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Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biol Evol 2023; 15:evad148. [PMID: 37728212 PMCID: PMC10510315 DOI: 10.1093/gbe/evad148] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Accepted: 08/03/2023] [Indexed: 09/21/2023] Open
Abstract
Bats are exceptional among mammals for their powered flight, extended lifespans, and robust immune systems and therefore have been of particular interest in comparative genomics. Using the Oxford Nanopore Technologies long-read platform, we sequenced the genomes of two bat species with key phylogenetic positions, the Jamaican fruit bat (Artibeus jamaicensis) and the Mesoamerican mustached bat (Pteronotus mesoamericanus), and carried out a comprehensive comparative genomic analysis with a diverse collection of bats and other mammals. The high-quality, long-read genome assemblies revealed a contraction of interferon (IFN)-α at the immunity-related type I IFN locus in bats, resulting in a shift in relative IFN-ω and IFN-α copy numbers. Contradicting previous hypotheses of constitutive expression of IFN-α being a feature of the bat immune system, three bat species lost all IFN-α genes. This shift to IFN-ω could contribute to the increased viral tolerance that has made bats a common reservoir for viruses that can be transmitted to humans. Antiviral genes stimulated by type I IFNs also showed evidence of rapid evolution, including a lineage-specific duplication of IFN-induced transmembrane genes and positive selection in IFIT2. In addition, 33 tumor suppressors and 6 DNA-repair genes showed signs of positive selection, perhaps contributing to increased longevity and reduced cancer rates in bats. The robust immune systems of bats rely on both bat-wide and lineage-specific evolution in the immune gene repertoire, suggesting diverse immune strategies. Our study provides new genomic resources for bats and sheds new light on the extraordinary molecular evolution in this critically important group of mammals.
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Affiliation(s)
- Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Oppenheim
- American Museum of Natural History, Institute for Comparative Genomics, New York, New York, USA
| | - Daniel J Becker
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael C Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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Dornelas M, Antão LH, Moyes F, Bates AE, Magurran AE, Adam D, Akhmetzhanova AA, Appeltans W, Arcos JM, Arnold H, Ayyappan N, Badihi G, Baird AH, Barbosa M, Barreto TE, Bässler C, Bellgrove A, Belmaker J, Benedetti‐Cecchi L, Bett BJ, Bjorkman AD, Błażewicz M, Blowes SA, Bloch CP, Bonebrake TC, Boyd S, Bradford M, Brooks AJ, Brown JH, Bruelheide H, Budy P, Carvalho F, Castañeda‐Moya E, Chen CA, Chamblee JF, Chase TJ, Siegwart Collier L, Collinge SK, Condit R, Cooper EJ, Cornelissen JHC, Cotano U, Kyle Crow S, Damasceno G, Davies CH, Davis RA, Day FP, Degraer S, Doherty TS, Dunn TE, Durigan G, Duffy JE, Edelist D, Edgar GJ, Elahi R, Elmendorf SC, Enemar A, Ernest SKM, Escribano R, Estiarte M, Evans BS, Fan T, Turini Farah F, Loureiro Fernandes L, Farneda FZ, Fidelis A, Fitt R, Fosaa AM, Daher Correa Franco GA, Frank GE, Fraser WR, García H, Cazzolla Gatti R, Givan O, Gorgone‐Barbosa E, Gould WA, Gries C, Grossman GD, Gutierréz JR, Hale S, Harmon ME, Harte J, Haskins G, Henshaw DL, Hermanutz L, Hidalgo P, Higuchi P, Hoey A, Van Hoey G, Hofgaard A, Holeck K, Hollister RD, Holmes R, Hoogenboom M, Hsieh C, Hubbell SP, Huettmann F, Huffard CL, Hurlbert AH, Macedo Ivanauskas N, Janík D, Jandt U, Jażdżewska A, Johannessen T, Johnstone J, Jones J, Jones FAM, Kang J, Kartawijaya T, Keeley EC, Kelt DA, Kinnear R, Klanderud K, Knutsen H, Koenig CC, Kortz AR, Král K, Kuhnz LA, Kuo C, Kushner DJ, Laguionie‐Marchais C, Lancaster LT, Min Lee C, Lefcheck JS, Lévesque E, Lightfoot D, Lloret F, Lloyd JD, López‐Baucells A, Louzao M, Madin JS, Magnússon B, Malamud S, Matthews I, McFarland KP, McGill B, McKnight D, McLarney WO, Meador J, Meserve PL, Metcalfe DJ, Meyer CFJ, Michelsen A, Milchakova N, Moens T, Moland E, Moore J, Mathias Moreira C, Müller J, Murphy G, Myers‐Smith IH, Myster RW, Naumov A, Neat F, Nelson JA, Paul Nelson M, Newton SF, Norden N, Oliver JC, Olsen EM, Onipchenko VG, Pabis K, Pabst RJ, Paquette A, Pardede S, Paterson DM, Pélissier R, Peñuelas J, Pérez‐Matus A, Pizarro O, Pomati F, Post E, Prins HHT, Priscu JC, Provoost P, Prudic KL, Pulliainen E, Ramesh BR, Mendivil Ramos O, Rassweiler A, Rebelo JE, Reed DC, Reich PB, Remillard SM, Richardson AJ, Richardson JP, van Rijn I, Rocha R, Rivera‐Monroy VH, Rixen C, Robinson KP, Ribeiro Rodrigues R, de Cerqueira Rossa‐Feres D, Rudstam L, Ruhl H, Ruz CS, Sampaio EM, Rybicki N, Rypel A, Sal S, Salgado B, Santos FAM, Savassi‐Coutinho AP, Scanga S, Schmidt J, Schooley R, Setiawan F, Shao K, Shaver GR, Sherman S, Sherry TW, Siciński J, Sievers C, da Silva AC, Rodrigues da Silva F, Silveira FL, Slingsby J, Smart T, Snell SJ, Soudzilovskaia NA, Souza GBG, Maluf Souza F, Castro Souza V, Stallings CD, Stanforth R, Stanley EH, Mauro Sterza J, Stevens M, Stuart‐Smith R, Rondon Suarez Y, Supp S, Yoshio Tamashiro J, Tarigan S, Thiede GP, Thorn S, Tolvanen A, Teresa Zugliani Toniato M, Totland Ø, Twilley RR, Vaitkus G, Valdivia N, Vallejo MI, Valone TJ, Van Colen C, Vanaverbeke J, Venturoli F, Verheye HM, Vianna M, Vieira RP, Vrška T, Quang Vu C, Van Vu L, Waide RB, Waldock C, Watts D, Webb S, Wesołowski T, White EP, Widdicombe CE, Wilgers D, Williams R, Williams SB, Williamson M, Willig MR, Willis TJ, Wipf S, Woods KD, Woehler EJ, Zawada K, Zettler ML, Hickler T. BioTIME: A database of biodiversity time series for the Anthropocene. Glob Ecol Biogeogr 2018; 27:760-786. [PMID: 30147447 PMCID: PMC6099392 DOI: 10.1111/geb.12729] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 05/08/2023]
Abstract
MOTIVATION The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. MAIN TYPES OF VARIABLES INCLUDED The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. SPATIAL LOCATION AND GRAIN BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). TIME PERIOD AND GRAIN BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. MAJOR TAXA AND LEVEL OF MEASUREMENT BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. SOFTWARE FORMAT .csv and .SQL.
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Affiliation(s)
- Maria Dornelas
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Laura H. Antão
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biology and CESAMUniversidade de Aveiro, Campus Universitário de SantiagoAveiroPortugal
| | - Faye Moyes
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Amanda E. Bates
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
- Department of Ocean Sciences, Memorial University of NewfoundlandSt John'sNewfoundland and LabradorCanada
| | - Anne E. Magurran
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Dušan Adam
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | | | - Ward Appeltans
- UNESCO, Intergovernmental Oceanographic Commission, IOC Project Office for IODEOostendeBelgium
| | | | - Haley Arnold
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | - Gal Badihi
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Andrew H. Baird
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - Miguel Barbosa
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biology and CESAMUniversidade de Aveiro, Campus Universitário de SantiagoAveiroPortugal
| | - Tiago Egydio Barreto
- Laboratório de Ecologia e Restauração Florestal, Fundação Espaço Eco, Piracicaba, São PauloBrazil
| | | | - Alecia Bellgrove
- School of Life and Environmental SciencesCentre for Integrative Ecology, Deakin UniversityWarrnamboolVictoriaAustralia
| | - Jonathan Belmaker
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | | | - Brian J. Bett
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Anne D. Bjorkman
- Section for Ecoinformatics and Biodiversity, Department of BioscienceAarhus UniversityAarhusDenmark
| | - Magdalena Błażewicz
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Shane A. Blowes
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Christopher P. Bloch
- Department of Biological SciencesBridgewater State UniversityBridgewaterMassachusetts
| | | | - Susan Boyd
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Matt Bradford
- CSIRO Land & WaterEcosciences Precinct, Dutton ParkQueenslandAustralia
| | - Andrew J. Brooks
- Marine Science Institute, University of CaliforniaSanta BarbaraCalifornia
| | - James H. Brown
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical Garden, Martin‐Luther‐University Halle‐WittenbergHalleGermany
| | - Phaedra Budy
- Department of Watershed Sciences and the Ecology Center, US Geological Survey, UCFWRU and Utah State UniversityLoganUtah
| | - Fernando Carvalho
- Universidade do Extremo Sul Catarinense (PPG‐CA)CriciúmaSanta CatarinaBrazil
| | - Edward Castañeda‐Moya
- Southeast Environmental Research Center (OE 148), Florida International UniversityMiamiFlorida
| | - Chaolun Allen Chen
- Coral Reef Ecology and Evolution LabBiodiversity Research Centre, Academia SinicaTaipeiTaiwan
| | | | - Tory J. Chase
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | | | | | - Richard Condit
- Center for Tropical Forest ScienceWashingtonDistrict of Columbia
| | - Elisabeth J. Cooper
- Biosciences Fisheries and EconomicsUiT‐ The Arctic University of NorwayTromsøNorway
| | - J. Hans C. Cornelissen
- Systems Ecology, Department of Ecological Science, Vrije UniversiteitAmsterdamThe Netherlands
| | | | - Shannan Kyle Crow
- The National Institute of Water and Atmospheric ResearchAucklandNew Zealand
| | - Gabriella Damasceno
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | | | - Robert A. Davis
- School of ScienceEdith Cowan UniversityJoondalupWestern AustraliaAustralia
| | - Frank P. Day
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
| | - Steven Degraer
- Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and ManagementBrusselsBelgium
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Tim S. Doherty
- School of ScienceEdith Cowan UniversityJoondalupWestern AustraliaAustralia
- School of Life and Environmental SciencesCentre for Integrative Ecology (Burwood Campus), Deakin UniversityGeelongVictoriaAustralia
| | | | - Giselda Durigan
- Divisão de Florestas e Estações Experimentais, Floresta Estadual de Assis, Laboratório de Ecologia e Hidrologia Florestal, Instituto FlorestalSão PauloBrazil
| | - J. Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian InstitutionWashington, District of Columbia
| | - Dor Edelist
- National Institute of Oceanography, Tel‐ShikmonaHaifaIsrael
| | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Robin Elahi
- Hopkins Marine Station, Stanford University, StanfordCalifornia
| | | | - Anders Enemar
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - S. K. Morgan Ernest
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFL
| | - Rubén Escribano
- Instituto Milenio de Oceanografía, Universidad de ConcepciónConcepciónChile
| | - Marc Estiarte
- CSIC, Global Ecology Unit CREAF‐CSIC‐UABBellaterraCataloniaSpain
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | - Brian S. Evans
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological ParkWashingtonDistrict of Columbia
| | - Tung‐Yung Fan
- National Museum of Marine Biology and AquariumPingtung CountyTaiwan
| | - Fabiano Turini Farah
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | - Luiz Loureiro Fernandes
- Departamento de Oceanografia e Ecologia, Universidade Federal do Espírito Santo, Vitória, Espírito SantoBrazil
| | - Fábio Z. Farneda
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Department of Ecology/PPGEFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Alessandra Fidelis
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | - Robert Fitt
- School of Biological SciencesUniversity of AberdeenAberdeenUnited Kingdom
| | - Anna Maria Fosaa
- Botanical Department, Faroese Museum of Natural HistoryTorshavnFaroe Islands
| | | | - Grace E. Frank
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | | | - Hernando García
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | | | - Or Givan
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Elizabeth Gorgone‐Barbosa
- Lab of Vegetation Ecology, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio ClaroBrazil
| | - William A. Gould
- USDA Forest Service, 65 USDA Forest Service, International Institute of Tropical ForestrySan JuanPuerto Rico
| | - Corinna Gries
- Center for Limnology, University of WisconsinMadisonWisconsin
| | - Gary D. Grossman
- The Warnell School of Forestry and Natural ResourcesUniversity of GeorgiaAthensGeorgia
| | - Julio R. Gutierréz
- Departamento de Biología, Facultad de Ciencias, Universidad de La SerenaLa SerenaChile
- Centro de Estudios Avanzados en Zonas Aridas (CEAZA)La SerenaChile
- Institute of Ecology and Biodiversity (IEB)SantiagoChile
| | - Stephen Hale
- U.S. Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology DivisionNarragansettRhode Island
| | - Mark E. Harmon
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - John Harte
- The Energy and Resources Group and The Department of Environmental Science, Policy and ManagementUniversity of CaliforniaBerkeleyCalifornia
| | - Gary Haskins
- Cetacean Research & Rescue UnitBanffUnited Kingdom
| | - Donald L. Henshaw
- U.S. Forest Service Pacific Northwest Research LaboratoryCorvallisOregon
| | - Luise Hermanutz
- Memorial University, St John'sNewfoundland and LabradorCanada
| | - Pamela Hidalgo
- Instituto Milenio de Oceanografía, Universidad de ConcepciónConcepciónChile
| | - Pedro Higuchi
- Laboratório de Dendrologia e Fitossociologia, Universidade do Estado de Santa CatarinaFlorianópolisSanta CatarinaBrazil
| | - Andrew Hoey
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - Gert Van Hoey
- Department of Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and FoodOostendeBelgium
| | | | - Kristen Holeck
- Department of Natural Resources and Cornell Biological Field StationCornell UniversityIthacaNew York
| | | | | | - Mia Hoogenboom
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
- Marine Biology and Aquaculture, College of Science and EngineeringJames Cook UniversityDouglasQueenslandAustralia
| | - Chih‐hao Hsieh
- Institute of Oceanography, National Taiwan UniversityTaipeiTaiwan
| | | | - Falk Huettmann
- EWHALE lab‐ Biology and Wildlife DepartmentInstitute of Arctic Biology, University of AlaskaFairbanksAlaska
| | | | - Allen H. Hurlbert
- Department of BiologyUniversity of North CarolinaChapel HillNorth Carolina
| | | | - David Janík
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Ute Jandt
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical Garden, Martin‐Luther‐University Halle‐WittenbergHalleGermany
| | - Anna Jażdżewska
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | | | - Jill Johnstone
- Department of BiologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Julia Jones
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State UniversityCorvallisOregon
| | - Faith A. M. Jones
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Jungwon Kang
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | | | - Douglas A. Kelt
- Department of WildlifeFish, and Conservation Biology, University of California, DavisDavisCalifornia
| | - Rebecca Kinnear
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
| | - Kari Klanderud
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesÅsNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | | | - Alessandra R. Kortz
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Kamil Král
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Linda A. Kuhnz
- Monterey Bay Aquarium Research InstituteMoss LandingCalifornia
| | - Chao‐Yang Kuo
- ARC Centre of Excellence for Coral Reef Studies, James Cook UniversityTownsvilleQueenslandAustralia
| | - David J. Kushner
- Channel Islands National Park, U. S. National Park ServiceCalifornia, VenturaCalifornia
| | | | | | - Cheol Min Lee
- Forest and Climate Change Adaptation LaboratoryCenter for Forest and Climate Change, National Institute of Forest ScienceSeoulRepublic of Korea
| | - Jonathan S. Lefcheck
- Department of Biological SciencesVirginia Institute of Marine Science, The College of William & Mary, Gloucester PointVirginia
| | - Esther Lévesque
- Département des sciences de l'environnementUniversité du Québec à Trois‐Rivières and Centre d’études nordiquesQuébecCanada
| | - David Lightfoot
- Department of BiologyMuseum of Southwestern Biology, University of New MexicoAlbuquerqueNew Mexico
| | - Francisco Lloret
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | | | - Adrià López‐Baucells
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Museu de Ciències Naturals de GranollersCatalunyaSpain
| | | | - Joshua S. Madin
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, KaneoheHawai‘iUSA
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | | | - Shahar Malamud
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Iain Matthews
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | - Brian McGill
- School of Biology and EcologySustainability Solutions Initiative, University of MaineOronoMaine
| | | | - William O. McLarney
- Stream Biomonitoring Program, Mainspring Conservation TrustFranklinNorth Carolina
| | - Jason Meador
- Stream Biomonitoring Program, Mainspring Conservation TrustFranklinNorth Carolina
| | | | | | - Christoph F. J. Meyer
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Ecosystems and Environment Research Centre (EERC), School of Environment and Life Sciences, University of SalfordSalfordUnited Kingdom
| | - Anders Michelsen
- Terrestrial Ecology Section, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Nataliya Milchakova
- Laboratory of Phytoresources, Kovalevsky Institute of Marine Biological Research of RAS (IMBR)SevastopolRussia
| | - Tom Moens
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Even Moland
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | - Jon Moore
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
- Aquatic Survey & Monitoring Ltd. ASMLDurhamUnited Kingdom
| | | | - Jörg Müller
- Bavarian Forest National ParkGrafenauGermany
- Field Station Fabrikschleichach, University of WürzburgRauhenebrachGermany
| | - Grace Murphy
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | | | - Andrew Naumov
- Zoological Institute, Russian Academy SciencesSt PetersburgRussia
| | - Francis Neat
- Marine Scotland, Marine LaboratoryScottish GovernmentEdinburghUnited Kingdom
| | - James A. Nelson
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisiana
| | - Michael Paul Nelson
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | | | - Natalia Norden
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | - Jeffrey C. Oliver
- University of Arizona Health Sciences Library, University of ArizonaTucsonArizona
| | - Esben M. Olsen
- Institute of Marine ResearchHisNorway
- Department of Natural Sciences, Faculty of Engineering and Science, Centre for Coastal Research, University of AgderKristiansandNorway
| | | | - Krzysztof Pabis
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Robert J. Pabst
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - Alain Paquette
- Center for Forest Research, Université du Québec à Montréal (UQAM)MontrealQuebecCanada
| | - Sinta Pardede
- Wildlife Conservation Society Indonesia ProgramBogorIndonesia
| | - David M. Paterson
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Shetland Oil Terminal Environmental Advisory Group (SOTEAG)St AndrewsUnited Kingdom
| | - Raphaël Pélissier
- UMR AMAP, IRD, CIRAD, CNRS, INRA, Montpellier UniversityMontpellierFrance
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF‐CSIC‐UABBellaterraCataloniaSpain
- CREAF, Universitat Autònoma de BarcelonaCerdanyola del VallèsCataloniaSpain
| | - Alejandro Pérez‐Matus
- Subtidal Ecology Laboratory & Center for Marine Conservation, Estación Costera de Investigaciones MarinasFacultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiagoCasillaChile
| | - Oscar Pizarro
- Australian Centre of Field Robotics, University of SydneySydneyNew South WalesAustralia
| | - Francesco Pomati
- Department of Aquatic EcologyEawag: Swiss Federal Institute of Aquatic Science and TechnologySwitzerland
| | - Eric Post
- Department of WildlifeFish, and Conservation Biology, University of California, DavisDavisCalifornia
| | | | - John C. Priscu
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMontana
| | - Pieter Provoost
- UNESCO, Intergovernmental Oceanographic Commission, IOC Project Office for IODEOostendeBelgium
| | | | | | - B. R. Ramesh
- Department of EcologyFrench Institute of PondicherryPuducherryIndia
| | | | - Andrew Rassweiler
- Channel Islands National Park, U. S. National Park ServiceCalifornia, VenturaCalifornia
| | - Jose Eduardo Rebelo
- Ichthyology Laboratory, Fisheries and AquacultureUniversity of AveiroAveiroPortugal
| | - Daniel C. Reed
- Marine Science Institute, University of CaliforniaSanta BarbaraCalifornia
| | - Peter B. Reich
- Department of Forest Resources, University of MinnesotaSt PaulMinnesota
- Hawkesbury Institute for the Environment, Western Sydney UniversityPenrithNew South WalesAustralia
| | - Suzanne M. Remillard
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisOregon
| | - Anthony J. Richardson
- CSIRO Oceans and AtmosphereQueensland, BioSciences Precinct (QBP)St Lucia, BrisbaneQldAustralia
- Centre for Applications in Natural Resource Mathematics, The University of QueenslandSt LuciaQueenslandAustralia
| | | | - Itai van Rijn
- School of Zoology, George S. Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Ricardo Rocha
- Centre for Ecology, Evolution and Environmental Changes – cE3c, Faculty of SciencesUniversity of LisbonLisbonPortugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Metapopulation Research Centre, Faculty of Biosciences, University of HelsinkiHelsinkiFinland
| | - Victor H. Rivera‐Monroy
- Department of Oceanography and Coastal Sciences, College of the Coast and EnvironmentLouisiana State UniversityBaton RougeLouisiana
| | - Christian Rixen
- Swiss Federal Institute for Forest, Snow and Landscape ResearchDavos DorfSwitzerland
| | | | - Ricardo Ribeiro Rodrigues
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | - Denise de Cerqueira Rossa‐Feres
- Departamento de Zoologia e Botânica, Universidade Estadual Paulista – UNESPCâmpus São José do Rio Preto, São José do Rio PretoBrazil
| | - Lars Rudstam
- Department of Natural Resources and Cornell Biological Field StationCornell UniversityIthacaNew York
| | - Henry Ruhl
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Catalina S. Ruz
- Subtidal Ecology Laboratory & Center for Marine Conservation, Estación Costera de Investigaciones MarinasFacultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiagoCasillaChile
| | - Erica M. Sampaio
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research InstituteManausBrazil
- Department of Animal Physiology, Eberhard Karls University TübingenTübingenGermany
| | - Nancy Rybicki
- National Research Program, U.S. Geological SurveyRestonVirginia
| | - Andrew Rypel
- Wisconsin Department of Natural Resources and Center for LimnologyUniversity of Wisconsin‐MadisonMadisonWisconsin
| | - Sofia Sal
- Department of Life SciencesImperial College LondonAscotBerkshireUnited Kingdom
| | - Beatriz Salgado
- Alexander von Humboldt Biological Resources Research InstituteBogotá DCColombia
| | | | - Ana Paula Savassi‐Coutinho
- Departamento de Ciências Biológicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloSão PauloBrazil
| | - Sara Scanga
- Department of BiologyUtica CollegeUticaNew York
| | - Jochen Schmidt
- The National Institute of Water and Atmospheric ResearchAucklandNew Zealand
| | - Robert Schooley
- Wildlife Ecology and Conservation, Department of Natural Resources and Environmental SciencesUniversity of IllinoisChampaignIllinois
| | | | - Kwang‐Tsao Shao
- Biodiversity Research Center, Academia SinicaNankang, TaipeiTaiwan
| | | | | | | | - Jacek Siciński
- Laboratory of Polar Biology and Oceanobiology, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Caya Sievers
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | - Ana Carolina da Silva
- Laboratório de Dendrologia e Fitossociologia, Universidade do Estado de Santa CatarinaFlorianópolisSanta CatarinaBrazil
| | | | | | - Jasper Slingsby
- Department of Biological Sciences, Centre for Statistics in Ecology, Environment and ConservationUniversity of CapeTownRondeboschSouth Africa
- Fynbos Node, South African Environmental Observation NetworkClaremontSouth Africa
| | - Tracey Smart
- Coastal Finfish Section, South Carolina Department of Natural Resources, Marine Resources Research InstituteCharlestonSouth Carolina
| | - Sara J. Snell
- Department of BiologyUniversity of North CarolinaChapel HillNorth Carolina
| | - Nadejda A. Soudzilovskaia
- Conservation Biology DepartmentInstitute of Environmental Studies, CML, Leiden UniversityLeidenThe Netherlands
| | - Gabriel B. G. Souza
- Laboratório de Biologia e Tecnologia Pesqueira, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | | | - Vinícius Castro Souza
- Laboratório de Ecologia e Restauração Florestal, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São PauloSão PauloBrazil
| | | | - Rowan Stanforth
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
| | | | | | - Maarten Stevens
- INBO, Research Institute for Nature and ForestBrusselsBelgium
| | - Rick Stuart‐Smith
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Yzel Rondon Suarez
- Centro de Estudos em Recursos Naturais, Universidade Estadual de Mato Grosso do SulDouradosMato Grosso do SulBrazil
| | - Sarah Supp
- School of Biology and EcologyUniversity of MaineOronoMaine
| | | | | | - Gary P. Thiede
- Department of Watershed Sciences and the Ecology Center, US Geological Survey, UCFWRU and Utah State UniversityLoganUtah
| | - Simon Thorn
- Field Station Fabrikschleichach, University of WürzburgRauhenebrachGermany
| | - Anne Tolvanen
- Natural Resources Institute Finland, University of OuluOuluFinland
| | | | - Ørjan Totland
- Department of BiologyUniversity of BergenBergenNorway
| | - Robert R. Twilley
- Department of Oceanography and Coastal Sciences, College of the Coast and EnvironmentLouisiana State UniversityBaton RougeLouisiana
| | | | - Nelson Valdivia
- Universidad Austral de Chile and Centro FONDAP en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL)ValdiviaChile
| | | | | | - Carl Van Colen
- Marine Biology Research Group, Ghent UniversityGentBelgium
| | - Jan Vanaverbeke
- Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and ManagementBrusselsBelgium
| | - Fabio Venturoli
- Escola de Agronomia, Universidade Federal de GoiásGoiâniaBrazil
| | - Hans M. Verheye
- Department of Environmental AffairsOceans and Coastal ResearchCape TownSouth Africa
- Department of Biological SciencesMarine Research InstituteUniversity of Cape TownCape TownSouth Africa
| | - Marcelo Vianna
- Laboratório de Biologia e Tecnologia Pesqueira, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Rui P. Vieira
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Tomáš Vrška
- Department of Forest Ecology, Silva Tarouca Research InstituteBrnoCzech Republic
| | - Con Quang Vu
- Institute of Ecology and Biological Resources, VASTHanoiVietnam
| | - Lien Van Vu
- Vietnam National Museum of NatureHanoiVietnam
- Graduate University of Science and Technology, VASTHanoiVietnam
| | - Robert B. Waide
- Department of BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Conor Waldock
- National Oceanography Centre, University of Southampton Waterfront CampusSouthamptonUnited Kingdom
| | - Dave Watts
- CSIRO Oceans and Atmosphere FlagshipHobartTasmaniaAustralia
| | - Sara Webb
- Biology Department, Drew UniversityMadisonNew Jersey
- Environmental Studies Department, Drew UniversityMadisonNew Jersey
| | | | - Ethan P. White
- Department of Wildlife Ecology & ConservationUniversity of FloridaGainesvilleFlorida
- Informatics Institute, University of FloridaGainesvilleFlorida
| | | | - Dustin Wilgers
- Department of Natural SciencesMcPherson CollegeMcPhersonKansas
| | - Richard Williams
- Australian Antarctic Division, Channel HighwayKingstonTasmaniaAustralia
| | - Stefan B. Williams
- Australian Centre of Field Robotics, University of SydneySydneyNew South WalesAustralia
| | | | - Michael R. Willig
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & EngineeringUniversity of ConnecticutMansfieldConnecticut
| | - Trevor J. Willis
- Institute of Marine Sciences, School of Biological Sciences, University of PortsmouthPortsmouthUnited Kingdom
| | - Sonja Wipf
- Research Team Mountain Ecosystems, WSL Institute for Snow and Avalanche Research SLFDavosSwitzerland
| | | | - Eric J. Woehler
- Institute for Marine and Antarctic Studies, University of TasmaniaHobartTasmaniaAustralia
| | - Kyle Zawada
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St. AndrewsSt AndrewsUnited Kingdom
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Michael L. Zettler
- Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, D‐18119 RostockGermany
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3
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [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] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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4
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Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JCJ, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJP, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JHL, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol 2014; 12:e1002005. [PMID: 25423365 PMCID: PMC4244043 DOI: 10.1371/journal.pbio.1002005] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [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: 02/21/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022] Open
Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
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Affiliation(s)
- Ariel D. Chipman
- The Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Carlo Brena
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniel S. T. Hughes
- EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock, Abt. Genetik, Rostock, Germany
| | | | - Nadia Znassi
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Francisca C. Almeida
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, San Miguel de Tucumán, Argentina
| | - Claudio R. Alonso
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Zivkos Apostolou
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas, Heraklion, Crete, Greece
| | - Peshtewani Aqrawi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wallace Arthur
- Department of Zoology, National University of Ireland, Galway, Ireland
| | | | - Kerstin P. Blankenburg
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniela Brites
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Marcus Coyle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter K. Dearden
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Louis Du Pasquier
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Elizabeth J. Duncan
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Dieter Ebert
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Cornelius Eibner
- Department of Zoology, National University of Ireland, Galway, Ireland
| | - Galina Erikson
- Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America
- Scripps Translational Science Institute, La Jolla, California, United States of America
| | | | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Liezl Francisco
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - William J. Gillis
- Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America
| | | | - Jack E. Green
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Sai Gubbala
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation, Barcelona, Spain
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Paul Havlak
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Luke Hayden
- Department of Zoology, National University of Ireland, Galway, Ireland
| | - Sophie Helbing
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jerome H. L. Hui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Julia P. Hunn
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Vera S. Hunnekuhl
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - LaRonda Jackson
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mehwish Javaid
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tamsin E. Jones
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tobias S. Kaiser
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Divya Kalra
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nathan J. Kenny
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Viktoriya Korchina
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christie L. Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - F. Bernhard Kraus
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- Department of Laboratory Medicine, University Hospital Halle (Saale), Halle (Saale), Germany
| | - François Lapraz
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sandra L. Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jie Lv
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Christigale Mandapat
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gerard Manning
- Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America
| | - Marco Mariotti
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation, Barcelona, Spain
| | - Robert Mata
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tittu Mathew
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tobias Neumann
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Irene Newsham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dinh N. Ngo
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fiona Ongeri
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - William J. Palmer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shobha Patil
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro Patraquim
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Christopher Pham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nicholas H. Putman
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Catherine Rabouille
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Olivia Mendivil Ramos
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Adelaide C. Rhodes
- Harte Research Institute, Texas A&M University Corpus Christi, Corpus Christi, Texas, United States of America
| | - Helen E. Robertson
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Matthew Ronshaugen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Nehad Saada
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alejandro Sánchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Steven E. Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrew M. Schurko
- Department of Biology, Hendrix College, Conway, Arkansas, United States of America
| | - Kenneth W. Siggens
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - DeNard Simmons
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anna Stief
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute for Biochemistry and Biology, University Potsdam, Potsdam-Golm, Germany
| | - Eckart Stolle
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life”, Vienna, Austria
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - James M. Williams
- Department of Biology, Hendrix College, Conway, Arkansas, United States of America
| | - Judith H. Willis
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yuanqing Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaoyan Zou
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniel Lawson
- EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Donna M. Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kim C. Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Mendivil Ramos O, Barker D, Ferrier DEK. Ghost loci imply Hox and ParaHox existence in the last common ancestor of animals. Curr Biol 2012; 22:1951-6. [PMID: 23022064 DOI: 10.1016/j.cub.2012.08.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 08/09/2012] [Accepted: 08/13/2012] [Indexed: 12/24/2022]
Abstract
Hox genes are renowned for patterning animal development, with widespread roles in developmental gene regulation. Despite this importance, their evolutionary origin remains obscure, due to absence of Hox genes (and their evolutionary sisters, the ParaHox genes) from basal lineages and because the phylogenies of these genes are poorly resolved. This has led to debate about whether Hox and ParaHox genes originated coincidently with the origin of animals or instead evolved after the divergence of the earliest animal lineages. Here we use genomic synteny and Monte Carlo-based simulations to resolve Hox/ParaHox origins, our approach being independent of poorly resolved homeodomain phylogenies and better able to accommodate gene loss. We show Trox-2 of placozoans occupies a ParaHox locus. In addition, a separate locus sharing synteny and hence homology with human Hox loci exists in the placozoan genome, but without a Hox-like gene in it. We call this second locus a "ghost" Hox locus, because it is homologous to the human Hox loci, but does not itself contain a Hox gene. Extending our approach to sponges, we discover distinct ghost Hox and ParaHox loci. Thus, distinct Hox and ParaHox loci were present in the last common ancestor of all living animal lineages.
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Affiliation(s)
- Olivia Mendivil Ramos
- The Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK
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Abstract
Three neonates with gram-negative bacillary meningitis were treated with moxalactam after therapy with ampicillin plus aminoglycoside, trimethoprim-sulfamethoxazole, or chloramphenicol failed to sterilize the CSF. Clinical improvement and CSF sterility occurred after therapy with moxalactam was initiated. Moxalactam concentrations in CSF exceeded MICs of each organism. All three patients were cured of their infection. Moxalactam appears to be an effective antibiotic for the treatment of neonatal gram-negative bacillary meningitis.
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