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A draft genome sequence of the elusive giant squid, Architeuthis dux

da Fonseca RR 1 , Couto A 2 , Machado AM 3 , Brejova B 4 , Albertin CB 5 , Silva F 3 Show all authors , Gardner P 6 , Baril T 7 , Hayward A 7 , Campos A 3 , Ribeiro ÂM 3 , Barrio-Hernandez I 8 , Hoving HJ 9 , Tafur-Jimenez R 10 , Chu C 11 , Frazão B 3 , Petersen B 12 , Peñaloza F 13 , Musacchia F 14 , Alexander GC 15 , Osório H 16 , Winkelmann I 17 , Simakov O 18 , Rasmussen S 19 , Rahman MZ 20 , Pisani D 21 , Vinther J 21 , Jarvis E 22 , Zhang G 23 , Strugnell JM 24 , Castro LFC 3 , Fedrigo O 25 , Patricio M 26 , Li Q 27 , Rocha S 2 , Antunes A 3 , Wu Y 28 , Ma B 29 , Sanges R 30 , Vinar T 4 , Blagoev B 8 , Sicheritz-Ponten T 12 , Nielsen R 17 , Gilbert MTP 17

Affiliations 

  • 1 Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
  • 2 Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
  • 3 CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Av. General Norton de Matos, 4450'208 Matosinhos, Portugal
  • 4 Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic
  • 5 Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA
  • 6 Department of Biochemistry, University of Otago, 710 Cumberland Street, North Dunedin, Dunedin 9016, New Zealand
  • 7 Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK
  • 8 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
  • 9 GEOMAR Helmholtz Centre for Ocean Research Kiel,Wischhofstraße 1-3, 24148 Kiel, Germany
  • 10 Instituto del Mar del Perú, Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao, Peru
  • 11 Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
  • 12 Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Batu 3 1/2, Butik Air Nasi, 08100 Bedong, Kedah, Malaysia
  • 13 Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México
  • 14 Genomic Medicine, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy
  • 15 GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708, USA
  • 16 i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
  • 17 Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
  • 18 Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14 (UZA1), A-1090 Vienna, Austria
  • 19 Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
  • 20 Bioinformatics Solutions Inc, 470 Weber St N Suite 204, Waterloo, ON N2L 6J2, Canada
  • 21 School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK
  • 22 Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
  • 23 Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
  • 24 Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia
  • 25 The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
  • 26 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
  • 27 BGI-Shenzhen, Shenzhen, China
  • 28 Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
  • 29 School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada
  • 30 Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
Gigascience, 2020 Jan 01;9(1).
PMID: 31942620 DOI: 10.1093/gigascience/giz152

Abstract

BACKGROUND: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea-dwelling species will allow several pending evolutionary questions to be unlocked.

FINDINGS: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.

CONCLUSIONS: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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