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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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438/ http://www.ncbi.nlm.nih.gov/pubmed/31942620 https://doi.org/10.1093/gigascience/giz152 |
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ftpubmed:oai:pubmedcentral.nih.gov:6962438 2023-05-15T13:53:48+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 2020-01-16 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438/ http://www.ncbi.nlm.nih.gov/pubmed/31942620 https://doi.org/10.1093/gigascience/giz152 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438/ http://www.ncbi.nlm.nih.gov/pubmed/31942620 http://dx.doi.org/10.1093/gigascience/giz152 © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY Data Note Text 2020 ftpubmed https://doi.org/10.1093/gigascience/giz152 2020-01-26T01:26:35Z 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. Text Antarc* Antarctic Arctic PubMed Central (PMC) Antarctic Arctic Pacific GigaScience 9 1 |
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Data Note |
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Data Note 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 |
topic_facet |
Data Note |
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. |
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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 |
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 |
publisher |
Oxford University Press |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438/ http://www.ncbi.nlm.nih.gov/pubmed/31942620 https://doi.org/10.1093/gigascience/giz152 |
geographic |
Antarctic Arctic Pacific |
geographic_facet |
Antarctic Arctic Pacific |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962438/ http://www.ncbi.nlm.nih.gov/pubmed/31942620 http://dx.doi.org/10.1093/gigascience/giz152 |
op_rights |
© The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1093/gigascience/giz152 |
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GigaScience |
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9 |
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1766259259987722240 |