0000-0002-0282-1000], Lowe, Christopher J [0000-0002-7789-8643], Rokhsar, Daniel S [0000-0002-8704-2224], and Apollo - University of Cambridge Repository

Subjects
0106 biological sciences, Evolution, General Science & Technology, Hemichordate, Synteny, 010603 evolutionary biology, 01 natural sciences, Article, Conserved sequence, Evolution, Molecular, 03 medical and health sciences, Chordata, Nonvertebrate, Transforming Growth Factor beta, Phylogenetics, Genetics, Animals, 14. Life underwater, Chordata, Phylogeny, Conserved Sequence, 030304 developmental biology, Comparative genomics, 0303 health sciences, Genome, Multidisciplinary, Deuterostome, biology, Phylum, Human Genome, Molecular, biology.organism_classification, Nonvertebrate, Multigene Family, Evolutionary developmental biology, Generic health relevance, Echinodermata, Signal Transduction
Abstract

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

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