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

Detalhes bibliográficos
Autor(a) principal: Fonseca, RR
Data de Publicação: 2020
Outros Autores: Couto, A, Machado, AM, Brejova, B, Albertin, CB, Silva, F, Gardner, P, Baril, T, Hayward, A, Campos, A, Ribeiro, ÂM, Barrio-Hernandez, I, Hoving, HJ, Tafur-Jimenez, R, Chu, C, Frazão, B, Petersen, B, Peñaloza, F, Musacchia, F, Alexander, GC, Osorio, 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
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: https://hdl.handle.net/10216/141445
Resumo: 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.
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spelling A draft genome sequence of the elusive giant squid, Architeuthis duxBackground: 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.Oxford University Press20202020-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10216/141445eng2047-217X10.1093/gigascience/giz152Fonseca, RRCouto, AMachado, AMBrejova, BAlbertin, CBSilva, FGardner, PBaril, THayward, ACampos, ARibeiro, ÂMBarrio-Hernandez, IHoving, HJTafur-Jimenez, RChu, CFrazão, BPetersen, BPeñaloza, FMusacchia, FAlexander, GCOsorio, HWinkelmann, ISimakov, ORasmussen, SRahman, MZPisani, DVinther, JJarvis, EZhang, GStrugnell, JMCastro, LFCFedrigo, OPatricio, MLi, QRocha, SAntunes, AWu, YMa, BSanges, RVinar, TBlagoev, BSicheritz-Ponten, TNielsen, RGilbert, MTPinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-29T14:46:52Zoai:repositorio-aberto.up.pt:10216/141445Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T00:08:18.522663Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv A draft genome sequence of the elusive giant squid, Architeuthis dux
title A draft genome sequence of the elusive giant squid, Architeuthis dux
spellingShingle A draft genome sequence of the elusive giant squid, Architeuthis dux
Fonseca, RR
title_short A draft genome sequence of the elusive giant squid, Architeuthis dux
title_full A draft genome sequence of the elusive giant squid, Architeuthis dux
title_fullStr A draft genome sequence of the elusive giant squid, Architeuthis dux
title_full_unstemmed A draft genome sequence of the elusive giant squid, Architeuthis dux
title_sort A draft genome sequence of the elusive giant squid, Architeuthis dux
author Fonseca, RR
author_facet 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, HJ
Tafur-Jimenez, R
Chu, C
Frazão, B
Petersen, B
Peñaloza, F
Musacchia, F
Alexander, GC
Osorio, 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
author_role author
author2 Couto, A
Machado, AM
Brejova, B
Albertin, CB
Silva, F
Gardner, P
Baril, T
Hayward, A
Campos, A
Ribeiro, ÂM
Barrio-Hernandez, I
Hoving, HJ
Tafur-Jimenez, R
Chu, C
Frazão, B
Petersen, B
Peñaloza, F
Musacchia, F
Alexander, GC
Osorio, 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
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv 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, HJ
Tafur-Jimenez, R
Chu, C
Frazão, B
Petersen, B
Peñaloza, F
Musacchia, F
Alexander, GC
Osorio, 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
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv https://hdl.handle.net/10216/141445
url https://hdl.handle.net/10216/141445
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 2047-217X
10.1093/gigascience/giz152
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
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