Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux"
The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusk 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 dwellin...
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ftdatacite:10.5524/100676 2023-05-15T14:05:20+02:00 Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" Rute, Da Fonseca R. Alvarina, Couto André, Machado M. Brona, Brejova Caroline, Albertin B. Filipe, Silva Paul, Gardner Tobias, Baril Alex, Hayward Alexandre, Campos Angela, Ribeiro M. Inigo, Barrio-Hernandez Henk-Jan, Hoving Ricardo, Tafur-Jimenez Chong, Chu Bárbara, Frazão Bent, Petersen Fernando, Penaloza Francesco, Musacchia Alexander Jr. C. Graham Hugo, Osório Winkelmann Inger Simakov Oleg Simon, Rasmussen Rahman Ziaur, M. Davide, Pisani Erich, Jarvis D Guojie, Zhang Jakob, Vinther Jan, Strugnell M. C. Castro Filipe, L. Fedrigo Olivier Mateus, Patricio Qiye, Li Sara, Rocha Agostinho, Antunes Yufeng, Wu Bin, Ma Remo, Sanges Tomas, Vinar Blagoy, Blagoev Sicheritz-Ponten Thomas Rasmus, Nielsen M.Thomas, Gilbert P 2020 https://dx.doi.org/10.5524/100676 http://gigadb.org/dataset/100676 en eng GigaScience Database https://dx.doi.org/10.1093/gigascience/giz152 CC0 1.0 Universal http://creativecommons.org/publicdomain/zero/1.0 CC0 Genomic Transcriptomic Proteomic cephalopod invertebrate genome assembly dataset Dataset GigaDB Dataset 2020 ftdatacite https://doi.org/10.5524/100676 https://doi.org/10.1093/gigascience/giz152 2021-11-05T12:55:41Z The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusk 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 unlocking several pending evolutionary questions. 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 three different tissue types from three other species of squid species (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. 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. Dataset Antarc* Antarctic Arctic DataCite Metadata Store (German National Library of Science and Technology) Antarctic Arctic Pacific |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
Genomic Transcriptomic Proteomic cephalopod invertebrate genome assembly |
spellingShingle |
Genomic Transcriptomic Proteomic cephalopod invertebrate genome assembly Rute, Da Fonseca R. Alvarina, Couto André, Machado M. Brona, Brejova Caroline, Albertin B. Filipe, Silva Paul, Gardner Tobias, Baril Alex, Hayward Alexandre, Campos Angela, Ribeiro M. Inigo, Barrio-Hernandez Henk-Jan, Hoving Ricardo, Tafur-Jimenez Chong, Chu Bárbara, Frazão Bent, Petersen Fernando, Penaloza Francesco, Musacchia Alexander Jr. C. Graham Hugo, Osório Winkelmann Inger Simakov Oleg Simon, Rasmussen Rahman Ziaur, M. Davide, Pisani Erich, Jarvis D Guojie, Zhang Jakob, Vinther Jan, Strugnell M. C. Castro Filipe, L. Fedrigo Olivier Mateus, Patricio Qiye, Li Sara, Rocha Agostinho, Antunes Yufeng, Wu Bin, Ma Remo, Sanges Tomas, Vinar Blagoy, Blagoev Sicheritz-Ponten Thomas Rasmus, Nielsen M.Thomas, Gilbert P Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
topic_facet |
Genomic Transcriptomic Proteomic cephalopod invertebrate genome assembly |
description |
The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusk 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 unlocking several pending evolutionary questions. 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 three different tissue types from three other species of squid species (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. 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 |
Dataset |
author |
Rute, Da Fonseca R. Alvarina, Couto André, Machado M. Brona, Brejova Caroline, Albertin B. Filipe, Silva Paul, Gardner Tobias, Baril Alex, Hayward Alexandre, Campos Angela, Ribeiro M. Inigo, Barrio-Hernandez Henk-Jan, Hoving Ricardo, Tafur-Jimenez Chong, Chu Bárbara, Frazão Bent, Petersen Fernando, Penaloza Francesco, Musacchia Alexander Jr. C. Graham Hugo, Osório Winkelmann Inger Simakov Oleg Simon, Rasmussen Rahman Ziaur, M. Davide, Pisani Erich, Jarvis D Guojie, Zhang Jakob, Vinther Jan, Strugnell M. C. Castro Filipe, L. Fedrigo Olivier Mateus, Patricio Qiye, Li Sara, Rocha Agostinho, Antunes Yufeng, Wu Bin, Ma Remo, Sanges Tomas, Vinar Blagoy, Blagoev Sicheritz-Ponten Thomas Rasmus, Nielsen M.Thomas, Gilbert P |
author_facet |
Rute, Da Fonseca R. Alvarina, Couto André, Machado M. Brona, Brejova Caroline, Albertin B. Filipe, Silva Paul, Gardner Tobias, Baril Alex, Hayward Alexandre, Campos Angela, Ribeiro M. Inigo, Barrio-Hernandez Henk-Jan, Hoving Ricardo, Tafur-Jimenez Chong, Chu Bárbara, Frazão Bent, Petersen Fernando, Penaloza Francesco, Musacchia Alexander Jr. C. Graham Hugo, Osório Winkelmann Inger Simakov Oleg Simon, Rasmussen Rahman Ziaur, M. Davide, Pisani Erich, Jarvis D Guojie, Zhang Jakob, Vinther Jan, Strugnell M. C. Castro Filipe, L. Fedrigo Olivier Mateus, Patricio Qiye, Li Sara, Rocha Agostinho, Antunes Yufeng, Wu Bin, Ma Remo, Sanges Tomas, Vinar Blagoy, Blagoev Sicheritz-Ponten Thomas Rasmus, Nielsen M.Thomas, Gilbert P |
author_sort |
Rute, Da Fonseca R. |
title |
Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
title_short |
Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
title_full |
Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
title_fullStr |
Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
title_full_unstemmed |
Supporting data for "A draft genome sequence of the elusive giant squid, Architeuthis dux" |
title_sort |
supporting data for "a draft genome sequence of the elusive giant squid, architeuthis dux" |
publisher |
GigaScience Database |
publishDate |
2020 |
url |
https://dx.doi.org/10.5524/100676 http://gigadb.org/dataset/100676 |
geographic |
Antarctic Arctic Pacific |
geographic_facet |
Antarctic Arctic Pacific |
genre |
Antarc* Antarctic Arctic |
genre_facet |
Antarc* Antarctic Arctic |
op_relation |
https://dx.doi.org/10.1093/gigascience/giz152 |
op_rights |
CC0 1.0 Universal http://creativecommons.org/publicdomain/zero/1.0 |
op_rightsnorm |
CC0 |
op_doi |
https://doi.org/10.5524/100676 https://doi.org/10.1093/gigascience/giz152 |
_version_ |
1766277157280022528 |