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

Author:

da Fonseca Rute R12ORCID,Couto Alvarina3,Machado Andre M4,Brejova Brona5,Albertin Carolin B6,Silva Filipe47,Gardner Paul8,Baril Tobias9,Hayward Alex9,Campos Alexandre4,Ribeiro Ângela M4,Barrio-Hernandez Inigo10,Hoving Henk-Jan11,Tafur-Jimenez Ricardo12,Chu Chong13,Frazão Barbara414,Petersen Bent1516,Peñaloza Fernando17,Musacchia Francesco18,Alexander Graham C19,Osório Hugo202122,Winkelmann Inger23,Simakov Oleg24,Rasmussen Simon25,Rahman M Ziaur26,Pisani Davide27,Vinther Jakob27,Jarvis Erich2829,Zhang Guojie30313233,Strugnell Jan M3435,Castro L Filipe C47,Fedrigo Olivier29,Patricio Mateus36,Li Qiye37,Rocha Sara338,Antunes Agostinho47ORCID,Wu Yufeng39,Ma Bin40,Sanges Remo4142,Vinar Tomas5,Blagoev Blagoy10,Sicheritz-Ponten Thomas1516,Nielsen Rasmus2343,Gilbert M Thomas P2344

Affiliation:

1. Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark

2. The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark

3. Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain

4. 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

5. Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic

6. Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA

7. Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal

8. Department of Biochemistry, University of Otago, 710 Cumberland Street, North Dunedin, Dunedin 9016, New Zealand

9. Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK

10. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark

11. GEOMAR Helmholtz Centre for Ocean Research Kiel,Wischhofstraße 1-3, 24148 Kiel, Germany

12. Instituto del Mar del Perú, Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao, Peru

13. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

14. IPMA, Fitoplâncton Lab, Rua C do Aeroporto, 1749-077, Lisboa, Portugal

15. 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

16. Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark

17. Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México

18. Genomic Medicine, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy

19. GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708, USA

20. i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal

21. IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal

22. Faculty of Medicine of the University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal

23. Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark

24. Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14 (UZA1), A-1090 Vienna, Austria

25. Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark

26. Bioinformatics Solutions Inc, 470 Weber St N Suite 204, Waterloo, ON N2L 6J2, Canada

27. School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK

28. Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA

29. The Rockefeller University, 1230 York Ave, New York, NY 10065, USA

30. Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark

31. China National Genebank, BGI-Shenzhen, Shenzhen 518083, China

32. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China

33. CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China

34. Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia

35. Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne Victoria 3086, Australia

36. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK

37. BGI-Shenzhen, Shenzhen, China

38. Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain

39. Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA

40. School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada

41. Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy

42. Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy

43. Departments of Integrative Biology and Statistics, University of California, 3040 Valley Life Sciences, Berkeley, CA 94720-3200, USA

44. Norwegian University of Science and Technology, University Museum, Høgskolering 1, 7491 Trondheim, Norway

Abstract

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.

Funder

Villum Fonden

Portuguese Science Foundation

Danish National Research Foundation

Rede Nacional de Espectrometria de Massa

COMPETE and North Portugal Regional Operational Programme

European Regional Development Fund

Wellcome Trust

European Molecular Biology Laboratory

Lundbeck Foundation

Novo Nordisk Foundation

Biotechnology and Biological Sciences Research Council

David and Lucile Packard Foundation

Netherlands Organization for Scientific Research

Deutsche Forschungsgemeinschaft

Vedecká Grantová Agentúra MŠVVaŠ SR a SAV

National Science Foundation

DeiC National Life Science Supercomputer

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Health Informatics

Cited by 41 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3