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

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A draft genome sequence of the elusive giant squid, Architeuthis dux.
GigaScience ( IF 9.2 ) Pub Date : 2020-01-01 , DOI: 10.1093/gigascience/giz152
Rute R da Fonseca _{1,

2} , Alvarina Couto ₃ , Andre M Machado ₄ , Brona Brejova ₅ , Carolin B Albertin ₆ , Filipe Silva _{4,

7} , Paul Gardner ₈ , Tobias Baril ₉ , Alex Hayward ₉ , Alexandre Campos ₄ , Ângela M Ribeiro ₄ , Inigo Barrio-Hernandez ₁₀ , Henk-Jan Hoving ₁₁ , Ricardo Tafur-Jimenez ₁₂ , Chong Chu ₁₃ , Barbara Frazão _{4,

14} , Bent Petersen _{15,

16} , Fernando Peñaloza ₁₇ , Francesco Musacchia ₁₈ , Graham C Alexander ₁₉ , Hugo Osório _{20,

21,

22} , Inger Winkelmann ₂₃ , Oleg Simakov ₂₄ , Simon Rasmussen ₂₅ , M Ziaur Rahman ₂₆ , Davide Pisani ₂₇ , Jakob Vinther ₂₇ , Erich Jarvis _{28,

29} , Guojie Zhang _{30,

31,

32,

33} , Jan M Strugnell _{34,

35} , L Filipe C Castro _{4,

7} , Olivier Fedrigo ₂₉ , Mateus Patricio ₃₆ , Qiye Li ₃₇ , Sara Rocha _{3,

38} , Agostinho Antunes _{4,

7} , Yufeng Wu ₃₉ , Bin Ma ₄₀ , Remo Sanges _{41,

42} , Tomas Vinar ₅ , Blagoy Blagoev ₁₀ , Thomas Sicheritz-Ponten _{15,

16} , Rasmus Nielsen _{23,

43} , M Thomas P Gilbert _{23,

44}

Affiliation

Center for Macroecology, Evolution and Climate (CMEC), GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark.
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain.
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.
Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovak Republic.
Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
Department of Biochemistry, University of Otago, 710 Cumberland Street, North Dunedin, Dunedin 9016, New Zealand.
Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK.
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
GEOMAR Helmholtz Centre for Ocean Research Kiel,Wischhofstraße 1-3, 24148 Kiel, Germany.
Instituto del Mar del Perú, Esq. Gamarra y Gral. Valle, Chucuito Apartado 22, Callao, Peru.
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
IPMA, Fitoplâncton Lab, Rua C do Aeroporto, 1749-077, Lisboa, Portugal.
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.
Evolutionary Genomics Section, Globe Institute, University of Copenhagen,Øster Farimagsgade 5, 1353 Copenhagen, Denmark.
Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, México.
Genomic Medicine, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy.
GCB Sequencing and Genomic Technologies Shared Resource, Duke University CIEMAS, 101 Science Drive, Durham, NC 27708, USA.
i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal.
IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal.
Faculty of Medicine of the University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal.
Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14 (UZA1), A-1090 Vienna, Austria.
Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
Bioinformatics Solutions Inc, 470 Weber St N Suite 204, Waterloo, ON N2L 6J2, Canada.
School of Biological Sciences and School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TG, UK.
Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
China National Genebank, BGI-Shenzhen, Shenzhen 518083, China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China.
CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu Kunming, Yunnan 650223, China.
Centre for Sustainable Tropical Fisheries & Aquaculture, James Cook University, Townsville, Douglas QLD 4814, Australia.
Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne Victoria 3086, Australia.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
BGI-Shenzhen, Shenzhen, China.
Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain.
Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.
School of Computer Science, University of Waterloo, 200 University Ave W, Waterloo, ON N2L 3G1, Canada.
Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
Departments of Integrative Biology and Statistics, University of California, 3040 Valley Life Sciences, Berkeley, CA 94720-3200, USA.
Norwegian University of Science and Technology, University Museum, Høgskolering 1, 7491 Trondheim, Norway.

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.

中文翻译：

难以捉摸的巨型鱿鱼Architeuthis dux的基因组序列草图。

背景技术巨型鱿鱼（Architeuthis dux； Steenstrup，1857）是一种神秘的大型软体动物，除北极和南极高水域外，在深海中具有环球分布。该物种难以捉摸，难以研究。因此，为该深海物种装配基因组将使一些悬而未决的进化问题得以解开。结果我们提出了一个基因组装配草案，其中包括200 Gb的Illumina读段，4 Gb的分子合成长读和108 Gb的芝加哥文库，最终大小与估计的2.7 Gb的基因组大小匹配，并且支架的N50为4.8 Mb 。我们还提出了一种替代组件，包括使用Pacific Biosciences平台生成的27 Gb原始读取。此外，我们对来自其他3种鱿鱼（Onychoteuthis bankii，Dosidicus gigas和Sthenoteuthis oualaniensis）的3种不同组织类型的同一个体和RNA的蛋白质组进行了测序，以协助基因组注释。我们注释了33,406个蛋白质编码基因，得到了证据的支持，BUSCO估计的基因组完整性达到了92％。重复区域覆盖基因组的49.17％。结论这个带注释的拟南芥基因组草案为研究该物种的独特特征提供了重要资源，包括其巨大的繁殖力和对深海环境的关键适应性。重复区域覆盖基因组的49.17％。结论这个带注释的拟南芥基因组草案为研究该物种的独特特征提供了重要资源，包括其巨大的繁殖力和对深海环境的关键适应性。重复区域覆盖基因组的49.17％。结论这个带注释的拟南芥基因组草图为研究该物种的独特特征提供了重要资源，包括其巨大的繁殖力和对深海环境的关键适应性。

更新日期：2020-01-16

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