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The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea\u2013dwelling species will allow several pending evolutionary questions to be unlocked.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Findings<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/gigascience\/giz152","type":"journal-article","created":{"date-parts":[[2020,1,16]],"date-time":"2020-01-16T05:07:01Z","timestamp":1579151221000},"source":"Crossref","is-referenced-by-count":48,"title":["A draft genome sequence of the elusive giant squid, <i>Architeuthis dux<\/i>"],"prefix":"10.1093","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2805-4698","authenticated-orcid":false,"given":"Rute R","family":"da Fonseca","sequence":"first","affiliation":[{"name":"Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen , Universitetsparken 15, 2100 Copenhagen,","place":["Denmark"]},{"name":"The Bioinformatics Centre, Department of Biology, University of Copenhagen , Ole Maal\u00f8es Vej 5, 2200 Copenhagen,","place":["Denmark"]}]},{"given":"Alvarina","family":"Couto","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology, University of Vigo , Vigo 36310,","place":["Spain"]}]},{"given":"Andre M","family":"Machado","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]}]},{"given":"Brona","family":"Brejova","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava , Mlynsk\u00e1 dolina, 842 48 Bratislava, Slovak Republic"}]},{"given":"Carolin B","family":"Albertin","sequence":"additional","affiliation":[{"name":"Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole , MA 02543,","place":["USA"]}]},{"given":"Filipe","family":"Silva","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]},{"name":"Department of Biology, Faculty of Sciences, University of Porto , Rua do Campo Alegre, 4169-007, Porto,","place":["Portugal"]}]},{"given":"Paul","family":"Gardner","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Otago , 710 Cumberland Street, North Dunedin, Dunedin 9016,","place":["New Zealand"]}]},{"given":"Tobias","family":"Baril","sequence":"additional","affiliation":[{"name":"Centre for Ecology and Conservation, University of Exeter , Penryn Campus, Penryn, Cornwall, TR10 9FE,","place":["UK"]}]},{"given":"Alex","family":"Hayward","sequence":"additional","affiliation":[{"name":"Centre for Ecology and Conservation, University of Exeter , Penryn Campus, Penryn, Cornwall, TR10 9FE,","place":["UK"]}]},{"given":"Alexandre","family":"Campos","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]}]},{"given":"\u00c2ngela M","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]}]},{"given":"Inigo","family":"Barrio-Hernandez","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense M,","place":["Denmark"]}]},{"given":"Henk-Jan","family":"Hoving","sequence":"additional","affiliation":[{"name":"GEOMAR Helmholtz Centre for Ocean Research Kiel ,Wischhofstra\u00dfe 1-3, 24148 Kiel,","place":["Germany"]}]},{"given":"Ricardo","family":"Tafur-Jimenez","sequence":"additional","affiliation":[{"name":"Instituto del Mar del Per\u00fa , Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao,","place":["Peru"]}]},{"given":"Chong","family":"Chu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston, MA,","place":["USA"]}]},{"given":"Barbara","family":"Fraz\u00e3o","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]},{"name":"IPMA, Fitopl\u00e2ncton Lab , Rua C do Aeroporto, 1749-077, Lisboa,","place":["Portugal"]}]},{"given":"Bent","family":"Petersen","sequence":"additional","affiliation":[{"name":"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,","place":["Malaysia"]},{"name":"Evolutionary Genomics Section, Globe Institute, University of Copenhagen ,\u00d8ster Farimagsgade 5, 1353 Copenhagen,","place":["Denmark"]}]},{"given":"Fernando","family":"Pe\u00f1aloza","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n Biom\u00e9dica en C\u00e1ncer, Instituto Nacional de Cancerolog\u00eda-Instituto de Investigaciones Biom\u00e9dicas, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Mexico City ,","place":["M\u00e9xico"]}]},{"given":"Francesco","family":"Musacchia","sequence":"additional","affiliation":[{"name":"Genomic Medicine, Telethon Institute of Genetics and Medicine , Via Campi Flegrei, 34, 80078 Pozzuoli, Naples,","place":["Italy"]}]},{"suffix":"Jr","given":"Graham C","family":"Alexander","sequence":"additional","affiliation":[{"name":"GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708,","place":["USA"]}]},{"given":"Hugo","family":"Os\u00f3rio","sequence":"additional","affiliation":[{"name":"i3S-Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto , Rua Alfredo Allen 208, 4200-135 Porto,","place":["Portugal"]},{"name":"IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto , Rua J\u00falio Amaral de Carvalho 45, 4200-135 Porto,","place":["Portugal"]},{"name":"Faculty of Medicine of the University of Porto , Alameda Prof. Hernani Monteiro, 4200-319 Porto,","place":["Portugal"]}]},{"given":"Inger","family":"Winkelmann","sequence":"additional","affiliation":[{"name":"Section for GeoGenetics, GLOBE Institute, University of Copenhagen , \u00d8ster Voldgade 5-7, 1350 Copenhagen,","place":["Denmark"]}]},{"given":"Oleg","family":"Simakov","sequence":"additional","affiliation":[{"name":"Department of Molecular Evolution and Development, University of Vienna , Althanstrasse 14 (UZA1), A-1090 Vienna,","place":["Austria"]}]},{"given":"Simon","family":"Rasmussen","sequence":"additional","affiliation":[{"name":"Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Blegdamsvej 3B, 2200 Copenhagen,","place":["Denmark"]}]},{"given":"M Ziaur","family":"Rahman","sequence":"additional","affiliation":[{"name":"Bioinformatics Solutions Inc , 470 Weber St N Suite 204, Waterloo, ON N2L 6J2,","place":["Canada"]}]},{"given":"Davide","family":"Pisani","sequence":"additional","affiliation":[{"name":"School of Biological Sciences and School of Earth Sciences, University of Bristol , 24 Tyndall Avenue, Bristol, BS8 1TG,","place":["UK"]}]},{"given":"Jakob","family":"Vinther","sequence":"additional","affiliation":[{"name":"School of Biological Sciences and School of Earth Sciences, University of Bristol , 24 Tyndall Avenue, Bristol, BS8 1TG,","place":["UK"]}]},{"given":"Erich","family":"Jarvis","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute , 4000 Jones Bridge Rd, Chevy Chase, MD 20815,","place":["USA"]},{"name":"The Rockefeller University , 1230 York Ave, New York, NY 10065,","place":["USA"]}]},{"given":"Guojie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Section for Ecology and Evolution, Department of Biology, University of Copenhagen , Universitetsparken 15, 2100 Copenhagen,","place":["Denmark"]},{"name":"China National Genebank , BGI-Shenzhen, Shenzhen 518083,","place":["China"]},{"name":"State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , 32 Jiaochang Donglu Kunming, Yunnan 650223,","place":["China"]},{"name":"CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , 32 Jiaochang Donglu Kunming, Yunnan 650223,","place":["China"]}]},{"given":"Jan M","family":"Strugnell","sequence":"additional","affiliation":[{"name":"Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University , Townsville, Douglas QLD 4814,","place":["Australia"]},{"name":"Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University , Melbourne Victoria 3086,","place":["Australia"]}]},{"given":"L Filipe C","family":"Castro","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. General Norton de Matos, 4450'208 Matosinhos,","place":["Portugal"]},{"name":"Department of Biology, Faculty of Sciences, University of Porto , Rua do Campo Alegre, 4169-007, Porto,","place":["Portugal"]}]},{"given":"Olivier","family":"Fedrigo","sequence":"additional","affiliation":[{"name":"The Rockefeller University , 1230 York Ave, New York, NY 10065,","place":["USA"]}]},{"given":"Mateus","family":"Patricio","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD,","place":["UK"]}]},{"given":"Qiye","family":"Li","sequence":"additional","affiliation":[{"name":"BGI-Shenzhen , Shenzhen,","place":["China"]}]},{"given":"Sara","family":"Rocha","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Genetics and Immunology, University of Vigo , Vigo 36310,","place":["Spain"]},{"name":"Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Terminal de Cruzeiros de Leix\u00f5es, Av. 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