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

Rute R da Fonseca, Alvarina Couto, Andre M Machado, Brona Brejova, Carolin B Albertin, Filipe Silva, Paul Gardner, Tobias Baril, Alex Hayward, Alexandre Campos, Ângela M Ribeiro, Inigo Barrio-Hernandez, Henk-Jan Hoving, Ricardo Tafur-Jimenez, Chong Chu, Barbara Frazão, Bent Petersen, Fernando Peñaloza, Francesco Musacchia, Graham C AlexanderHugo Osório, Inger Winkelmann, Oleg Simakov, Simon Rasmussen, M Ziaur Rahman, Davide Pisani, Jakob Vinther, Erich Jarvis, Guojie Zhang, Jan M Strugnell, L Filipe C Castro, Olivier Fedrigo, Mateus Patricio, Qiye Li, Sara Rocha, Agostinho Antunes, Yufeng Wu, Bin Ma, Remo Sanges, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, M Thomas P Gilbert

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

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.

OriginalsprogEngelsk
TidsskriftGigaScience
Vol/bind9
Udgave nummer1
ISSN2047-217X
DOI
StatusUdgivet - 1. jan. 2020

Fingeraftryk

Decapodiformes
Genes
Gigantism
Genome Size
Mollusca
Nucleic Acid Repetitive Sequences
Molluscs
Proteome
Proteins
Libraries
RNA
Scaffolds
Tissue

Bibliografisk note

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

Citer dette

da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., ... Gilbert, M. T. P. (2020). A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience, 9(1). https://doi.org/10.1093/gigascience/giz152
da Fonseca, Rute R ; Couto, Alvarina ; Machado, Andre M ; Brejova, Brona ; Albertin, Carolin B ; Silva, Filipe ; Gardner, Paul ; Baril, Tobias ; Hayward, Alex ; Campos, Alexandre ; Ribeiro, Ângela M ; Barrio-Hernandez, Inigo ; Hoving, Henk-Jan ; Tafur-Jimenez, Ricardo ; Chu, Chong ; Frazão, Barbara ; Petersen, Bent ; Peñaloza, Fernando ; Musacchia, Francesco ; Alexander, Graham C ; Osório, Hugo ; Winkelmann, Inger ; Simakov, Oleg ; Rasmussen, Simon ; Rahman, M Ziaur ; Pisani, Davide ; Vinther, Jakob ; Jarvis, Erich ; Zhang, Guojie ; Strugnell, Jan M ; Castro, L Filipe C ; Fedrigo, Olivier ; Patricio, Mateus ; Li, Qiye ; Rocha, Sara ; Antunes, Agostinho ; Wu, Yufeng ; Ma, Bin ; Sanges, Remo ; Vinar, Tomas ; Blagoev, Blagoy ; Sicheritz-Ponten, Thomas ; Nielsen, Rasmus ; Gilbert, M Thomas P. / A draft genome sequence of the elusive giant squid, Architeuthis dux. I: GigaScience. 2020 ; Bind 9, Nr. 1.
@article{8e55e6b5e08f441384b5bcf114b0d606,
title = "A draft genome sequence of the elusive giant squid, Architeuthis dux",
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.",
author = "{da Fonseca}, {Rute R} and Alvarina Couto and Machado, {Andre M} and Brona Brejova and Albertin, {Carolin B} and Filipe Silva and Paul Gardner and Tobias Baril and Alex Hayward and Alexandre Campos and Ribeiro, {{\^A}ngela M} and Inigo Barrio-Hernandez and Henk-Jan Hoving and Ricardo Tafur-Jimenez and Chong Chu and Barbara Fraz{\~a}o and Bent Petersen and Fernando Pe{\~n}aloza and Francesco Musacchia and Alexander, {Graham C} and Hugo Os{\'o}rio and Inger Winkelmann and Oleg Simakov and Simon Rasmussen and Rahman, {M Ziaur} and Davide Pisani and Jakob Vinther and Erich Jarvis and Guojie Zhang and Strugnell, {Jan M} and Castro, {L Filipe C} and Olivier Fedrigo and Mateus Patricio and Qiye Li and Sara Rocha and Agostinho Antunes and Yufeng Wu and Bin Ma and Remo Sanges and Tomas Vinar and Blagoy Blagoev and Thomas Sicheritz-Ponten and Rasmus Nielsen and Gilbert, {M Thomas P}",
note = "{\circledC} The Author(s) 2020. Published by Oxford University Press.",
year = "2020",
month = "1",
day = "1",
doi = "10.1093/gigascience/giz152",
language = "English",
volume = "9",
journal = "GigaScience",
issn = "2047-217X",
publisher = "BioMed Central",
number = "1",

}

da Fonseca, RR, Couto, A, Machado, AM, Brejova, B, Albertin, CB, Silva, F, Gardner, P, Baril, T, Hayward, A, Campos, A, Ribeiro, ÂM, Barrio-Hernandez, I, Hoving, H-J, Tafur-Jimenez, R, Chu, C, Frazão, B, Petersen, B, Peñaloza, F, Musacchia, F, Alexander, GC, Osório, H, Winkelmann, I, Simakov, O, Rasmussen, S, Rahman, MZ, Pisani, D, Vinther, J, Jarvis, E, Zhang, G, Strugnell, JM, Castro, LFC, Fedrigo, O, Patricio, M, Li, Q, Rocha, S, Antunes, A, Wu, Y, Ma, B, Sanges, R, Vinar, T, Blagoev, B, Sicheritz-Ponten, T, Nielsen, R & Gilbert, MTP 2020, 'A draft genome sequence of the elusive giant squid, Architeuthis dux', GigaScience, bind 9, nr. 1. https://doi.org/10.1093/gigascience/giz152

A draft genome sequence of the elusive giant squid, Architeuthis dux. / da Fonseca, Rute R; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe; Gardner, Paul; Baril, Tobias; Hayward, Alex; Campos, Alexandre; Ribeiro, Ângela M; Barrio-Hernandez, Inigo; Hoving, Henk-Jan; Tafur-Jimenez, Ricardo; Chu, Chong; Frazão, Barbara; Petersen, Bent; Peñaloza, Fernando; Musacchia, Francesco; Alexander, Graham C; Osório, Hugo; Winkelmann, Inger; Simakov, Oleg; Rasmussen, Simon; Rahman, M Ziaur; Pisani, Davide; Vinther, Jakob; Jarvis, Erich; Zhang, Guojie; Strugnell, Jan M; Castro, L Filipe C; Fedrigo, Olivier; Patricio, Mateus; Li, Qiye; Rocha, Sara; Antunes, Agostinho; Wu, Yufeng; Ma, Bin; Sanges, Remo; Vinar, Tomas; Blagoev, Blagoy; Sicheritz-Ponten, Thomas; Nielsen, Rasmus; Gilbert, M Thomas P.

I: GigaScience, Bind 9, Nr. 1, 01.01.2020.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - A draft genome sequence of the elusive giant squid, Architeuthis dux

AU - da Fonseca, Rute R

AU - Couto, Alvarina

AU - Machado, Andre M

AU - Brejova, Brona

AU - Albertin, Carolin B

AU - Silva, Filipe

AU - Gardner, Paul

AU - Baril, Tobias

AU - Hayward, Alex

AU - Campos, Alexandre

AU - Ribeiro, Ângela M

AU - Barrio-Hernandez, Inigo

AU - Hoving, Henk-Jan

AU - Tafur-Jimenez, Ricardo

AU - Chu, Chong

AU - Frazão, Barbara

AU - Petersen, Bent

AU - Peñaloza, Fernando

AU - Musacchia, Francesco

AU - Alexander, Graham C

AU - Osório, Hugo

AU - Winkelmann, Inger

AU - Simakov, Oleg

AU - Rasmussen, Simon

AU - Rahman, M Ziaur

AU - Pisani, Davide

AU - Vinther, Jakob

AU - Jarvis, Erich

AU - Zhang, Guojie

AU - Strugnell, Jan M

AU - Castro, L Filipe C

AU - Fedrigo, Olivier

AU - Patricio, Mateus

AU - Li, Qiye

AU - Rocha, Sara

AU - Antunes, Agostinho

AU - Wu, Yufeng

AU - Ma, Bin

AU - Sanges, Remo

AU - Vinar, Tomas

AU - Blagoev, Blagoy

AU - Sicheritz-Ponten, Thomas

AU - Nielsen, Rasmus

AU - Gilbert, M Thomas P

N1 - © The Author(s) 2020. Published by Oxford University Press.

PY - 2020/1/1

Y1 - 2020/1/1

N2 - 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.

AB - 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.

U2 - 10.1093/gigascience/giz152

DO - 10.1093/gigascience/giz152

M3 - Journal article

C2 - 31942620

VL - 9

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 1

ER -

da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F et al. A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience. 2020 jan 1;9(1). https://doi.org/10.1093/gigascience/giz152