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

Animals Biological Evolution Chromatography, Liquid Computational Biology / methods DNA Transposable Elements Decapodiformes / genetics Gene Expression Profiling Genome Genomics / methods Molecular Sequence Annotation Multigene Family RNA, Untranslated Tandem Mass Spectrometry Transcriptome Whole Genome Sequencing
cephalopod genome assembly invertebrate

Journal

GigaScience
ISSN: 2047-217X
Titre abrégé: Gigascience
Pays: United States
ID NLM: 101596872

Informations de publication

Date de publication:
01 01 2020
Historique:
received: 24 06 2019
revised: 27 10 2019
accepted: 05 12 2019
entrez: 17 1 2020
pubmed: 17 1 2020
medline: 8 10 2020
Statut: ppublish

Résumé

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. 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. 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.

Sections du résumé

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.

Identifiants

DOI: 10.1093/gigascience/giz152 PMID: 31942620 PMC: PMC6962438
pubmed: 31942620
pii: 5697198
doi: 10.1093/gigascience/giz152
pmc: PMC6962438
pii:
doi:

Substances chimiques

DNA Transposable Elements 0
RNA, Untranslated 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Wellcome Trust
ID : WT108749/Z/15/Z
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N020146/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M009122/1
Pays : United Kingdom

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press.

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Auteurs

Rute R da Fonseca (RR)

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.

Alvarina Couto (A)

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

Andre M Machado (AM)

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.

Brona Brejova (B)

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

Carolin B Albertin (CB)

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

Filipe Silva (F)

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

Paul Gardner (P)

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

Tobias Baril (T)

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

Alex Hayward (A)

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

Alexandre Campos (A)

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.

Ângela M Ribeiro (ÂM)

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.

Inigo Barrio-Hernandez (I)

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

Henk-Jan Hoving (HJ)

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

Ricardo Tafur-Jimenez (R)

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

Chong Chu (C)

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

Barbara Frazão (B)

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

Bent Petersen (B)

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.

Fernando Peñaloza (F)

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

Francesco Musacchia (F)

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

Graham C Alexander (GC)

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

Hugo Osório (H)

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.

Inger Winkelmann (I)

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

Oleg Simakov (O)

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

Simon Rasmussen (S)

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

M Ziaur Rahman (MZ)

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

Davide Pisani (D)

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

Jakob Vinther (J)

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

Erich Jarvis (E)

Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.

Guojie Zhang (G)

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.

Jan M Strugnell (JM)

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.

L Filipe C Castro (LFC)

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

Olivier Fedrigo (O)

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

Mateus Patricio (M)

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

Qiye Li (Q)

BGI-Shenzhen, Shenzhen, China.

Sara Rocha (S)

Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain.
Biomedical Research Center (CINBIO), University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain.

Agostinho Antunes (A)

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

Yufeng Wu (Y)

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

Bin Ma (B)

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

Remo Sanges (R)

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.

Tomas Vinar (T)

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

Blagoy Blagoev (B)

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

Thomas Sicheritz-Ponten (T)

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.

Rasmus Nielsen (R)

Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Departments of Integrative Biology and Statistics, University of California, 3040 Valley Life Sciences, Berkeley, CA 94720-3200, USA.

M Thomas P Gilbert (MTP)

Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Norwegian University of Science and Technology, University Museum, Høgskolering 1, 7491 Trondheim, Norway.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Chromatographie › Chromatographie en phase liquide › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Séquences répétées dispersées › Éléments transposables d'ADN › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Eucaryotes › Animaux › Invertébrés › Mollusca › Cephalopoda › Decapodiformes › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Famille multigénique › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Techniques d'investigation › Techniques de chimie analytique › Spectrométrie de masse › Spectrométrie de masse en tandem › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › A draft genome sequence of the elusive giant...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Analyse de séquence d'ADN › Séquençage du génome entier › A draft genome sequence of the elusive giant...