A draft genome sequence of the elusive giant squid, Architeuthis dux
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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 |
eu_rights_str_mv |
openAccess |
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) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799136008722186241 |