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Zemel BM, Nevue AA, Tavares LES, Dagostin A, Lovell PV, Jin DZ, Mello CV, von Gersdorff H. Motor cortex analogue neurons in songbirds utilize Kv3 channels to generate ultranarrow spikes. eLife 2023; 12:e81992. [PMID: 37158590 PMCID: PMC10241522 DOI: 10.7554/elife.81992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Complex motor skills in vertebrates require specialized upper motor neurons with precise action potential (AP) firing. To examine how diverse populations of upper motor neurons subserve distinct functions and the specific repertoire of ion channels involved, we conducted a thorough study of the excitability of upper motor neurons controlling somatic motor function in the zebra finch. We found that robustus arcopallialis projection neurons (RAPNs), key command neurons for song production, exhibit ultranarrow spikes and higher firing rates compared to neurons controlling non-vocal somatic motor functions (dorsal intermediate arcopallium [AId] neurons). Pharmacological and molecular data indicate that this striking difference is associated with the higher expression in RAPNs of high threshold, fast-activating voltage-gated Kv3 channels, that likely contain Kv3.1 (KCNC1) subunits. The spike waveform and Kv3.1 expression in RAPNs mirror properties of Betz cells, specialized upper motor neurons involved in fine digit control in humans and other primates but absent in rodents. Our study thus provides evidence that songbirds and primates have convergently evolved the use of Kv3.1 to ensure precise, rapid AP firing in upper motor neurons controlling fast and complex motor skills.
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Affiliation(s)
- Benjamin M Zemel
- Vollum Institute, Oregon Health and Science UniversityPortlandUnited States
| | - Alexander A Nevue
- Department of Behavioral Neuroscience, Oregon Health and Science UniversityPortlandUnited States
| | - Leonardo ES Tavares
- Vollum Institute, Oregon Health and Science UniversityPortlandUnited States
- Department of Physics, Pennsylvania State UniversityUniversity ParkUnited States
| | - Andre Dagostin
- Vollum Institute, Oregon Health and Science UniversityPortlandUnited States
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science UniversityPortlandUnited States
| | - Dezhe Z Jin
- Department of Physics, Pennsylvania State UniversityUniversity ParkUnited States
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science UniversityPortlandUnited States
| | - Henrique von Gersdorff
- Vollum Institute, Oregon Health and Science UniversityPortlandUnited States
- Oregon Hearing Research Center, Oregon Health and Science UniversityPortlandUnited States
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Haimson B, Meir O, Sudakevitz-Merzbach R, Elberg G, Friedrich S, Lovell PV, Paixão S, Klein R, Mello CV, Klar A. Natural loss of function of ephrin-B3 shapes spinal flight circuitry in birds. Sci Adv 2021; 7:7/24/eabg5968. [PMID: 34117069 PMCID: PMC8195482 DOI: 10.1126/sciadv.abg5968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 05/11/2023]
Abstract
Flight in birds evolved through patterning of the wings from forelimbs and transition from alternating gait to synchronous flapping. In mammals, the spinal midline guidance molecule ephrin-B3 instructs the wiring that enables limb alternation, and its deletion leads to synchronous hopping gait. Here, we show that the ephrin-B3 protein in birds lacks several motifs present in other vertebrates, diminishing its affinity for the EphA4 receptor. The avian ephrin-B3 gene lacks an enhancer that drives midline expression and is missing in galliforms. The morphology and wiring at brachial levels of the chicken embryonic spinal cord resemble those of ephrin-B3 null mice. Dorsal midline decussation, evident in the mutant mouse, is apparent at the chick brachial level and is prevented by expression of exogenous ephrin-B3 at the roof plate. Our findings support a role for loss of ephrin-B3 function in shaping the avian brachial spinal cord circuitry and facilitating synchronous wing flapping.
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Affiliation(s)
- Baruch Haimson
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oren Meir
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Reut Sudakevitz-Merzbach
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Gerard Elberg
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Samantha Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Sónia Paixão
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rüdiger Klein
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA.
| | - Avihu Klar
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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3
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Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Towards complete and error-free genome assemblies of all vertebrate species. Nature 2021; 592:737-746. [PMID: 33911273 PMCID: PMC8081667 DOI: 10.1038/s41586-021-03451-0] [Citation(s) in RCA: 584] [Impact Index Per Article: 194.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/12/2021] [Indexed: 02/02/2023]
Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA, USA
| | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcela Uliano-Silva
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | | | | | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mark Chaisson
- University of Southern California, Los Angeles, CA, USA
| | - Gregory L Gedman
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Lindsey J Cantin
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Iliana Bista
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center, Dresden, Germany
| | - Sadye Paez
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- School of Biology, University of St Andrews, St Andrews, UK
| | - Tanya M Lama
- University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, MA, USA
| | - Frank Grutzner
- School of Biological Science, The Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Dave Burt
- UQ Genomics, University of Queensland, Brisbane, Queensland, Australia
| | - Julia M George
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - David Iorns
- The Genetic Rescue Foundation, Wellington, New Zealand
| | - Andrew Digby
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Daryl Eason
- Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
| | - Bruce Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - George Turner
- School of Natural Sciences, Bangor University, Gwynedd, UK
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Maximilian Wagner
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Gavin J P Naylor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK
- Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | | | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic, Ivanić-Grad, Croatia
| | | | - Zemin Ning
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Dovetail Genomics, Santa Cruz, CA, USA
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jay Ghurye
- Dovetail Genomics, Santa Cruz, CA, USA
- Department of Computer Science, University of Maryland College Park, College Park, MD, USA
| | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | | | | | | | | | - Dengfeng Guan
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, IL, USA
| | - David F Clayton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Farooq O Al-Ajli
- Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
- Qatar Falcon Genome Project, Doha, Qatar
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc., Seoul, Republic of Korea
| | | | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
- Goethe-University, Faculty of Biosciences, Frankfurt, Germany
| | | | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Paul Medvedev
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Karen Clark
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kevin Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Woori Kwak
- eGnome, Inc., Seoul, Republic of Korea
- Hoonygen, Seoul, Korea
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Luis Nassar
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Guojie Zhang
- China National Genebank, BGI-Shenzhen, Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Robert W Murphy
- Centre for Biodiversity, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Federica Di Palma
- Department of Biological Sciences, Earlham Institute, University of East Anglia, Norwich, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Tandy Warnow
- Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Oliver A Ryder
- San Diego Zoo Global, Escondido, CA, USA
- Department of Evolution, Behavior, and Ecology, University of California San Diego, La Jolla, CA, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Stephen J O'Brien
- Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Harris A Lewin
- The Genome Center, University of California Davis, Davis, CA, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA, USA
| | | | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology, Dresden, Germany.
- Faculty of Computer Science, Technical University Dresden, Dresden, Germany.
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA.
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Lovell PV, Wirthlin M, Kaser T, Buckner AA, Carleton JB, Snider BR, McHugh AK, Tolpygo A, Mitra PP, Mello CV. ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and brain evolution studies. J Comp Neurol 2020; 528:2099-2131. [PMID: 32037563 DOI: 10.1002/cne.24879] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/14/2022]
Abstract
An in-depth understanding of the genetics and evolution of brain function and behavior requires a detailed mapping of gene expression in functional brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchatlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the brain of zebra finches. ZEBrA is a first of its kind gene expression brain atlas for a bird species and a first for any sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June 2019) are presented in alignment with an annotated histological atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among many fundamental themes.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Taylor Kaser
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Alexa A Buckner
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Julia B Carleton
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | - Brian R Snider
- Center for Spoken Language Understanding, Institute on Development and Disability, Oregon Health and Science University, Portland, Oregon
| | - Anne K McHugh
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
| | | | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon
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5
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Abstract
BACKGROUND Vocal learning, the ability to learn to produce vocalizations through imitation, relies on specialized brain circuitry known in songbirds as the song system. While the connectivity and various physiological properties of this system have been characterized, the molecular genetic basis of neuronal excitability in song nuclei remains understudied. We have focused our efforts on examining voltage-gated ion channels to gain insight into electrophysiological and functional features of vocal nuclei. A previous investigation of potassium channel genes in zebra finches (Taeniopygia guttata) revealed evolutionary modifications unique to songbirds, as well as transcriptional specializations in the song system [Lovell PV, Carleton JB, Mello CV. BMC Genomics 14:470 2013]. Here, we expand this approach to sodium, calcium, and chloride channels along with their modulatory subunits using comparative genomics and gene expression analysis encompassing microarrays and in situ hybridization. RESULTS We found 23 sodium, 38 calcium, and 33 chloride channel genes (HGNC-based classification) in the zebra finch genome, several of which were previously unannotated. We determined 15 genes are missing relative to mammals, including several genes (CLCAs, BEST2) linked to olfactory transduction. The majority of sodium and calcium but few chloride channels showed differential expression in the song system, among them SCN8A and CACNA1E in the direct motor pathway, and CACNG4 and RYR2 in the anterior forebrain pathway. In several cases, we noted a seemingly coordinated pattern across multiple nuclei (SCN1B, SCN3B, SCN4B, CACNB4) or sparse expression (SCN1A, CACNG5, CACNA1B). CONCLUSION The gene families examined are highly conserved between avian and mammalian lineages. Several cases of differential expression likely support high-frequency and burst firing in specific song nuclei, whereas cases of sparse patterns of expression may contribute to the unique electrophysiological signatures of distinct cell populations. These observations lay the groundwork for manipulations to determine how ion channels contribute to the neuronal excitability properties of vocal learning systems.
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Affiliation(s)
- Samantha R. Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Peter V. Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Taylor M. Kaser
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
| | - Claudio V. Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR USA
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Mello CV, Kaser T, Buckner AA, Wirthlin M, Lovell PV. Molecular architecture of the zebra finch arcopallium. J Comp Neurol 2019; 527:2512-2556. [PMID: 30919954 DOI: 10.1002/cne.24688] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/23/2022]
Abstract
The arcopallium, a key avian forebrain region, receives inputs from numerous brain areas and is a major source of descending sensory and motor projections. While there is evidence of arcopallial subdivisions, the internal organization or the arcopallium is not well understood. The arcopallium is also considered the avian homologue of mammalian deep cortical layers and/or amygdalar subdivisions, but one-to-one correspondences are controversial. Here we present a molecular characterization of the arcopallium in the zebra finch, a passerine songbird species and a major model organism for vocal learning studies. Based on in situ hybridization for arcopallial-expressed transcripts (AQP1, C1QL3, CBLN2, CNTN4, CYP19A1, ESR1/2, FEZF2, MGP, NECAB2, PCP4, PVALB, SCN3B, SCUBE1, ZBTB20, and others) in comparison with cytoarchitectonic features, we have defined 20 distinct regions that can be grouped into six major domains (anterior, posterior, dorsal, ventral, medial, and intermediate arcopallium, respectively; AA, AP, AD, AV, AM, and AI). The data also help to establish the arcopallium as primarily pallial, support a unique topography of the arcopallium in passerines, highlight similarities between the vocal robust nucleus of the arcopallium (RA) and AI, and provide insights into the similarities and differences of cortical and amygdalar regions between birds and mammals. We also propose the use of AMV (instead of nucleus taenia/TnA), AMD, AD, and AI as initial steps toward a universal arcopallial nomenclature. Besides clarifying the internal organization of the arcopallium, the data provide a coherent basis for further functional and comparative studies of this complex avian brain region.
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Affiliation(s)
- Claudio V Mello
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Taylor Kaser
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Alexa A Buckner
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
| | - Peter V Lovell
- Department of Behavioral Neuroscience, OHSU, Portland, Oregon
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Lovell PV, Huizinga NA, Getachew A, Mees B, Friedrich SR, Wirthlin M, Mello CV. Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. BMC Res Notes 2018; 11:309. [PMID: 29776372 PMCID: PMC5960091 DOI: 10.1186/s13104-018-3402-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/07/2018] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. DATA DESCRIPTION We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr_un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Nicole A Huizinga
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Abel Getachew
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Brianna Mees
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | | | - Morgan Wirthlin
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.,Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.
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8
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Lovell PV, Huizinga NA, Friedrich SR, Wirthlin M, Mello CV. The constitutive differential transcriptome of a brain circuit for vocal learning. BMC Genomics 2018; 19:231. [PMID: 29614959 PMCID: PMC5883274 DOI: 10.1186/s12864-018-4578-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/02/2018] [Indexed: 01/25/2023] Open
Abstract
Background The ability to imitate the vocalizations of other organisms, a trait known as vocal learning, is shared by only a few organisms, including humans, where it subserves the acquisition of speech and language, and 3 groups of birds. In songbirds, vocal learning requires the coordinated activity of a set of specialized brain nuclei referred to as the song control system. Recent efforts have revealed some of the genes that are expressed in these vocal nuclei, however a thorough characterization of the transcriptional specializations of this system is still missing. We conducted a rigorous and comprehensive analysis of microarrays, and conducted a separate analysis of 380 genes by in situ hybridizations in order to identify molecular specializations of the major nuclei of the song system of zebra finches (Taeniopygia guttata), a songbird species. Results Our efforts identified more than 3300 genes that are differentially regulated in one or more vocal nuclei of adult male birds compared to the adjacent brain regions. Bioinformatics analyses provided insights into the possible involvement of these genes in molecular pathways such as cellular morphogenesis, intrinsic cellular excitability, neurotransmission and neuromodulation, axonal guidance and cela-to-cell interactions, and cell survival, which are known to strongly influence the functional properties of the song system. Moreover, an in-depth analysis of specific gene families with known involvement in regulating the development and physiological properties of neuronal circuits provides further insights into possible modulators of the song system. Conclusion Our study represents one of the most comprehensive molecular characterizations of a brain circuit that evolved to facilitate a learned behavior in a vertebrate. The data provide novel insights into possible molecular determinants of the functional properties of the song control circuitry. It also provides lists of compelling targets for pharmacological and genetic manipulations to elucidate the molecular regulation of song behavior and vocal learning. Electronic supplementary material The online version of this article (10.1186/s12864-018-4578-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Nicole A Huizinga
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA.,Current affiliation: Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA.
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Abstract
The genomics era has brought along the completed sequencing of a large number of bird genomes that cover a broad range of the avian phylogenetic tree (>30 orders), leading to major novel insights into avian biology and evolution. Among recent findings, the discovery that birds lack a large number of protein coding genes that are organized in highly conserved syntenic clusters in other vertebrates is very intriguing, given the physiological importance of many of these genes. A considerable number of them play prominent endocrine roles, suggesting that birds evolved compensatory genetic or physiological mechanisms that allowed them to survive and thrive in spite of these losses. While further studies are needed to establish the exact extent of avian gene losses, these findings point to birds as potentially highly relevant model organisms for exploring the genetic basis and possible therapeutic approaches for a wide range of endocrine functions and disorders.
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Affiliation(s)
- C V Mello
- Dept. Behavioral Neuroscience, Oregon Health & Science University, L470, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
| | - P V Lovell
- Dept. Behavioral Neuroscience, Oregon Health & Science University, L470, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
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10
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Abstract
While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that specific groups of syntenic protein-coding genes are missing in birds. This is a response to the Correspondence article: https://www.dx.doi.org/10.1186/s13059-017-1231-1
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97017, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97017, USA.
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11
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Dagostin AA, Lovell PV, Hilscher MM, Mello CV, Leão RM. Control of Phasic Firing by a Background Leak Current in Avian Forebrain Auditory Neurons. Front Cell Neurosci 2015; 9:471. [PMID: 26696830 PMCID: PMC4674572 DOI: 10.3389/fncel.2015.00471] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/19/2015] [Indexed: 12/02/2022] Open
Abstract
Central neurons express a variety of neuronal types and ion channels that promote firing heterogeneity among their distinct neuronal populations. Action potential (AP) phasic firing, produced by low-threshold voltage-activated potassium currents (VAKCs), is commonly observed in mammalian brainstem neurons involved in the processing of temporal properties of the acoustic information. The avian caudomedial nidopallium (NCM) is an auditory area analogous to portions of the mammalian auditory cortex that is involved in the perceptual discrimination and memorization of birdsong and shows complex responses to auditory stimuli We performed in vitro whole-cell patch-clamp recordings in brain slices from adult zebra finches (Taeniopygia guttata) and observed that half of NCM neurons fire APs phasically in response to membrane depolarizations, while the rest fire transiently or tonically. Phasic neurons fired APs faster and with more temporal precision than tonic and transient neurons. These neurons had similar membrane resting potentials, but phasic neurons had lower membrane input resistance and time constant. Surprisingly phasic neurons did not express low-threshold VAKCs, which curtailed firing in phasic mammalian brainstem neurons, having similar VAKCs to other NCM neurons. The phasic firing was determined not by VAKCs, but by the potassium background leak conductances, which was more prominently expressed in phasic neurons, a result corroborated by pharmacological, dynamic-clamp, and modeling experiments. These results reveal a new role for leak currents in generating firing diversity in central neurons.
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Affiliation(s)
- André A Dagostin
- Department of Physiology, School of Medicine of Ribeirão Preto, University of São Paulo Ribeirão Preto, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland OR, USA
| | - Markus M Hilscher
- Brain Institute, Federal University of Rio Grande do Norte Natal, Brazil ; Institute for Analysis and Scientific Computing, Vienna University of Technology Vienna, Austria
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland OR, USA
| | - Ricardo M Leão
- Department of Physiology, School of Medicine of Ribeirão Preto, University of São Paulo Ribeirão Preto, Brazil
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12
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Abstract
Hron et al. provide transcriptome evidence that three (1.1 %) of the 274 genes reported by Lovell et al. as missing in birds may actually be 'hidden' as a result of high GC content. Although this factor may explain some gene absences from genomic assemblies, we believe it is insufficient to account for the extensive syntenic losses described in Lovell et al. Please see related article: www.dx.doi.org/10.1186/s13059-015-0724-z.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Lucia Carbone
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- Oregon National Primate Research Center, West Campus, Oregon Health and Science University, Portland, OR, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA.
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13
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Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 2015; 15:565. [PMID: 25518852 PMCID: PMC4290089 DOI: 10.1186/s13059-014-0565-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 12/12/2022] Open
Abstract
Background Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. Results Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. Conclusions Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0565-1) contains supplementary material, which is available to authorized users.
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14
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Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MTP, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science 2014; 346:1256846. [PMID: 25504733 DOI: 10.1126/science.1256846] [Citation(s) in RCA: 279] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes.
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Affiliation(s)
- Andreas R Pfenning
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
| | - Erina Hara
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Osceola Whitney
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Miriam V Rivas
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Rui Wang
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Petra L Roulhac
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ganeshkumar Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - Jacquelyn Mouncastle
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - J Will Thompson
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Erik J Soderblom
- Duke Proteomics and Metabolomics Core Facility, Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masaki Kato
- Laboratory for Symbolic Cognitive Development, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute, and Duke University Medical Center, Durham, NC 27710, USA.
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15
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Wirthlin M, Lovell PV, Jarvis ED, Mello CV. Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics 2014; 15:1082. [PMID: 25494627 PMCID: PMC4377847 DOI: 10.1186/1471-2164-15-1082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/09/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with this success, as well as with characteristic songbird traits such as vocal learning and the brain circuits that underlie this behavior, has proven difficult, in part due to the small number of avian genomes available until recently. Here we performed a comparative analysis of 48 avian genomes to identify genomic features that are unique to songbirds, as well as an initial assessment of function by investigating their tissue distribution and predicted protein domain structure. RESULTS Using BLAT alignments and gene synteny analysis, we curated a large set of Ensembl gene models that were annotated as novel or duplicated in the most commonly studied songbird, the Zebra finch (Taeniopygia guttata), and then extended this analysis to 47 additional avian and 4 non-avian genomes. We identified 10 novel genes uniquely present in songbird genomes. A refined map of chromosomal synteny disruptions in the Zebra finch genome revealed that the majority of these novel genes localized to regions of genomic instability associated with apparent chromosomal breakpoints. Analyses of in situ hybridization and RNA-seq data revealed that a subset of songbird-unique genes is expressed in the brain and/or other tissues, and that 2 of these (YTHDC2L1 and TMRA) are highly differentially expressed in vocal learning-associated nuclei relative to the rest of the brain. CONCLUSIONS Our study reveals novel genes unique to songbirds, including some that may subserve their unique vocal control system, substantially improves the quality of Zebra finch genome annotations, and contributes to a better understanding of how genomic features may have evolved in conjunction with the emergence of the songbird lineage.
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Affiliation(s)
| | | | | | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97214, USA.
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16
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Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MPC, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014; 346:1320-31. [PMID: 25504713 PMCID: PMC4405904 DOI: 10.1126/science.1253451] [Citation(s) in RCA: 1095] [Impact Index Per Article: 109.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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Affiliation(s)
- Erich D Jarvis
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA.
| | - Siavash Mirarab
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andre J Aberer
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Bo Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Benoit Nabholz
- CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Université Montpellier II Montpellier, France
| | - Jason T Howard
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Claudia C Weber
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Rute R da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Jianwen Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Long Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Nitish Narula
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ganesh Ganapathy
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Bastien Boussau
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Université de Lyon, F-69622 Villeurbanne, France
| | - Md Shamsuzzoha Bayzid
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Volodymyr Zavidovych
- Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Bhanu Rekepalli
- Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mikkel Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bent Lindow
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA
| | - David Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Richard E Green
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Michael W Bruford
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK
| | - Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Andrew Dixon
- International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mads Frost Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark
| | - Frederick H Sheldon
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
| | - Maria Paula Cruz Schneider
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil
| | - Francisco Prosdocimi
- Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil
| | - José Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Amhed Missael Vargas Velazquez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Bent Petersen
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - Thomas Sicheritz-Ponten
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark
| | - An Pas
- Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates
| | - Tom Bailey
- Dubai Falcon Hospital, Dubai, United Arab Emirates
| | - Paul Scofield
- Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand
| | - Michael Bunce
- Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Qi Zhou
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Polina Perelman
- Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia
| | - Amy C Driskell
- Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Zijun Xiong
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yongli Zeng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenyu Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Binghang Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Kui Wu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Xiao
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiong Yinqi
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiuemei Zheng
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Linnea Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Michael Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA
| | - Jon Fjeldsa
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - F Keith Barker
- Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA
| | - Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Warren Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA
| | - Stephen O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA
| | - David Haussler
- Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - John McCormack
- Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Dave Burt
- Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden
| | - Per Alström
- Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany
| | - David P Mindell
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Edward L Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Tandy Warnow
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Wang Jun
- BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Olson CR, Wirthlin M, Lovell PV, Mello CV. Proper care, husbandry, and breeding guidelines for the zebra finch, Taeniopygia guttata. Cold Spring Harb Protoc 2014; 2014:1243-8. [PMID: 25342067 DOI: 10.1101/pdb.prot084780] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The zebra finch Taeniopygia guttata castanotis is a songbird commonly used in the laboratory, particularly for studies of vocal learning, neurobiology, and physiology. Within the laboratory, it is important to adopt careful husbandry practices that allow for normal development of the birds. For example, their song is a learned trait, passed culturally from adult males to juveniles, and thus its learning can be influenced by the health and social conditions of the birds present in the laboratory. Here we present guidelines for the successful maintenance and breeding of captive zebra finches.
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Affiliation(s)
- Christopher R Olson
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
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Karten HJ, Brzozowska-Prechtl A, Lovell PV, Tang DD, Mello CV, Wang H, Mitra PP. Digital atlas of the zebra finch (Taeniopygia guttata) brain: a high-resolution photo atlas. J Comp Neurol 2014; 521:3702-15. [PMID: 23896990 DOI: 10.1002/cne.23443] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 03/12/2013] [Accepted: 07/18/2013] [Indexed: 11/06/2022]
Abstract
We describe a set of new comprehensive, high-quality, high-resolution digital images of histological sections from the brain of male zebra finches (Taeniopygia guttata) and make them publicly available through an interactive website (http://zebrafinch.brainarchitecture.org/). These images provide a basis for the production of a dimensionally accurate and detailed digital nonstereotaxic atlas. Nissl- and myelin-stained brain sections are provided in the transverse, sagittal, and horizontal planes, with the transverse plane approximating the more traditional Frankfurt plane. In addition, a separate set of brain sections in this same plane is stained for tyrosine hydroxylase, revealing the distribution of catecholaminergic neurons (dopaminergic, noradrenergic, and adrenergic) in the songbird brain. For a subset of sagittal sections we also prepared a corresponding set of drawings, defining and annotating various nuclei, fields, and fiber tracts that are visible under Nissl and myelin staining. This atlas of the zebra finch brain is expected to become an important tool for birdsong research and comparative studies of brain organization and evolution.
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Affiliation(s)
- Harvey J Karten
- Department of Neuroscience, University of California at San Diego, La Jolla, California, 92093
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Lovell PV, Carleton JB, Mello CV. Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations. BMC Genomics 2013; 14:470. [PMID: 23845108 PMCID: PMC3711925 DOI: 10.1186/1471-2164-14-470] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/19/2013] [Indexed: 02/08/2023] Open
Abstract
Background A fundamental question in molecular neurobiology is how genes that determine basic neuronal properties shape the functional organization of brain circuits underlying complex learned behaviors. Given the growing availability of complete vertebrate genomes, comparative genomics represents a promising approach to address this question. Here we used genomics and molecular approaches to study how ion channel genes influence the properties of the brain circuitry that regulates birdsong, a learned vocal behavior with important similarities to human speech acquisition. We focused on potassium (K-)Channels, which are major determinants of neuronal cell excitability. Starting with the human gene set of K-Channels, we used cross-species mRNA/protein alignments, and syntenic analysis to define the full complement of orthologs, paralogs, allelic variants, as well as novel loci not previously predicted in the genome of zebra finch (Taeniopygia guttata). We also compared protein coding domains in chicken and zebra finch orthologs to identify genes under positive selective pressure, and those that contained lineage-specific insertions/deletions in functional domains. Finally, we conducted comprehensive in situ hybridizations to determine the extent of brain expression, and identify K-Channel gene enrichments in nuclei of the avian song system. Results We identified 107 K-Channel finch genes, including 6 novel genes common to non-mammalian vertebrate lineages. Twenty human genes are absent in songbirds, birds, or sauropsids, or unique to mammals, suggesting K-Channel properties may be lineage-specific. We also identified specific family members with insertions/deletions and/or high dN/dS ratios compared to chicken, a non-vocal learner. In situ hybridization revealed that while most K-Channel genes are broadly expressed in the brain, a subset is selectively expressed in song nuclei, representing molecular specializations of the vocal circuitry. Conclusions Together, these findings shed new light on genes that may regulate biophysical and excitable properties of the song circuitry, identify potential targets for the manipulation of the song system, and reveal genomic specializations that may relate to the emergence of vocal learning and associated brain areas in birds.
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Mello CV, Lovell PV. No small feat: microRNA responses during vocal communication in songbirds. BMC Biol 2011; 9:35. [PMID: 21627855 PMCID: PMC3104949 DOI: 10.1186/1741-7007-9-35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 05/31/2011] [Indexed: 11/30/2022] Open
Abstract
Simply hearing the song produced by another bird of the same species triggers the regulation of microRNAs (miRNAs) in high-order auditory parts of the zebra finch brain. Some of the identified miRNAs appear to be unique to birds, possibly to songbirds. These findings, reported in BMC Genomics, highlight the complexities of gene regulation associated with vocal communication and point to possible key regulators of song-triggered gene networks. See research article:http://www.biomedcentral.com/1471-2164/12/277
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Abstract
The gene encoding cholecystokinin (Cck) is abundantly expressed in the mammalian brain and has been associated with such functions as feeding termination and satiety, locomotion and self-stimulation, the modulation of anxiety-like behaviors, and learning and memory. Here we describe the brain expression and song regulation of Cck in the brain of the adult male zebra finch (Taeniopygia guttata), a songbird species. Using in situ hybridization we demonstrate that Cck is highly expressed in several discrete brain regions, most prominently the caudalmost portion of the hippocampal formation, the caudodorsal nidopallial shelf and the caudomedial nidopallium (NCM), the core or shell regions of dorsal thalamic nuclei, dopaminergic cell groups in the mesencephalon and pons, the principal nucleus of the trigeminal nerve, and the dorsal raphe. Cck was largely absent in song control system, a group of nuclei required for vocal learning and song production in songbirds, although sparse labeling was detected throughout the striatum, including song nucleus area X. We also show that levels of Cck mRNA and the number of labeled cells increase in the NCM of males and females following auditory stimulation with conspecific song. Double labeling further reveals that the majority of Cck cells, excluding those in the reticular nucleus of the thalamus, are non-GABAergic. Together, these data provide the first comprehensive characterization of Cck expression in a songbird, and suggest a possible involvement of Cck regulation in important aspects of birdsong biology, such as perceptual processing, auditory memorization, and/or vocal-motor control of song production.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA
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Lovell PV, Olson CR, Mello CV. Singing under the influence: examining the effects of nutrition and addiction on a learned vocal behavior. Mol Neurobiol 2011; 44:175-84. [PMID: 21340665 DOI: 10.1007/s12035-011-8169-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/03/2011] [Indexed: 02/04/2023]
Abstract
The songbird model is widely established in a number of laboratories for the investigation of the neurobiology and development of vocal learning. While vocal learning is rare in the animal kingdom, it is a trait that songbirds share with humans. The neuroanatomical and physiological organization of the brain circuitry that controls learned vocalizations has been extensively characterized, particularly in zebra finches (Taeniopygia guttata). Recently, several powerful molecular and genomic tools have become available in this organism, making it an attractive choice for neurobiologists interested in the neural and genetic basis of a complex learned behavior. Here, we briefly review some of the main features of vocal learning and associated brain structures in zebra finches and comment on some examples that illustrate how themes related to nutrition and addiction can be explored using this model organism.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, 3181 Sam Jackson Park Rd L470, Portland, OR 97239, USA
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Kong L, Lovell PV, Heger A, Mello CV, Ponting CP. Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata. Mol Biol Evol 2010; 27:1923-34. [PMID: 20237222 DOI: 10.1093/molbev/msq080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Genes encoding protein kinases tend to evolve slowly over evolutionary time, and only rarely do they appear as recent duplications in sequenced vertebrate genomes. Consequently, it was a surprise to find two families of kinase genes that have greatly and recently expanded in the zebra finch (Taeniopygia guttata) lineage. In contrast to other amniotic genomes (including chicken) that harbor only single copies of p21-activated serine/threonine kinase 3 (PAK3) and proviral integration site 1 (PIM1) genes, the zebra finch genome appeared at first to additionally contain 67 PAK3-like (PAK3L) and 51 PIM1-like (PIM1L) protein kinase genes. An exhaustive analysis of these gene models, however, revealed most to be incomplete, owing to the absence of terminal exons. After reprediction, 31 PAK3L genes and 10 PIM1L genes remain, and all but three are predicted, from the retention of functional sites and open reading frames, to be enzymatically active. PAK3L, but not PIM1L, gene sequences show evidence of recurrent episodes of positive selection, concentrated within structures spatially adjacent to N- and C-terminal protein regions that have been discarded from zebra finch PAK3L genes. At least seven zebra finch PAK3L genes were observed to be expressed in testis, whereas two sequences were found transcribed in the brain, one broadly including the song nuclei and the other in the ventricular zone and in cells resembling Bergmann's glia in the cerebellar Purkinje cell layer. Two PIM1L sequences were also observed to be expressed with broad distributions in the zebra finch brain, one in both the ventricular zone and the cerebellum and apparently associated with glial cells and the other showing neuronal cell expression and marked enrichment in midbrain/thalamic nuclei. These expression patterns do not correlate with zebra finch-specific features such as vocal learning. Nevertheless, our results show how ancient and conserved intracellular signaling molecules can be co-opted, following duplication, thereby resulting in lineage-specific functions, presumably affecting the zebra finch testis and brain.
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Affiliation(s)
- Lesheng Kong
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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Wood WE, Olson CR, Lovell PV, Mello CV. Dietary retinoic acid affects song maturation and gene expression in the song system of the zebra finch. Dev Neurobiol 2008; 68:1213-24. [PMID: 18548487 DOI: 10.1002/dneu.20642] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Vitamin A, an essential nutrient, is required in its acidic form (retinoic acid) for normal embryogenesis and neuronal development, typically within well-defined concentration ranges. In zebra finches, a songbird species, localized retinoic acid synthesis in the brain is important for the development of song, a learned behavior sharing significant commonalities with speech acquisition in humans. We tested how dietary retinoic acid affects the development of song behavior and the brain's system for song control. Supplemental doses of retinoic acid given to juveniles during the critical period for song learning resulted in more variable or plastic-like songs when the birds reached adulthood, compared to the normal songs of vehicle-fed controls. We also observed that several genes (brinp1, nrgn, rxr-alpha, and sdr2/scdr9) had altered levels of expression in specific nuclei of the song system when comparing the experimental and control diet groups. Interestingly, we found significant correlations between gene expression levels in nuclei of the anterior forebrain pathway (lMAN and area X) and the degree of variability in the recorded songs. We observed, however, no major morphological effects such as changes in the volumes of song nuclei. Overall, our results lend further support to a fundamental role of retinoic acid in song maturation and point to possible molecular pathways associated with this action. The data also demonstrate that dietary content of Vitamin A can affect the maturation of a naturally learned complex behavior.
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Affiliation(s)
- William E Wood
- Neurological Sciences Institute, Oregon Health and Science University, Beaverton, Oregon 97006, USA
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Lovell PV, Clayton DF, Replogle KL, Mello CV. Birdsong "transcriptomics": neurochemical specializations of the oscine song system. PLoS One 2008; 3:e3440. [PMID: 18941504 PMCID: PMC2563692 DOI: 10.1371/journal.pone.0003440] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 09/22/2008] [Indexed: 11/18/2022] Open
Abstract
Background Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system. Methodology/Principal Findings Using high-throughput functional genomics we have identified ∼200 novel molecular markers of adult zebra finch HVC, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood. Conclusions/Significance Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning.
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Affiliation(s)
- Peter V. Lovell
- Neurological Sciences Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - David F. Clayton
- Cell & Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Kirstin L. Replogle
- Cell & Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Claudio V. Mello
- Neurological Sciences Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
- * E-mail:
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Replogle K, Arnold AP, Ball GF, Band M, Bensch S, Brenowitz EA, Dong S, Drnevich J, Ferris M, George JM, Gong G, Hasselquist D, Hernandez AG, Kim R, Lewin HA, Liu L, Lovell PV, Mello CV, Naurin S, Rodriguez-Zas S, Thimmapuram J, Wade J, Clayton DF. The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics 2008; 9:131. [PMID: 18366674 PMCID: PMC2329646 DOI: 10.1186/1471-2164-9-131] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 03/18/2008] [Indexed: 11/10/2022] Open
Abstract
Background Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. Results We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500–15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. Conclusion Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.
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Affiliation(s)
- Kirstin Replogle
- Cell & Developmental Biology, Univ, of Illinois, Urbana, IL, USA.
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Pinaud R, Saldanha CJ, Wynne RD, Lovell PV, Mello CV. The excitatory thalamo-"cortical" projection within the song control system of zebra finches is formed by calbindin-expressing neurons. J Comp Neurol 2008; 504:601-18. [PMID: 17722049 DOI: 10.1002/cne.21457] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The learning and production of vocalizations in songbirds are controlled by a system of interconnected brain nuclei organized into a direct vocal motor pathway and an anterior forebrain (pallium-basal ganglia-thalamo-pallial) loop. Here we show that the thalamo-pallial ("thalamo-cortical") projection (from the medial part of the dorsolateral thalamic nucleus to the lateral magnocellular nucleus of the anterior nidopallium--DLM to LMAN) within the anterior forebrain loop is composed of cells positive for the calcium-binding protein calbindin. We show that the vast majority of cells within DLM express calbindin, based both on immunocytochemistry (ICC) for calbindin protein and in situ hybridization for calb mRNA. Using a combination of tract-tracing and ICC we show that the neurons that participate in the DLM-to-LMAN projection are calbindin-positive. We also demonstrate that DLM is devoid of cells expressing mRNA for the GABAergic marker zGAD65. This observation confirms that the calbindin-expressing cells in DLM are not GABAergic, in accordance with previous electrophysiological data indicating that the DLM-to-LMAN projection is excitatory. Furthermore, we use ICC to determine the trajectory of the fibers within the DLM-to-LMAN projection, and to demonstrate a sex difference in calbindin expression levels in the fibers of the DLM-to-LMAN projection. Our findings provide a clear-cut neurochemical signature for a critical projection in the songbird vocal control pathways that enable song learning.
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Affiliation(s)
- Raphael Pinaud
- Neurological Sciences Institute, Oregon Health & Science University, Beaverton, Oregon 97006, USA
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King JT, Lovell PV, Rishniw M, Kotlikoff MI, Zeeman ML, McCobb DP. Beta2 and beta4 subunits of BK channels confer differential sensitivity to acute modulation by steroid hormones. J Neurophysiol 2006; 95:2878-88. [PMID: 16436475 DOI: 10.1152/jn.01352.2005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Membrane-associated receptors for rapid, steroidal neuromodulation remain elusive. Estradiol has been reported to facilitate activation of voltage- and Ca(2+)-dependent BK potassium channels encoded by Slo, if associated with beta1 subunits. We show here that 1) multiple members of the beta family confer sensitivity to multiple steroids on BK channels, 2) that beta subunits differentiate between steroids, and 3) that different betas have distinct relative preferences for particular steroids. Expressed in HEK 293 cells, inside-out patches with channels composed of Slo-alpha alone showed no steroid sensitivity. Cells expressing alphabeta4 exhibited potent, rapid, reversible, and dose-dependent potentiation by corticosterone (CORT; a glucocorticoid), and were potentiated to a lesser degree by other sex and stress steroids. In contrast, alphabeta2 channels were potentiated more strongly by dehydroepiandrosterone (DHEA; an enigmatic, stress-related adrenal androgen), and to a lesser extent by CORT, estradiol, testosterone, and DHEA-S. Cholesterol had no effect on any BK channel compositions tested. Conductance-voltage plots of channels composed of alpha plus beta2 or beta4 subunits were shifted in the negative direction by steroids, indicating greater activation at negative voltages. Thus our results argue that the variety of Slo-beta subunit coexpression patterns occurring in vivo expands the repertoire of Slo channel gating in yet another dimension not fully appreciated, rendering BK gating responsive to dynamic fluctuations in a multiple of steroid hormones.
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Affiliation(s)
- J T King
- Department of Neurobiology and Behavior, Cornell University, W153 Mudd Hall, Ithaca, NY 14853, USA
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Abstract
Although adrenal glucocorticoids cortisol and corticosterone (CORT) have numerous "genomic" effects on adrenomedullary chromaffin cells, acute modulatory actions remain largely unknown, despite rapid stress-related changes in secretion. We report that 1 microM glucocorticoids rapidly modulate gating of chromaffin cell BK channels and action potential firing. In general, CORT, or the analog dexamethasone (DEX), increased channel activity in inside-out bovine patches, an effect not blocked by the glucocorticoid receptor (GR) antagonist RU38486. By contrast, these steroids could profoundly inhibit BK activation in many rat patches, while facilitating activation in others. We show that BK inhibition arises from a negative shift in the voltage dependence of BK inactivation paralleling that for activation. We report that rat cells characteristically exhibit greater repetitive firing ability than bovine cells in the absence of glucocorticoids. In both species, steroid application typically increased firing responses to smaller current injections, attributable to BK-enhanced repolarization and Na+ channel deinactivation. However, in rat cells, where BK inactivation is generally faster and more complete, glucocorticoids tended to dampen responses to stronger stimuli. Thus, in the context of natural variation in BK gating, glucocorticoids can either promote or limit firing responses. We suggest that steroids exploit BK gating variety to tailor catecholamine output in a species- and context-specific fashion.
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Affiliation(s)
- Peter V Lovell
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
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Mahmoud SF, Bezzerides AL, Riba R, Lai GJ, Lovell PV, Hara Y, McCobb DP. Accurate quantitative RT-PCR for relative expression of Slo splice variants. J Neurosci Methods 2002; 115:189-98. [PMID: 11992670 DOI: 10.1016/s0165-0270(02)00015-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Much interest has been shown in the use of multi-template reverse transcription-polymerase chain reaction (RT-PCR) as a quantitative instrument for low-abundance mRNAs. A desire to achieve finely-graded quantification of the stress- and hormone-related regulation of one splicing decision in an ion channel gene motivated us to test the reliability of simultaneous amplification of two splice variants with one pair of flanking constitutive primers. Unexpectedly indiscriminate heteroduplexing between the two amplification products, despite a large length difference, and their tight comigration with one homoduplex, mandated a rigorously-denaturing electrophoresis protocol. Conveniently, a new fluorescent dye with high affinity for single-stranded DNA has become available. Though the dye has a good dynamic range, we found that dye and gel saturation compounded by the length difference between products introduced an asymmetrical error into the calculation of relative abundance. Avoiding several pitfalls, dye calibration could be used to correct the error. We also found that differences in the amplification efficiency of the two templates were not constant, but dependent on the initial template ratio, requiring a non-linear correction. Together these improvements gave us very consistent quantitative results, and thus advance our analysis of hormonal mechanisms underlying the regulation of alternative splicing of an ion channel critically involved in stress responses.
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Affiliation(s)
- Sahar F Mahmoud
- Department of Neurobiology and Behavior, Cornell University, W153 Mudd Hall, Ithaca, NY 14853, USA
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Lovell PV, McCobb DP. Pituitary control of BK potassium channel function and intrinsic firing properties of adrenal chromaffin cells. J Neurosci 2001; 21:3429-42. [PMID: 11331373 PMCID: PMC6762506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
The discovery that the hypothalamic-pituitary-adrenocortical (HPA) endocrine stress axis controls an alternative splicing decision in chromaffin Slo-encoded BK (big potassium) channels raised the possibility that activation of the HPA could serve as a mechanism to tune the intrinsic electrical properties of epinephrine-secreting adrenal chromaffin cells. To test this, we compared BK functional properties and cell excitability in chromaffin cells from normal and hypophysectomized (pituitary-ablated) rats. Hypophysectomy was found to alter the voltage dependence and kinetics of BK gating, making channels less accessible for activation from rest. Perforated-patch recordings revealed changes in action potential waveform and repetitive firing properties. The maximum number of spikes that could be elicited with a 2 sec depolarizing current pulse was reduced by approximately 50% by hypophysectomy. The results indicate that pituitary hormones can adapt the mechanics of adrenal catecholamine release by tailoring BK channel function.
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Affiliation(s)
- P V Lovell
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
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Abstract
Both bovine and rat adrenal chromaffin cells have served as pioneering model systems in cellular neurophysiology, including in the study of large conductance calcium- and voltage-dependent K(+) (BK) channels. We now report that while BK channels dominate the outward current profile of both species, specific gating properties vary widely across cell populations, and the distributions of these properties differ dramatically between species. Although BK channels were first described in bovine chromaffin cells, rapidly inactivating ones were discovered in rat chromaffin cells. We report that bovine cells can also exhibit inactivating BK channels with varying properties similar to those in rat cells. However, a much smaller proportion of bovine cells exhibit inactivating BK current, the proportion of the total current that inactivates is usually smaller, and the rate of inactivation is often much slower. Other gating features differ as well; the voltage dependence of channel activation is much more positive for bovine cells, and their rates of activation and deactivation are faster and slower, respectively. Modeling studies suggest that channel heterogeneity is consistent with varying tetrameric combinations of inactivation-competent versus -incompetent subunits. The results suggest that chromaffin BK channel functional nuances represent an important level for evolutionary tailoring of autonomic stress responses.
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Affiliation(s)
- P V Lovell
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
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