A draft genome sequence of the elusive giant squid, Architeuthis dux
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...
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2020
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Online Access: | https://portal.findresearcher.sdu.dk/da/publications/8e55e6b5-e08f-4413-84b5-bcf114b0d606 https://doi.org/10.1093/gigascience/giz152 https://findresearcher.sdu.dk/ws/files/159859399/giz152.pdf |
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ftsydanskunivpub:oai:sdu.dk:publications/8e55e6b5-e08f-4413-84b5-bcf114b0d606 2023-05-15T13:56:04+02:00 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 2020-01 application/pdf https://portal.findresearcher.sdu.dk/da/publications/8e55e6b5-e08f-4413-84b5-bcf114b0d606 https://doi.org/10.1093/gigascience/giz152 https://findresearcher.sdu.dk/ws/files/159859399/giz152.pdf eng eng info:eu-repo/semantics/openAccess da Fonseca , R R , Couto , A , Machado , A M , Brejova , B , Albertin , C B , Silva , F , Gardner , P , Baril , T , Hayward , A , Campos , A , Ribeiro , Â M , Barrio-Hernandez , I , Hoving , H-J , Tafur-Jimenez , R , Chu , C , Frazão , B , Petersen , B , Peñaloza , F , Musacchia , F , Alexander , G C , Osório , H , Winkelmann , I , Simakov , O , Rasmussen , S , Rahman , M Z , Pisani , D , Vinther , J , Jarvis , E , Zhang , G , Strugnell , J M , Castro , L F C , 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 , M T P 2020 , ' A draft genome sequence of the elusive giant squid, Architeuthis dux ' , GigaScience , vol. 9 , no. 1 , giz152 . https://doi.org/10.1093/gigascience/giz152 article 2020 ftsydanskunivpub https://doi.org/10.1093/gigascience/giz152 2022-08-14T10:19:27Z 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. Article in Journal/Newspaper Antarc* Antarctic Arctic University of Southern Denmark Research Portal Antarctic Arctic Pacific GigaScience 9 1 |
institution |
Open Polar |
collection |
University of Southern Denmark Research Portal |
op_collection_id |
ftsydanskunivpub |
language |
English |
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. |
format |
Article in Journal/Newspaper |
author |
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 |
spellingShingle |
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 |
author_facet |
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 |
author_sort |
da Fonseca, Rute R |
title |
A draft genome sequence of the elusive giant squid, Architeuthis dux |
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 |
draft genome sequence of the elusive giant squid, architeuthis dux |
publishDate |
2020 |
url |
https://portal.findresearcher.sdu.dk/da/publications/8e55e6b5-e08f-4413-84b5-bcf114b0d606 https://doi.org/10.1093/gigascience/giz152 https://findresearcher.sdu.dk/ws/files/159859399/giz152.pdf |
geographic |
Antarctic Arctic Pacific |
geographic_facet |
Antarctic Arctic Pacific |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_source |
da Fonseca , R R , Couto , A , Machado , A M , Brejova , B , Albertin , C B , Silva , F , Gardner , P , Baril , T , Hayward , A , Campos , A , Ribeiro , Â M , Barrio-Hernandez , I , Hoving , H-J , Tafur-Jimenez , R , Chu , C , Frazão , B , Petersen , B , Peñaloza , F , Musacchia , F , Alexander , G C , Osório , H , Winkelmann , I , Simakov , O , Rasmussen , S , Rahman , M Z , Pisani , D , Vinther , J , Jarvis , E , Zhang , G , Strugnell , J M , Castro , L F C , 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 , M T P 2020 , ' A draft genome sequence of the elusive giant squid, Architeuthis dux ' , GigaScience , vol. 9 , no. 1 , giz152 . https://doi.org/10.1093/gigascience/giz152 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1093/gigascience/giz152 |
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GigaScience |
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9 |
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