1
|
Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, Vikhrev IV, Breton S, Castro LFC, da Fonseca RR, Geist J, Österling ME, Prié V, Teixeira A, Gan HM, Simakov O, Froufe E. The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). DNA Res 2021; 28:6182681. [PMID: 33755103 PMCID: PMC8088596 DOI: 10.1093/dnares/dsab002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.
Collapse
Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,CIBIO/InBIO-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.,IUCN SSC Mollusc Specialist Group, c/o IUCN, Cambridge, England
| | - André M Machado
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal.,MED-Mediterranean Institute for Agriculture, Environment and Development, CEBAL-Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal.,MED-Mediterranean Institute for Agriculture, Environment and Development, CEBAL-Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal
| | - Ivan N Bolotov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk 163000, Russia
| | - Ilya V Vikhrev
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk 163000, Russia
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - L Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Juergen Geist
- Aquatic Systems Biology Unit, Technical University of Munich, TUM School of Life Sciences, D-85354 Freising, Germany
| | - Martin E Österling
- Department of Environmental and Life Sciences-Biology, Karlstad University, 651 88 Karlstad, Sweden
| | - Vincent Prié
- Research Associate, Institute of Systematics, Evolution, Biodiversity (ISYEB), National Museum of Natural History (MNHN), CNRS, SU, EPHE, 75005 Paris, France
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Han Ming Gan
- GeneSEQ Sdn Bhd, Bandar Bukit Beruntung, Rawang 48300, Selangor, Malaysia
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, 1010 Vienna, Austria
| | - Elsa Froufe
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| |
Collapse
|
2
|
Lopes-Lima M, Sousa R, Geist J, Aldridge DC, Araujo R, Bergengren J, Bespalaya Y, Bódis E, Burlakova L, Van Damme D, Douda K, Froufe E, Georgiev D, Gumpinger C, Karatayev A, Kebapçi Ü, Killeen I, Lajtner J, Larsen BM, Lauceri R, Legakis A, Lois S, Lundberg S, Moorkens E, Motte G, Nagel KO, Ondina P, Outeiro A, Paunovic M, Prié V, von Proschwitz T, Riccardi N, Rudzīte M, Rudzītis M, Scheder C, Seddon M, Şereflişan H, Simić V, Sokolova S, Stoeckl K, Taskinen J, Teixeira A, Thielen F, Trichkova T, Varandas S, Vicentini H, Zajac K, Zajac T, Zogaris S. Conservation status of freshwater mussels in Europe: state of the art and future challenges. Biol Rev Camb Philos Soc 2016; 92:572-607. [DOI: 10.1111/brv.12244] [Citation(s) in RCA: 320] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Manuel Lopes-Lima
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto; Rua dos Bragas 289 4050-123 Porto Portugal
- IUCN SSC Mollusc Specialist Group; c/o 219 Huntingdon Road Cambridge CB3 0DL U.K
| | - Ronaldo Sousa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto; Rua dos Bragas 289 4050-123 Porto Portugal
- Centre of Molecular and Environmental Biology (CMBA), University of Minho; Campus de Gualtar 4710-057 Braga Portugal
| | - Juergen Geist
- Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management; Technische Universität München; Mühlenweg 22 85350 Freising Germany
| | - David C. Aldridge
- Aquatic Ecology Group, Department of Zoology; University of Cambridge; Downing Street Cambridge CB2 3EJ U.K
| | - Rafael Araujo
- Museo Nacional de Ciencias Naturales-CSIC; C/José Gutiérrez Abascal 2 28006 Madrid Spain
| | - Jakob Bergengren
- Water Unit, County Administration Board Jönköping; SE-551 86 Jönköping Sweden
| | - Yulia Bespalaya
- Institute of Ecological Problems of the North of Ural Branch of Russian Academy of Sciences; 163000 Arkhangelsk Russia
| | - Erika Bódis
- MTA Centre for Ecological Research, Danube Research Institute; Jávorka S. u. 14 2131 Göd Hungary
| | - Lyubov Burlakova
- Great Lakes Center, Buffalo State College; 1300 Elmwood Ave. Buffalo NY 14222 U.S.A
| | - Dirk Van Damme
- Research Unit Palaeontology; Geological Institute, Universiteit Gent; Krijgslaan 281 (S8-B) B-9000 Gent Belgium
| | - Karel Douda
- Department of Zoology and Fisheries; Faculty of Agrobiology Food and Natural Resources, Czech University of Life Sciences Prague; Kamycka 129 Prague CZ 165 Czech Republic
| | - Elsa Froufe
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto; Rua dos Bragas 289 4050-123 Porto Portugal
| | - Dilian Georgiev
- Department of Ecology and Environmental Conservation; University of Plovdiv; Tzar Assen Str. 24 BG-4000 Plovdiv Bulgaria
| | - Clemens Gumpinger
- Consultants in Aquatic Ecology and Engineering (Technisches Büro für Gewässerökologie) - Blattfisch; Gabelsbergerstraße 7 4600 Wels Austria
| | - Alexander Karatayev
- Great Lakes Center, Buffalo State College; 1300 Elmwood Ave. Buffalo NY 14222 U.S.A
| | - Ümit Kebapçi
- Biology Department of Art and Science Faculty, Mehmet Akif Ersoy University; Burdur Turkey
| | - Ian Killeen
- 123, Rathdown Park, Greystones County Wicklow Ireland
| | - Jasna Lajtner
- Department of Zoology, Division of Biology; Faculty of Science, University of Zagreb; Rooseveltov trg 6 HR-10000 Zagreb Croatia
| | - Bjørn M. Larsen
- Norwegian Institute for Nature Research (NINA); PO Box 5685 Sluppen NO-7485 Trondheim Norway
| | - Rosaria Lauceri
- CNR ISE - Institute of Ecosystem Study; Largo Tonolli 50 28922 Verbania Italy
| | - Anastasios Legakis
- Zoological Museum, Department of Biology; University of Athens; Athens Greece
| | - Sabela Lois
- Departamento de Zooloxía e A.F.; Fac. Veterinaria, Universidade de Santiago de Compostela (USC); 27002 Lugo Spain
| | - Stefan Lundberg
- Swedish museum of Natural History; PO Box 50007 SE-104 05 Stockholm Sweden
| | | | - Gregory Motte
- CRNFB - Centre de Recherche de la Nature, des Forêts et du Bois; Gembloux Belgium
| | - Karl-Otto Nagel
- Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Abteilung Marine Zoologie/Sektion Malakologie; Senckenberganlage 25 60325 Frankfurt/Main Germany
| | - Paz Ondina
- Departamento de Zooloxía e A.F.; Fac. Veterinaria, Universidade de Santiago de Compostela (USC); 27002 Lugo Spain
| | - Adolfo Outeiro
- Departamento de Zooloxía e A.F.; Fac. Veterinaria, Universidade de Santiago de Compostela (USC); 27002 Lugo Spain
| | - Momir Paunovic
- Institute for Biological Research ‘Sinisa Stankovic’, University of Belgrade; 142 Bulevar despota Stefana 11000 Belgrade Serbia
| | - Vincent Prié
- Equipe ‘Exploration de la Biodiversité’, USM 603/UMR 7138 ‘Systématique, Adaptation, Evolution’, Muséum National d'Histoire Naturelle; Case Postale 51, 55, Rue Buffon 75231 Paris Cedex 05 France
- iotope; 22 Bd Maréchal Foch 34 140 Mèze France
| | - Ted von Proschwitz
- Göteborg Natural History Museum, Invetebrate Zoology; Box 7283 402 35 Göteborg Sweden
| | - Nicoletta Riccardi
- CNR ISE - Institute of Ecosystem Study; Largo Tonolli 50 28922 Verbania Italy
| | - Mudīte Rudzīte
- Museum of Zoology, University of Latvia; Kronvalda Bulv. 4 Rīga LV-1586 Latvia
| | - Māris Rudzītis
- Museum of Geology, University of Latvia; Alberta 10 Rīga LV-1010 Latvia
| | - Christian Scheder
- Consultants in Aquatic Ecology and Engineering (Technisches Büro für Gewässerökologie) - Blattfisch; Gabelsbergerstraße 7 4600 Wels Austria
| | - Mary Seddon
- IUCN SSC Mollusc Specialist Group; c/o 219 Huntingdon Road Cambridge CB3 0DL U.K
| | - Hülya Şereflişan
- Faculty of Marine Sciences and Technology, Mustafa Kemal University; 31200 İskenderun Hatay Turkey
| | - Vladica Simić
- Department of Hydroecology and Water Protection; Faculty of Science, Institute of Biology and Ecology, University of Kragujevac; 34000 Kragujevac Serbia
| | - Svetlana Sokolova
- Institute of Ecological Problems of the North of Ural Branch of Russian Academy of Sciences; 163000 Arkhangelsk Russia
| | - Katharina Stoeckl
- Aquatic Systems Biology Unit, Department of Ecology and Ecosystem Management; Technische Universität München; Mühlenweg 22 85350 Freising Germany
| | - Jouni Taskinen
- Department of Biological and Environmental Science; University of Jyväskylä; PO Box 35 (YAC-315.2) FI-40014 Jyväskylä Finland
| | - Amílcar Teixeira
- CIMO - Mountain Research Centre, School of Agriculture, Polytechnic Institute of Bragança; Campus de Santa Apolónia, Apartado 1172 5301-854 Bragança Portugal
| | - Frankie Thielen
- Natur & Ëmwelt/Fondation Hëllef fir d'Natur; Kierchestrooss 2 L-9753 Heinerscheid Luxembourg
| | - Teodora Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences; 2 Gagarin Str. Sofia 1113 Bulgaria
| | - Simone Varandas
- CITAB - Centre for Research and Technology of Agro-Environment and Biological Sciences; Forestry Department, University of Trás-os-Montes and Alto Douro; Apartado 1013 5001-811 Vila Real Portugal
| | | | - Katarzyna Zajac
- Institute of Nature Conservation, Polish Academy of Sciences; 31-120 Kraków Mickiewicza 33 Poland
| | - Tadeusz Zajac
- Institute of Nature Conservation, Polish Academy of Sciences; 31-120 Kraków Mickiewicza 33 Poland
| | - Stamatis Zogaris
- Hellenic Centre For Marine Research - Institute of Marine Biological Sciences and Inland Waters; 46, 7 km Athens-Sounio Anavissos Attiki Greece
| |
Collapse
|